Office of

Energy

Projects

March 2015

FERC/DEIS—0259

DRAFT ENVIRONMENTAL IMPACT STATEMENT

FOR HYDROPOWER LICENSES

Merced River Hydroelectric Project—FERC Project No. 2179-043–California

Merced Falls Hydroelectric Project—FERC Project No. 2467-020–California

Federal Energy Regulatory Commission

Office of Energy Projects

Division of Hydropower Licensing

888 First Street, NE

Washington, D.C. 20426

March 2015
This page intentionally left blank.
FEDERAL ENERGY REGULATORY COMMISSION

WASHINGTON, D.C. 20426

OFFICE OF ENERGY PROJECTS

To the Agency or Individual Addressed:

Reference: Draft Environmental Impact Statement

Attached is the draft environmental impact statement (draft EIS) for the Merced 

River Hydroelectric Project No. 2179) and the Merced Falls Hydroelectric Project No. 

2467). The Merced River Project is located on the main stem of the Merced River in 

Mariposa County, about 23 miles northeast of the city of Merced, California. It occupies 

3,154.9 acres of federal land administered by the U.S. Department of Interior, Bureau of 

Land Management (BLM) as part of the Sierra Resource Management Area. The Merced 

Falls Project is located on the Merced River on the border of Merced and Mariposa 

Counties, California. It occupies approximately 1.0 acre of federal lands administered by 

BLM.

This draft EIS documents the view of governmental agencies, non-governmental 

organizations, affected Indian tribes, the public, the license applicants, and Federal 

Energy Regulatory Commission (Commission) staff. It contains staff evaluations of the 

applicants’ proposals and the alternatives for relicensing the Merced River and Merced 

Falls Hydroelectric Projects.

Before the Commission makes licensing decisions, it will take into account all 

concerns relevant to the public interest. The draft EIS will be part of the record from 

which the Commission will make its decisions. The draft EIS was sent to the U.S. 

Environmental Protection Agency and made available to the public on or about April 15, 

2015.

Copies of the draft EIS are available for review in the Commission’s Public 

Reference Branch, Room 2A, located at 888 First Street, N.E., Washington D.C. 20426. 

The draft EIS also may be viewed on the Internet at www.ferc.gov/docsfiling/elibrary.asp. Please call (202) 502-8222 for assistance.
Any comments should be filed by May 29, 2015. Comments may be filed 

electronically via the Internet. See 18 Code of Federal Regulations 385.2001(a)(1)(iii) 

and the instructions on the Commission’s web site: http://www.ferc.gov/docsfiling/efiling.asp. Commenters can submit brief comments up to 6,000 characters, 

without prior registration, using the eComment system at http://www.ferc.gov/docsfiling/ecomment.asp. You must include your name and contact information at the end of 

your comments. For assistance, please contact FERC Online Support. Although the 

Commission strongly encourages electronic filing, documents may also be paperfiled. To paper-file, mail an original and five copies to: Kimberly D. Bose, Secretary, 

Federal Energy Regulatory Commission, 888 First Street, NE, Washington, DC 20426.

Attachment: Draft Environmental Impact Statement
iii

COVER SHEET

a. Title:

Relicensing the Merced River Hydroelectric Project, FERC Project 

No. 2179, and the Merced Falls Hydroelectric Project, FERC 

Project No. 2467

b. Subject: Draft Environmental Impact Statement

c. Lead Agency: Federal Energy Regulatory Commission

d. Abstract: The Merced River Project (FERC No. 2179-043) is located in 

Mariposa County, California. The existing project affects 

3,154.9 acres of federal land administered by the U.S. Department 

of the Interior, Bureau of Land Management (BLM). It generates 

an average of about 387 gigawatt-hours (GWh) of energy annually. 

The Merced Irrigation District (Merced ID) proposes to implement 

measures to protect and enhance environmental conditions. Merced 

ID proposes no new capacity and no new construction at the project.

The staff’s recommendation is to relicense the project as proposed, 

with certain modifications, and additional measures recommended 

by the agencies.

The Merced Falls Project (FERC No. 2467-020) is located on the 

border of Merced and Mariposa Counties, California. It occupies 

1.0 acre of federal land administered by BLM, and generates an 

average of about 14.4 GWh of energy annually. 

Pacific Gas & Electric (PG&E) proposes to implement measures to 

protect and enhance environmental conditions. PG&E proposes no 

new capacity and no new construction at the project.

The staff’s recommendation is to relicense the project as proposed, 

with certain modifications, and additional measures recommended 

by the agencies.

e. Contact: Matthew Buhyoff

Federal Energy Regulatory 

Commission

Office of Energy Projects

888 First Street, N.E.

Washington, D.C. 20426

(202) 502-6824

Annie Jones

Federal Energy Regulatory 

Commission

Office of General Counsel

888 First Street, N.E.

Washington, D.C. 20426

(202) 502-6453
iv

f. Transmittal: This draft environmental impact statement to relicense the Merced

River and Merced Falls Hydroelectric Projects is being made 

available for public comment on or about April 15, 2015, as 

required by the National Environmental Policy Act of 19691and the 

Commission’s Regulations Implementing the National 

Environmental Policy Act (18 CFR, Part 380).

 

1 National Environmental Policy Act of 1969, amended (Pub. L. 91-190, 42 U.S.C. 

4321-4347, January 1, 1970, as amended by Pub. L. 94-52, July 3, 1975, Pub. L. 94-83, 

August 9, 1975, and Pub. L. 97-258, §4(b), September 13, 1982).
v

FOREWORD

The Federal Energy Regulatory Commission (Commission), pursuant to the 

Federal Power Act (FPA)2and the U.S. Department of Energy Organization Act3is 

authorized to issue licenses for up to 50 years for the construction and operation of nonfederal hydroelectric development subject to its jurisdiction, on the necessary conditions:

That the project adopted...shall be such as in the judgment of the Commission will 

be best adapted to a comprehensive plan for improving or developing a waterway or 

waterways for the use or benefit of interstate or foreign commerce, for the improvement 

and utilization of water-power development, for the adequate protection, mitigation, and 

enhancement of fish and wildlife (including related spawning grounds and habitat), and 

for other beneficial public uses, including irrigation, flood control, water supply, and 

recreational and other purposes referred to in section 4(e)...4

The Commission may require such other conditions not inconsistent with the FPA 

as may be found necessary to provide for the various public interests to be served by the 

project.5 Compliance with such conditions during the licensing period is required. The 

Commission’s Rules of Practice and Procedure allow any person objecting to a licensee’s 

compliance or noncompliance with such conditions to file a complaint noting the basis 

for such objection for the Commission’s consideration.6

 

2 16 U.S.C. §791(a)-825r, as amended by the Electric Consumers Protection Act of 

1986, Pub. L. 99-495 (1986), the Energy Policy Act of 1992, Pub. L. 102-486 (1992), and 

the Energy Policy Act of 2005, Pub. L. 109-58 (2005).

3 Pub. L. 95-91, 91 Stat. 556 (1977).

4 16 U.S.C. §803(a).

5 16 U.S.C. §803(g).

6 18 C.F.R. §385.206 (2014).
vi

This page intentionally left blank.
vii

TABLE OF CONTENTS

COVER SHEET .................................................................................................................iii

FOREWORD....................................................................................................................... v

LIST OF FIGURES..........................................................................................................xiii

LIST OF TABLES...........................................................................................................xvii

ACRONYMS AND ABBREVIATIONS......................................................................... xxi

EXECUTIVE SUMMARY ............................................................................................xxiii

1.0 INTRODUCTION.................................................................................................... 1

1.1 APPLICATION............................................................................................. 1

1.1.1 Merced River Project....................................................................... 1

1.1.2 Merced Falls Project........................................................................ 1

1.2 PURPOSE OF ACTION AND NEED FOR POWER.................................. 6

1.2.1 Purpose of Action ............................................................................ 6

1.2.2 Need for Power................................................................................ 7

1.3 STATUTORY AND REGULATORY REQUIREMENTS ......................... 7

1.3.1 Merced River Project....................................................................... 7

1.3.1.1 Federal Power Act .......................................................... 7

1.3.1.2 Clean Water Act.............................................................. 9

1.3.1.3 Endangered Species Act ................................................. 9

1.3.1.4 Coastal Zone Management Act .................................... 10

1.3.1.5 National Historic Preservation Act............................... 10

1.3.1.6 Wild and Scenic Rivers Act.......................................... 11

1.3.1.7 Magnuson-Stevens Fishery Conservation and 

Management Act........................................................... 11

1.3.2 Merced Falls Project...................................................................... 12

1.3.2.1 Federal Power Act ........................................................ 12

1.3.2.2 Clean Water Act............................................................ 12

1.3.2.3 Endangered Species Act ............................................... 13

1.3.2.4 Coastal Zone Management Act .................................... 13

1.3.2.5 National Historic Preservation Act............................... 13

1.3.2.6 Wild and Scenic Rivers Act.......................................... 14

1.3.2.7 Magnuson-Stevens Fishery Conservation and 

Management Act........................................................... 14

1.4 PUBLIC REVIEW AND COMMENT....................................................... 14

1.4.1 Merced River Project..................................................................... 14

1.4.1.1 Scoping ......................................................................... 14

1.4.1.2 Interventions ................................................................. 15
viii

1.4.1.3 Comments on the Application ...................................... 16

1.4.2 Merced Falls Project...................................................................... 16

1.4.2.1 Scoping ......................................................................... 16

1.4.2.2 Interventions ................................................................. 16

1.4.2.3 Comments on the Application ...................................... 17

2.0 PROPOSED ACTION AND ALTERNATIVES................................................... 19

2.1 NO-ACTION ALTERNATIVE.................................................................. 19

2.1.1 Merced River Project..................................................................... 19

2.1.1.1 Existing Project Facilities............................................. 19

2.1.1.2 Existing Project Boundary............................................ 22

2.1.1.3 Project Safety................................................................ 22

2.1.1.4 Existing Project Operation............................................ 23

2.1.1.5 Existing Environmental Measures................................ 24

2.1.2 Merced Falls Project...................................................................... 26

2.1.2.1 Existing Project Facilities............................................. 26

2.1.2.2 Existing Project Boundary............................................ 27

2.1.2.3 Project Safety................................................................ 27

2.1.2.4 Existing Project Operation............................................ 27

2.1.2.5 Existing Environmental Measures................................ 28

2.2 APPLICANT’S PROPOSAL...................................................................... 28

2.2.1 Merced River Project..................................................................... 28

2.2.1.1 Proposed Project Facilities............................................ 28

2.2.1.2 Proposed Project Boundary .......................................... 31

2.2.1.3 Proposed Project Operation .......................................... 32

2.2.1.4 Proposed Environmental Measures .............................. 32

2.2.1.5 Modifications to Applicant’s Proposal—Mandatory 

Conditions..................................................................... 36

2.2.2 Merced Falls Project...................................................................... 42

2.2.2.1 Proposed Project Facilities............................................ 42

2.2.2.2 Proposed Project Boundary .......................................... 42

2.2.2.3 Proposed Project Operation .......................................... 42

2.2.2.4 Proposed Environmental Measures .............................. 42

2.2.2.5 Modifications to Applicant’s Proposal—Mandatory 

Conditions..................................................................... 43

2.3 STAFF ALTERNATIVE ............................................................................ 44

2.3.1 Merced River Project..................................................................... 44

2.3.2 Merced Falls Project...................................................................... 51

2.4 STAFF ALTERNATIVE WITH MANDATORY CONDITIONS ............ 52

2.4.1 Merced River Project..................................................................... 52

2.4.2 Merced Falls Project...................................................................... 53

2.5 ALTERNATIVES CONSIDERED BUT ELIMINATED FROM 

DETAILED ANALYSIS ............................................................................ 53
ix

2.5.1 Issuing a Non-Power License........................................................ 53

2.5.2 Federal Government Takeover of the Projects.............................. 53

2.5.3 Retiring the Projects...................................................................... 53

3.0 ENVIRONMENTAL ANALYSIS......................................................................... 55

3.1 GENERAL DESCRIPTION OF THE RIVER BASIN .............................. 55

3.2 SCOPE OF CUMULATIVE EFFECTS ANALYSIS ................................ 59

3.2.1 Geographic Scope.......................................................................... 60

3.2.2 Temporal Scope............................................................................. 61

3.3 PROPOSED ACTION AND ACTION ALTERNATIVES ....................... 61

3.3.1 Aquatic Resources......................................................................... 62

3.3.1.1 Affected Environment................................................... 62

3.3.1.2 Environmental Effects ................................................ 133

3.3.1.3 Cumulative Effects ..................................................... 219

3.3.2 Terrestrial Resources................................................................... 222

3.3.2.1 Affected Environment................................................. 222

3.3.2.2 Environmental Effects ................................................ 245

3.3.3 Threatened and Endangered Species........................................... 264

3.3.3.1 Affected Environment................................................. 264

3.3.3.2 Environmental Effects ................................................ 282

3.3.3.3 Cumulative Effects ..................................................... 298

3.3.4 Recreation Resources .................................................................. 300

3.3.4.1 Affected Environment................................................. 300

3.3.4.2 Environmental Effects ................................................ 314

3.3.5 Land Use...................................................................................... 331

3.3.5.1 Affected Environment................................................. 331

3.3.5.2 Environmental Effects ................................................ 337

3.3.6 Cultural Resources....................................................................... 344

3.3.6.1 Affected Environment................................................. 344

3.3.6.2 Environmental Effects ................................................ 353

3.3.7 Aesthetic Resources..................................................................... 357

3.3.7.1 Affected Environment................................................. 357

3.3.7.2 Environmental Effects ................................................ 358

3.4 NO-ACTION ALTERNATIVE................................................................ 360

4.0 DEVELOPMENTAL ANALYSIS ...................................................................... 361

4.1 POWER AND DEVELOPMENTAL BENEFITS OF THE PROJECT... 361

4.2 COMPARISON OF ALTERNATIVES.................................................... 363

4.2.1 Merced River Project................................................................... 363

4.2.1.1 No-action Alternative ................................................. 364

4.2.1.2 Merced ID’s Proposal ................................................. 365

4.2.1.3 Staff Alternative.......................................................... 365

4.2.1.4 Staff Alternative with Mandatory Conditions ............ 365
x

4.2.2 Merced Falls Project.................................................................... 366

4.2.2.1 No-action Alternative ................................................. 366

4.2.2.2 Applicant’s Proposal................................................... 367

4.2.2.3 Staff Alternative.......................................................... 367

4.3 COST OF ENVIRONMENTAL MEASURES......................................... 367

4.3.1 Merced River Project................................................................... 368

4.3.2 Merced Falls Project.................................................................... 375

5.0 CONCLUSIONS AND RECOMMENDATIONS............................................... 379

5.1 COMPREHENSIVE DEVELOPMENT AND RECOMMENDED 

ALTERNATIVE ....................................................................................... 379

5.1.1 Merced River Project................................................................... 379

5.1.1.1 Measures Proposed by Merced ID.............................. 380

5.1.1.2 Additional Measures Recommended by Staff............ 386

5.1.1.3 Measures Not Recommended by Staff ....................... 424

5.1.2 Merced Falls Project.................................................................... 440

5.1.2.1 Measures Proposed by PG&E .................................... 441

5.1.2.2 Additional Measures Recommended by Staff............ 442

5.1.2.3 Measures Not Recommended by Staff ....................... 451

5.2 UNAVOIDABLE ADVERSE EFFECTS................................................. 456

5.3 SUMMARY OF SECTION 10(J) RECOMMENDATIONS AND 4(E) 

CONDITIONS........................................................................................... 456

5.3.1 Fish and Wildlife Agency Recommendations............................. 456

5.3.1.1 Merced River Project.................................................. 457

5.3.1.2 Merced Falls Project ................................................... 488

5.3.2 Land Management Agencies’ Section 4(e) Conditions............... 497

5.3.2.1 Merced River Project.................................................. 497

5.4 CONSISTENCY WITH COMPREHENSIVE PLANS............................ 498

5.4.1 Applicable to Both Projects......................................................... 498

5.4.2 Applicable Only to Merced River Project................................... 500

6.0 LITERATURE CITED......................................................................................... 501

7.0 LIST OF PREPARERS ........................................................................................ 513

7.1 FEDERAL ENERGY REGULATORY COMMISSION......................... 513

7.2 LOUIS BERGER GROUP AND STILLWATER SCIENCES................ 513
xi

APPENDIX A—Merced River Draft License Articles

APPENDIX B—Merced Fall Draft License Articles

APPENDIX C—List of Commenters on the Merced River Project Application

APPENDIX D—Bureau of Land Management Preliminary Conditions

APPENDIX E—Preliminary Water Quality Certification Conditions for the Merced 

River Hydroelectric Project

APPENIDX F—Preliminary Water Quality Certification Conditions for the Merced Falls 

Hydroelectric Project
xii

This page intentionally left blank.
xiii

LIST OF FIGURES

Figure 1-1. Location of Merced River Hydroelectric Project.......................................... 2

Figure 1-2. Merced River and Merced Falls Hydroelectric Projects and vicinity........... 3

Figure 1-3. Location of the Merced Falls Hydroelectric Project ..................................... 4

Figure 1-4. Merced Falls Hydroelectric Project............................................................... 5

Figure 3-1. Merced River Basin and subbasins ............................................................. 56

Figure 3-2. Mean daily releases from New Exchequer powerhouse and dam, 

Merced ID’s synthesized mean daily unregulated flow at New 

Exchequer dam, and Lake McClure daily reservoir elevations in water 

year 2006, a representative wet water year ................................................. 64

Figure 3-3. Mean daily releases from McSwain powerhouse and dam, Merced ID’s 

synthesized mean daily unregulated flow at McSwain dam, and 

McSwain reservoir daily reservoir elevations in water year 2006, a 

representative wet water year...................................................................... 65

Figure 3-4. Mean daily releases from New Exchequer powerhouse and dam, 

Merced ID’s synthesized mean daily unregulated flow at New 

Exchequer dam, and Lake McClure daily reservoir elevations in water 

year 2000, a representative normal water year............................................ 66

Figure 3-5. Mean daily releases from McSwain powerhouse and dam, Merced ID’s 

synthesized mean daily unregulated flow at McSwain dam, and 

McSwain reservoir daily reservoir elevations in water year 2000, a 

representative normal water year ................................................................ 67

Figure 3-6. Mean daily releases from New Exchequer powerhouse and dam, 

Merced ID’s synthesized mean daily unregulated flow at New 

Exchequer dam, and Lake McClure daily reservoir elevations in water 

year 1990, a representative dry water year.................................................. 68

Figure 3-7. Mean daily releases from McSwain powerhouse and dam, Merced ID’s 

synthesized mean daily unregulated flow at McSwain dam, and 

McSwain reservoir daily reservoir elevations in water year 1990, a 

representative dry water year ...................................................................... 69

Figure 3-8. Annual flow duration curve for the Merced Falls Project for the period 

of record (January 1, 1916 to September 30, 2009).................................... 75
xiv

Figure 3-9. Water temperature in Lake McClure near the dam (August 2004 through 

December 2006) .......................................................................................... 83

Figure 3-10. Water temperature in Lake McClure near the dam (January 2007 

through January 2009)................................................................................. 84

Figure 3-11. Water temperature in Lake McClure near the dam (March 2010 through 

February 2011) ............................................................................................ 85

Figure 3-12. Water temperature in McSwain reservoir near the dam (August 2004 

through December 2006)............................................................................. 86

Figure 3-13. Water temperature in McSwain reservoir near the dam (January 2007 

through January 2009)................................................................................. 87

Figure 3-14. Water temperature in McSwain reservoir near the dam (March 2010 

through February 2011)............................................................................... 88

Figure 3-15. Dissolved oxygen in Lake McClure near the dam (August 2004 through 

December 2006) .......................................................................................... 89

Figure 3-16. Dissolved oxygen in Lake McClure near the dam (January 2007 through 

January 2009) .............................................................................................. 90

Figure 3-17. Dissolved oxygen in Lake McClure near the dam (March 2010 through 

February 2011) ............................................................................................ 91

Figure 3-18. Dissolved oxygen in McSwain reservoir near the dam (August 2004 

through December 2006)............................................................................. 92

Figure 3-19. Dissolved oxygen in McSwain reservoir near the dam (January 2007 

through January 2009)................................................................................. 93

Figure 3-20. Dissolved oxygen in McSwain reservoir near the dam (March 2010 

through February 2011)............................................................................... 94

Figure 3-21. Daily average water temperatures recorded in the Merced River between 

Briceburg (RM 87.9) and the San Joaquin River confluence in water 

year 2006, a representative wet water year ................................................. 97

Figure 3-22. Daily average water temperatures recorded in the Merced River between 

Briceburg (RM 87.9) and the San Joaquin River confluence in water 

year 2008, a representative dry water year.................................................. 98
xv

Figure 3-23. Estimated fall-run Chinook salmon escapement in the Merced River 

from 1970 through 2010, showing fish of natural and hatchery origin for 

years 1981through 2007. ........................................................................... 113

Figure 3-24. Habitat suitability (weighted usable area) for all rainbow trout life 

stages in the riverine sub-reach downstream of Merced Falls dam .......... 116

Figure 3-25. Habitat suitability (weighted usable area) for the lamprey guild, 

Sacramento sucker, and sculpin guild in the riverine sub-reach 

downstream of Merced Falls dam ............................................................. 117

Figure 3-26. Habitat suitability (weighted usable area) for rainbow trout, in the 

impoundment sub-reach downstream of Merced Falls dam ..................... 118

Figure 3-27. Habitat suitability (weighted usable area) for lamprey ammocoete, 

Sacramento sucker juvenile and adult, and sculpin guild juvenile and 

adult in the impoundment sub-reach downstream of Merced Falls dam .. 119

Figure 3-28. Habitat suitability (weighted usable area) for steelhead in sub-reach 1 

downstream of Crocker-Huffman diversion dam...................................... 120

Figure 3-29. Habitat suitability (weighted usable area) for Chinook salmon in subreach 1 downstream of Crocker-Huffman diversion dam......................... 121

Figure 3-30. Habitat suitability (weighted usable area) for hardhead and Sacramento 

splittail in sub-reach 1 downstream of Crocker-Huffman diversion dam. 122

Figure 3-31. Habitat suitability (weighted usable area) for steelhead in sub-reach 2 

downstream of Crocker-Huffman diversion dam...................................... 123

Figure 3-32. Habitat suitability (weighted usable area) for Chinook salmon in subreach 2 downstream of Crocker-Huffman diversion dam......................... 124

Figure 3-33. Habitat suitability (weighted usable area) for hardhead and Sacramento 

splittail in sub-reach 2 downstream of Crocker-Huffman diversion dam. 125

Figure 3-34. Habitat suitability (weighted usable area) for steelhead in sub-reach 3 

downstream of Crocker-Huffman diversion dam...................................... 126

Figure 3-35. Habitat suitability (weighted usable area A) for Chinook salmon in subreach 3 downstream of Crocker-Huffman diversion dam......................... 127

Figure 3-36. Habitat suitability (weighted usable area) for hardhead and splittail in 

sub-reach 1 downstream of Crocker-Huffman diversion dam.................. 128
xvi

Figure 3-37. Comparison of lower Merced River water temperatures in 2004 (a 

critically dry water year) under 115,000 acre-feet (Merced ID’s 

proposed measure) and 265,000 acre-feet (California DFW) 

recommended measure) minimum pool alternatives at Crocker Huffman 

diversion dam (RM 52) and Snelling Bridge (RM 46.5). ......................... 184

Figure 3-38. Water surface elevation of Lake McClure in different water year types.. 303

Figure 3-39. Water surface elevation of McSwain reservoir in different water year 

types........................................................................................................... 304

Figure 3-40. Trails located within the project boundary at Lake McClure ................... 307

Figure 3-41. Map of recreation areas at Merced Falls Project....................................... 312

Figure 3-42. Areas of critical environmental concern identified in Sierra Resource 

Management Plan ...................................................................................... 334

Figure 3-43. Land proposed for exclusion from the project boundary.......................... 338

Figure 3-44. Map of proposed project boundary changes ............................................. 343
xvii

LIST OF TABLES

Table 2-1. Water storage characteristics of Merced River Hydropower Project 

reservoirs ..................................................................................................... 19

Table 2-2. Characteristics of powerhouses associated with the Merced River 

Hydropower Project .................................................................................... 20

Table 3-1. Hydrology for selected sites associated with the Merced River Project..... 70

Table 3-2. Maximum end-of-month storage in Lake McClure for flood control......... 73

Table 3-3. Current minimum flow requirements in the Merced River downstream 

of Crocker-Huffman diversion dam, as measured at Shaffer Bridge.......... 76

Table 3-4. Water quality objectives to support designated beneficial uses in the 

project area .................................................................................................. 78

Table 3-5. Estimated usable cold-water storage volume (acre-feet) in Lake 

McClure below the 15.0°C (59.0°F) isotherm ............................................ 82

Table 3-6. Summary of relative abundance, length, weight, and relative to 

condition factor for fish species collected in Lake McClure in 2010 ....... 103

Table 3-7. Summary of relative abundance, length, and weight of all fish species 

collected at McSwain reservoir in 2010.................................................... 105

Table 3-8. Comparison of alternative water-year type classifications. ...................... 143

Table 3-9. Proposed and recommended minimum and target flows (cfs) by water 

year type during the irrigation season (March through October).............. 145

Table 3-10. Proposed and recommended minimum and target flows (cfs) by water 

year type during non-irrigation season (November-February) as 

measured at Shaffer Bridge ....................................................................... 148

Table 3-11. Effective habitat analysis results showing percent of maximum habitat 

that is unavailable over the life stage period due to thermal conditions 

associated with various flow measures ..................................................... 153

Table 3-12. Average monthly unregulated flow by year type (cfs).............................. 158
xviii

Table 3-13. Comparison of 7DADM simulated water temperature guideline 

exceedance between the environmental baseline conditions and 

proposed and recommended flow regimes for all life stages of Central 

Valley steelhead and fall-run Chinook salmon between CrockerHuffman diversion dam (RM 52.0), Snelling Bridge (RM 46.4), 

Highway 59 Bridge (RM 42.0), and Shaffer Bridge (RM 32.8)............... 164

Table 3-14. Stakeholder recommendations for discrete spring and fall pulse flow 

volumes (acre-feet).................................................................................... 174

Table 3-15. Predicted water supply shortage and carryover storage compared to 

baseline conditions.................................................................................... 181

Table 3-16. Occurrences of noxious and invasive plants identified on the Merced 

River Project vegetation study area........................................................... 225

Table 3-17. Special-status plant species identified in the Merced River Hydroelectric 

Project study area ...................................................................................... 228

Table 3-18. Sensitive wildlife species known to occur or with potential habitat that 

occurs in or within 0.25 mile of the Merced River Project boundary....... 231

Table 3-19. Occurrences of noxious and invasive plants identified in the Merced 

Falls Project vegetation study area............................................................ 241

Table 3-20. Sensitive wildlife species known to occur or with potential habitat 

occurring within the Merced Falls Hydroelectric Project area ................. 244

Table 3-21. Summary of sites assessed for federally threatened and endangered fairy 

shrimp in areas of project-related activities .............................................. 270

Table 3-22. Recreation facilities and capacities at project recreation areas................. 306

Table 3-23. Recreation capacity estimates for Merced Falls Project ........................... 313

Table 3-24. Schedule for rehabilitating existing and constructing new recreation 

facilities..................................................................................................... 321

Table 3-25. Land ownership in the project boundary................................................... 331

Table 3-26. Mariposa County land use categories applicable to land located in the 

vicinity of the Project ................................................................................ 332

Table 3-27. Land ownership in the project boundary................................................... 336
xix

Table 4-1. Parameters for the economic analysis of the Merced River Hydroelectric 

Project........................................................................................................ 362

Table 4-2. Parameters for the economic analysis of the Merced Falls Hydroelectric 

Project........................................................................................................ 363

Table 4-3. Summary of the annual cost of alternative power and annual project cost 

for the alternatives for the Merced River Hydroelectric Project............... 364

Table 4-4. Summary of the annual cost of alternative power and annual project cost 

for the alternatives for the Merced Falls Hydroelectric Project................ 366

Table 4-5. Cost of proposed and recommended measures for the Merced River 

Hydroelectric Project................................................................................. 368

Table 4-6. Cost of proposed and recommended environmental mitigation and 

enhancement measures for the Merced Falls Hydroelectric Project......... 375

Table 5-1. Comparison of alternative water-year type classifications. ...................... 390

Table 5-2. Staff-recommended minimum flows (cfs) by water year type.................. 396

Table 5-3. Comparison of estimated effects and costs of flow regimes associated 

with proposed and recommended flow regimes compared to existing 

conditions .................................................................................................. 398

Table 5-4. Fish and wildlife agency recommendations for the Merced River 

Hydroelectric Project................................................................................. 458

Table 5-5. Fish and wildlife agency recommendations for the Merced Falls 

Hydroelectric Project................................................................................. 489

Table 5-6. Bureau of Land Management preliminary section 4(e) conditions for the 

Merced River Hydroelectric Project ......................................................... 497
xx

This page intentionally left blank.
xxi

ACRONYMS AND ABBREVIATIONS

ACEC area of critical environmental concern

AD Anno Domini

Advisory Council Advisory Council on Historic Preservation

APE area of potential effects

Basin Plan Water Quality Control Plan for the Sacramento River and 

the San Joaquin River Basins

BC Before Christ

BLM U.S. Department of Interior, Bureau of Land Management

BMI benthic macroinvertebrate

BMP best management practice

oC degrees Celsius

California DEC California Data Exchange Center

California DFA California Department of Food and Agriculture

California DFW California Department of Fish and Wildlife

California DWR California Department of Water Resources

California OEHHA California Office of Environmental Health Hazard 

Assessment

California SHPO California State Historic Preservation Officer

Central Valley Water Board Central Valley Regional Water Quality Control Board

cfs cubic feet per second

CFR Code of Federal Regulations

Commission Federal Energy Regulatory Commission

Corps U.S. Army Corps of Engineers

CWA Clean Water Act

CZMA Coastal Zone Management Act

D50 median particle size

DO dissolved oxygen

DPS distinct population segment

EFH Essential Fish Habitat

EIS environmental impact statement

EPA U.S. Environmental Protection Agency

EPT Ephemeroptera, Plecoptera, and Trichoptera

ESA Endangered Species Act

oF degrees Fahrenheit

FERC Federal Energy Regulatory Commission

Forest Service U.S. Department of Agriculture, Forest Service

FPA Federal Power Act

FR Federal Register

FWS U.S. Department of the Interior, Fish and Wildlife Service

GIS Geographic Information System

GWh gigawatt-hour
xxii

Hornitos Bridge Hornitos Road County Bridge

HPMP Historic Properties Management Plan

kW kilowatt

LWD large woody debris

LWM large woody material

mg/L milligrams per liter

Merced Falls Project Merced Falls Hydroelectric Project

Merced ID Merced Irrigation District

Merced River Project Merced River Hydroelectric Project

mm millimeter

msl mean sea level

MW megawatt

MWh megawatt-hour

National Register National Register of Historic Places

NEPA National Environmental Policy Act

NERC North American Electric Reliability Corporation

NHPA National Historic Preservation Act of 1966

NMWSE normal maximum water surface elevation

NMFS National Marine Fisheries Service

NTU nephelometric turbidity unit

NWR National Wildlife Refuge

ORV off-road vehicle(s)

PA Programmatic Agreement

Park Service U.S. Department of the Interior, National Park Service

PG&E Pacific Gas and Electric Company

ppb parts per billion

RM river mile

RST rotary screw trap

SD1 Scoping Document 1

SD2 Scoping Document 2

TCP traditional cultural property

μg/L micrograms per liter

USGS U.S. Department of the Interior, Geological Survey

Water Board California State Water Resources Control Board

WQC water quality certification

WUA weighted usable area
xxiii

EXECUTIVE SUMMARY

On February 26, 2012, Merced Irrigation District (Merced ID) filed an application 

for a new license with the Federal Energy Regulatory Commission (Commission) for the 

continued operation and maintenance of its 101.25-megawatt (MW) Merced River 

Hydroelectric Project. The Merced River Project is located on the main stem of the 

Merced River in Mariposa County, about 23 miles northeast of the city of Merced, 

California. It occupies 3,154.9 acres of federal land administered by the U.S. Department 

of the Interior, Bureau of Land Management (BLM). It generates an average of about 

387 gigawatt-hours (GWh) of energy annually. Merced ID proposes no new capacity and 

no new construction at the project.

On February 8, 2012, Pacific Gas and Electric Company (PG&E) filed an 

application for a new license with the Commission for the continued operation and 

maintenance of its 3.4-MW Merced Falls Hydroelectric Project. The Merced Falls 

Project is located on the Merced River on the border of Merced and Mariposa Counties, 

California. It occupies 1.0 acre of federal land administered by BLM and generates an 

average of about 14.4 GWh of energy annually. PG&E proposes no new capacity and no 

new construction at the project.

The applications for the two projects are being processed together because they: 

(1) are located contiguously on the Merced River; (2) the Merced Falls Project’s 

operation depends entirely on flows released by the upstream Merced River Project; and 

(3) downstream of the Merced River Project, the environmental effects of both projects 

are interrelated.

Project Description and Operation

Merced River Project

The Merced River Project consists of the following two developments (listed from 

upstream to downstream): 

New Exchequer Development

The New Exchequer development is located on the Merced River at river mile 

(RM) 62.5 and consists of: (1) the New Exchequer dam—a rock structure with a 

reinforced concrete upstream face, 490 feet high and 1,220 feet long that impounds Lake 

McClure; (2) an ogee-type, concrete spillway with a 1,080-foot-long, ungated section and 

a 240-foot-long, gated section with six radial gates that are 40 feet wide and 30 feet high; 

(3) an earth-and-rock dike that is 62 feet high and 1,500 feet long; (4) an intake structure 

located upstream of the dam in Lake McClure; (5) a concrete-lined power tunnel that is 

383 feet long and 18 feet in diameter; (6) a concrete-encased, steel penstock that is 982 

feet long and 16 feet in diameter; (7) an above-ground concrete powerhouse that is 75 

feet by 91 feet and discharges directly to the Merced River; and (8) a low-level outlet, 

consisting of a 945.5-foot long, 108-inch-diameter powerhouse bypass pipe with a 
xxiv

Howell-Bunger valve that runs from the New Exchequer power tunnel to McSwain 

reservoir north of the New Exchequer powerhouse. There is no transmission line 

associated with either development. Two PG&E-owned transmission lines connect the 

project to PG&E’s interconnected system at the step-up transformer in the powerhouse 

switchyards. 

Merced ID maintains four recreation areas at Lake McClure: (1) McClure Point, 

which includes a campground, picnic area, swim beach, marina, and boat ramp; 

(2) Barrett Cove, which includes a campground, swim beach, marina with two boat 

ramps, and overflow parking; (3) Horseshoe Bend, which includes a campground, swim 

beach, and boat ramp; and (4) Bagby, which includes a campground, boat ramp, and 

Shepherd’s Point primitive area.

The New Exchequer development is operated in a seasonal store-and-release mode 

with the elevation of the impoundment fluctuating on an annual basis to retain snowmelt 

from springtime runoff for flood control, water supply, recreation, hydropower, and 

environmental purposes. In spring and summer, water levels are maintained relatively 

high for recreation at Lake McClure. From March through October, Merced ID releases 

water primarily for downstream water supply. These releases are also used for 

hydropower generation at the New Exchequer and McSwain powerhouses. The normal 

operational maximum and minimum reservoir elevations for Lake McClure are 867 feet 

and 630 feet, respectively.

The New Exchequer development diverts all flows from Lake McClure through 

the intake, power tunnel, penstock, powerhouse, and low-level outlet and then directly 

releases the flows to McSwain reservoir, which is part of the McSwain development. 

McSwain Development

The McSwain development is located on the Merced River at RM 56.3, and 

consists of: (1) McSwain dam—an embankment structure with a central impervious core 

of rolled fill between shoulders of cobbles or crushed rock—that is 80 feet high and 1,620 

feet long and impounds McSwain reservoir; (2) an ungated concrete overflow spillway 

that is 802 feet long; (3) an intake structure that is integral with the dam; (4) a concrete 

lined power tunnel that is 160 feet long and 15 feet in diameter that leads to; (5) a steel 

penstock that is 160 feet long and 15 feet in diameter; (6) an above-ground, concrete 

powerhouse that is 72 feet by 72 feet and discharges directly into the Merced River and 

(7) a low-level outlet, consisting of a 360-foot-long, 9-foot diameter steel powerhouse 

bypass pipe that runs from the McSwain power tunnel to Merced Falls reservoir with a 

fixed wheel gate at its upstream end and an 8-foot-diameter Howell-Bunger valve on its 

downstream end. There is no transmission line associated with the project. The project 

connects to PG&E’s interconnected system at the step-up transformer in the powerhouse 

switchyard.
xxv

Merced ID maintains the McSwain recreation area at this development, which 

includes a campground, picnic area, group picnic area, informal day use area, swim 

beach, marina, and boat ramp.

The McSwain development is typically operated as a re-regulating afterbay7for 

flows released from Lake McClure. This operation allows the New Exchequer 

powerhouse to be used to meet peak power demands or perform load-following functions 

while still maintaining a steady flow release to the lower Merced River. The normal 

operational maximum and minimum reservoir elevations for McSwain reservoir are 

399.0 feet and 391.5 feet, respectively. Water surface elevations below the normal 

minimum do occur, but they are generally due to atypical operating conditions, such as 

unplanned outages, inspections, or work on the dam.

The McSwain development diverts all flows from McSwain reservoir through the 

intake, power tunnel, penstock, powerhouse, and low-level outlet, and then directly to the 

Merced Falls impoundment.

Merced Falls Project

The Merced Falls Project is located on the Merced River at RM 55 and consists of: 

(1) the 1-mile-long Merced Falls impoundment with approximately 900 acre-feet of 

storage capacity, a useable storage capacity of approximately 579 acre-feet, a total 

surface area of approximately 65 acres, and a normal impoundment elevation of 344 feet 

above mean sea level; (2) a 34-foot-high concrete gravity dam with a crest length of 575 

feet; (3) three radial gates, each 20 feet long and 13.5 feet high; (4) a 1,000-foot-long 

earthen levee with a crest width of 8 feet; (5) an adjacent intake structure with a debris 

rack; (6) a non-operable fish ladder; and (7) powerhouse facilities consisting of a steel 

building housing a 3.4-MW turbine/generator unit and a vertical Kaplan-type

four-blade turbine. 

The Merced Falls project is operated in a run-of-river mode. Inflow to the project 

passes through the impoundment, which is kept at a constant water elevation and then 

either through the powerhouse or the dam’s radial gates. Flows of up to approximately 

1,750 cubic feet per second (cfs) are diverted through the powerhouse, and then 

discharged to the Merced River via the tailrace. When water inflows exceed 2,200 cfs, 

the project spills water through the radial gates. The main section of the dam,

approximately 535.5 feet long, is topped with needle beams. During flood events with 

flows greater than 12,250 cfs, the needle beams can be dropped, allowing the 575-footlong concrete section of the dam to act as a spillway.

 

7 The term afterbay as used here is a reservoir of a hydroelectric power plant at the 

outlet of the turbines.
xxvi

Proposed Facilities

Neither Merced ID nor PG&E propose any upgrades or new project facilities.

Proposed Environmental Measures 

Merced River Project

Merced ID proposes the following environmental measures:

General Measures (could apply to more than one resource area)

 Consult annually (at a minimum) with BLM regarding measures needed to 

ensure protection and use of resources on federal land administered by 

BLM and affected by the project.

 Consult with BLM regarding any potential future new facilities on federal 

land.

 Consult with BLM regarding any potential future new ground-disturbing 

activities on or directly affecting BLM lands that were not specifically 

addressed in the Commission’s National Environmental Policy Act 

(NEPA) process.

Aquatic Resources

 Develop a plan to coordinate project operation with the downstream, runof-river Merced Falls Project to assure implementation of flow-related 

measures at the two projects.

 Develop an erosion control and restoration plan at least 90 days in advance 

of initiating construction of project facilities on BLM-managed land.

 Develop a recreation facilities construction hazardous material spill 

prevention, control, and countermeasures plan at least 90-days in advance 

of initiating construction of recreation facilities.

 Deliver 15,000 acre-feet of water to Merced National Wildlife Refuge 

(NWR) at a single delivery point during Merced ID’s irrigation season.

 Operate the project for flood control in accordance with the rules and 

regulations specified by the U.S. Army Corps of Engineers (Corps).

 Provide minimum flows (from 40 to 180 cfs as measured at Shaffer Bridge 

depending on time of year and water year type).
xxvii

 Provide target flows (from 50 to 225 cfs as measured at Shaffer Bridge, 

depending on time of year and water year type).

 Limit all controllable flow rate changes above a base flow of 200 cfs 

during any 1-hour period to not more than double or less than half the 

amount of the controlled release from McSwain dam at the start of the 

change.

 Continue to determine water year type using Merced 60-20-20 Index.

8

 Notify the California State Water Resources Control Board (Water Board), 

BLM, the U.S. Fish and Wildlife Service (FWS), the National Marine 

Fisheries Service (NMFS), and the California Department of Fish and 

Wildlife (California DFW) by March 10 of the second or subsequent 

dry/critically dry water year if Merced ID has drought concerns (i.e., if 

there may not be sufficient water to meet both environmental and 

irrigation demands). By May 1 of these same years (i.e., the second or 

subsequent dry/critically dry water years), consult with the agencies to 

discuss the project’s operational plans to manage drought conditions and 

file a drought plan with the Commission with a request for expedited 

approval.

 Maintain the Lake McClure minimum pool at elevation 640 feet9and the 

minimum pool of McSwain reservoir at or above elevation 388 feet, unless 

drawdowns are needed to maintain required minimum flows.

 

8 Merced ID established a five-level water year classification system for the 

Merced River. The 60-20-20 Index is based on the unregulated inflow to Lake McClure. 

The five-water year classifications are: wet, above normal, below normal, dry, and 

critical and are calculated as 60 percent of the current year’s April through July inflow 

plus 20 percent of the current year’s October through March inflow plus 20 percent of the 

previous year’s index.

9 An elevation of 640 feet in Lake McClure corresponds to a volume of 115,000 

acre-feet.
xxviii

 Operate four water temperature monitoring recorders at suitable sites in the 

Merced River downstream of Crocker-Huffman diversion dam, as selected 

by a technical advisory committee.10 

 Continuously monitor anadromous fish migrating into the Merced River at 

an Alaskan weir or similar device to be installed and operated from 

October 1 through December 31, using a VAKI RiverwaterTM system, and 

identify the time and direction of migration, size, sex, marks, and other 

attributes. Monitor juvenile anadromous fish outmigration from the 

Merced River from January 1 through May 31 with a rotary screw trap 

(RST) and document the total number and, for a representative subsample 

of the catch, size, weight, and life stage. 

 Establish a Merced River anadromous fish committee (also known as a 

technical advisory committee), consisting of representatives from NMFS, 

FWS, California DFW, the Water Board, and a non-governmental 

organization, that would meet four times a year to facilitate Merced ID’s 

implementation of license conditions that pertain to monitoring 

anadromous fish. An annual report would be filed with the Commission 

by January 1 of each year documenting the activities of the committee 

during the previous calendar year.

 Implement the amended Aquatic Invasive Species Management Plan filed 

on April 23, 2014, and supplemented on September 5, 2014, to provide 

guidance for the prevention of aquatic invasive species in project 

reservoirs.

 Develop a large woody debris (LWD) management plan that excludes 

BLM-managed land from any stockpiling activities to provide LWD to the 

Merced River downstream of Crocker-Huffman diversion dam to enhance 

aquatic habitat.

 

10 Merced ID proposes to establish a Merced River anadromous fish committee to 

include, by invitation, representatives from NMFS, FWS, California DFW, the Water 

Board, and a non-governmental organization member selected by Merced ID that would 

participate at its own expense. Merced ID would organize four committee meetings each 

year to review the results of draft annual reports pertaining to Chinook salmon and 

Oncorhynchus mykiss (O. mykiss) downstream of Crocker-Huffman diversion dam and to 

identify potential modifications to monitoring methods and protocols. In this draft 

environmental impact statement (EIS), O. mykiss refers to both the anadromous 

(steelhead) and resident (rainbow trout) form of this species.
xxix

Terrestrial Resources

 Implement the Invasive Species Management Plan on federal land, filed 

with the final license application and amended on September 22, 2014.

 Implement the Vegetation Management Plan on federal land, filed with the 

final license application, as amended, to protect special-status plants and 

minimize project effects on sensitive habitats.

 Avoid the use of pesticides and herbicides on land administered by BLM 

without the prior written approval of BLM.

 Implement the Bald Eagle Management Plan, filed with the license 

application.

 Document all known bat roosts at project facilities, and if bats could be 

subject to human disturbance, install exclusion devices.

 Implement the Limestone Salamanders Sensitive Areas Management Plan, 

filed with the license application.

 Record observations of western pond turtles to conserve this special-status 

species and its habitats on BLM lands.

Threatened and Endangered Species

 Provide annual training for project operation and maintenance staff to 

identify special-status species and sensitive areas that should be protected 

and non-native species to be treated.

 On an annual basis, review special-status species lists and assess potential 

project effects on any newly listed special-status species, and if necessary,

consult with the agencies to develop and implement protection measures.

 Avoid the use of burrow fumigants and rodenticides in habitat of the 

California tiger salamander and the San Joaquin kit fox when performing 

project maintenance activities.

Recreation Resources

 Implement the Recreation Facilities Plan, amended on September 22, 

2014. 

 Provide real-time recreation information on the California Data Exchange 

Center (California DEC), including:

– flow information for the Merced River below Merced Falls, Dry Creek 

near the city of Snelling, and the Merced River near the cities of 

Snelling, Cressey, and Stevinson;

– elevations for Lake McClure and McSwain reservoir; and
xxx

– flow information for the Merced River at Shaffer Bridge (U.S. 

Department of the Interior, Geological Survey [USGS] gage no. 

11271290). 

 Construct a parking area and install river access directional signage at the 

existing gravel-surfaced parking area at Merced Falls Road near CrockerHuffman diversion dam.

 Develop a conceptual plan to align the existing Merced River Trail to a 

new trail segment that would follow along the shoreline of Lake McClure 

and McSwain reservoir.

 Annually stock rainbow trout, fingerling kokanee, and Chinook salmon in 

Lake McClure and McSwain reservoir for recreational fishing.

Land Use

 Implement the Transportation Management Plan, filed on September 22, 

2014, to ensure project roads are adequately maintained.

 Implement the Fire Prevention and Response Plan, revised on September 

22, 2014, to provide for management, reporting, and the prevention of 

wildfires at the project.

Cultural Resources

 Implement the Historic Properties Management Plan (HPMP) upon filing 

to manage project effects on properties eligible for listing on the National 

Register of Historic Places (National Register).

Aesthetic Resources

 Implement the Visual Resource Plan, filed on September 22, 2014, to 

ensure visual quality objectives at the project are met through monitoring 

and consultation.

Merced Falls Project

PG&E proposes the following environmental measures.

Aquatic Resources

 Conduct annual fall fish sampling in the reach of the Merced River 

downstream of Merced Falls dam and upstream of Crocker-Huffman dam 

(Merced Falls reach) to monitor fish populations.

 Continue to periodically rake the project’s intake racks to clear them of 

LWD, and place the removed material on the debris chute at the dam to 

allow the debris to pass downstream.
xxxi

Water Resources

 Develop and implement a long-term water quality monitoring program to 

monitor dissolved oxygen and temperature in the Merced Falls reach to 

confirm adherence to water quality standards.

Recreation

 Continue to operate and maintain the existing recreation facilities at the 

Merced Falls impoundment area, including the River’s Edge Fishing 

Access area and the car-top boat launch at Merced Falls Fishing Access 

area.

 Develop and post directional and safety signage at the project’s informal 

canoe portage trail.

 Develop a fish stocking plan in consultation with California DFW that 

includes stocking 11,000 adult-sized rainbow trout at the Merced Falls 

impoundment for the first 2 years following license issuance and a plan for 

stocking (schedule and type and amount of fish) for the rest of the license 

term.

Cultural Resources

 Implement the HPMP filed on October 6, 2014.

Alternatives Considered

This draft environmental impact statement (EIS) analyzes the effects of continued 

project operation and recommends conditions for any new licenses that may be issued for 

these projects. In addition to Merced ID’s and PG&E’s proposals, we consider three 

alternatives for each project: (1) Merced ID’s and PG&E’s proposals with staff 

modifications (staff alternative); (2) the staff alternative with all mandatory conditions

filed by BLM and the Water Board; and (3) no action, meaning the projects would 

continue to be operated as they presently are with no changes.

Staff Alternative—Merced River Project

Under the staff alternative, the project would include most of Merced ID’s 

proposed measures, as outlined above with the exception of Merced ID’s proposed 

minimum and target flows, its proposed review of special-status species lists, and its 

proposal to consult annually with BLM regarding measures needed to ensure protection 

and use of resources on federal land administered by BLM and affected by the project. 

Under the staff alternative, the project would also include most of BLM’s mandatory 

section 4(e) conditions and the Water Board’s mandatory water quality certification 

conditions with the exception of the following due to cost and project nexus 

considerations: (1) annual funding costs incurred by BLM; (2) annual consultation to 
xxxii

review the project status for newly listed species; (3) a fish passage or habitat restoration 

plan; and (4) a review of federally listed and special-status species lists. 

Under the staff alternative, the project would also include the following additional 

measures and modifications.

Aquatic Resources

 Expand the scope of the proposed technical advisory committee beyond 

measures that pertain only to anadromous fish downstream of CrockerHuffman diversion dam (e.g., topics that pertain to resident fish, aquatic 

and terrestrial monitoring results, and actions that could affect BLMmanaged land, including Lake McClure water level management); 

establish guidelines for conducting meetings that provide ground rules for 

decision making; and add BLM and the U.S. Department of the Interior, 

National Park Service (Park Service) to the entities invited to participate 

on the committee.

 Add the Water Board, BLM, FWS, California DFW, NMFS, and the Park 

Service to the entities invited to consult on the proposed coordinated 

operation plan for the projects.

 Add the Water Board, California DFW, and FWS to the entities invited to 

consult on the proposed site-specific erosion control and restoration plans 

and expand the plans to apply to all construction on land within the project 

boundary.

 Include, at a minimum, the following elements in the proposed erosion 

control and restoration plans: (1) a description of best management 

practices (BMPs) that would be applied in specific circumstances, 

(2) provisions for inspecting erosion control measures while they are in 

place, (3) emergency protocols for erosion and sedimentation control, 

(4) site stabilization techniques that would be used once construction is 

completed, and (5) a description of when and what type of water quality 

monitoring of surface waters would occur during and after grounddisturbing activities. Identifying such measures and protocols in the 

erosion control and restoration plans would assure that erosion does not 

unacceptably degrade water quality adjacent to construction and other 

ground-disturbance sites. 

 In addition to monitoring ramping rates associated with releases from 

McSwain dam, monitor flows and stage at 1-hour intervals at the existing

gage immediately downstream of Crocker-Huffman diversion dam and 

provide annual reports to the Commission from both gages after review by 

the technical advisory committee. Monitoring flows at both locations 

would document compliance with the recommended ramping rate at 
xxxiii

McSwain dam and establish a relationship between the ramping rates at 

McSwain dam and the ramping rates downstream of Crocker-Huffman 

diversion dam and would provide data on whether or not the ramping rate 

protocol should be adjusted in the future. 

 Include, at a minimum, the following elements in the proposed

construction and non-routine maintenance hazardous material spill 

prevention, control, and countermeasure plans: (1) a description of the 

BMPs for contaminant control that would be applied in specific 

circumstances; (2) emergency protocols for spill containment and 

remediation; (3) the location of emergency cleanup equipment in the event 

of contaminant release; (4) identification of entities to be contacted in the 

event of a spill; (5) designated equipment refueling and maintenance areas;

(6) provisions requiring equipment to be cleaned and inspected prior to 

entering a construction site; (7) post-spill water quality monitoring 

protocols; and (8) a listing of applicable local, state, and federal 

regulations that pertain to prevention of spills and protection of water 

quality. Identifying such measures and protocols in the hazardous 

materials spill prevention, control, and countermeasure plans would assure 

that surface water and groundwater are protected from contaminants.

 Use the Hughes method to determine water year type rather than the 

currently used and proposed Merced 60-20-20 Index to better designate

water year types based on both forecasted and observed runoff and avoid 

biases on below normal water conditions.

 Release the instantaneous minimum flows as measured at Shaffer Bridge 

and shown in table 5-2 for the purpose of enhancing physical habitat, 

density-dependent conditions, and water temperature for Chinook salmon 

and O. mykiss.

 Maintain a minimum flow of 25 cfs at all times from New Exchequer dam

to ensure that the channel is not dewatered.

 Develop a water temperature monitoring plan in consultation with the 

technical advisory committee and monitor water temperature at four to 

eight sites (rather than limiting the number of sites to four) from CrockerHuffman diversion dam, downstream to Shaffer Bridge.

 Release a fall pulse flow of 1,000 cfs measured at Shaffer Bridge, during 

October or November until a total volume of 12,500 acre-feet is released

to attract adult anadromous salmonids to the mouth of the Merced River 

and stimulate upstream migration to the primary spawning area between 

Crocker-Huffman diversion dam and Shaffer Bridge. The timing of the 

beginning of the release would be determined by the technical advisory 

committee.
xxxiv

 Release a spring pulse flow of 30,000 acre-feet during wet, above normal, 

and below normal water years. This spring pulse flow would consist of 

flows equal to or above 1,000 cfs, measured at Shaffer Bridge, of 9 days 

and peak flows that hold for 2 or 3 days, with a gradually ascending and 

descending hydrograph. 

– During dry and critically dry water years, release a spring pulse flow of 

10,000 acre-feet. 

– After a minimum of two dry or critically dry water years, consult with 

the technical advisory committee and make recommendations to the 

Commission regarding whether anadromous fish outmigration data 

supports changing the 10,000 acre-feet pulse flow release. The spring 

pulse flow would stimulate outmigration of rearing anadromous 

salmonids and inundate riparian floodplains, which would provide 

benefits to salmonid habitat. 

– The timing of the onset of the spring pulse flow release would be 

determined by the technical advisory committee.

 Annually report Lake McClure stage and acre-feet of storage to the 

Commission to document compliance with water management measures 

and, when applicable, drought management plans.

 File the proposed drought plans, developed after two or more consecutive 

dry or critically dry water years, with the Commission for approval.

 Develop a drought management plan in consultation with the technical 

advisory committee that identifies the measures that would be considered 

to address droughts when they occur, decision paths regarding how 

management options for a specific drought would be decided, and a listing 

of Commission, BLM, and water quality certification (WQC) license 

conditions that would require variances with drought management options. 

Approval of this management plan would expedite approval of the 

proposed drought-specific plan, which would be time-sensitive.

 Develop a Merced NWR water delivery plan, in consultation with FWS 

and California DFW, to ensure to the extent practical, the delivery of 

15,000 acre-feet of water to the refuge during times of the year when this 

water would provide the most benefit to wildlife.

 Develop, in consultation with the technical advisory committee, an 

anadromous fish monitoring plan that includes the attributes Merced ID 

proposes to monitor. Include in the plan the proposed monitoring station 

locations, the rationale for selecting those locations, and corrective actions 

that could be taken, including assisting with fish rescue efforts, if 

monitoring shows the project is adversely affecting anadromous fish.
xxxv

 Add the technical advisory committee and California Department of 

Transportation to the entities invited to consult on the large woody 

material (LWM) management plan.

 Develop a gravel augmentation plan in consultation with the technical 

advisory committee that (1) provides for the annual placement of 2,600 

cubic yards of gravel in the lower Merced River; (2) identifies the range of 

particle sizes to be used for augmentation; (3) identifies gravel harvesting 

sites; (4) includes provisions for restoring harvest sites to mitigate for any 

aesthetic or ecological impact associated with gravel harvesting;

(5) includes the protocol for selecting augmentation sites between Merced 

Falls dam and Shaffer Bridge; (6) provides for monitoring and mapping 

augmented gravel; and (7) provides for annual reporting.

 Modify the Amended Aquatic Invasive Species Management Plan to 

include provisions for documenting observations of quagga and zebra 

mussels, New Zealand mudsnails, Asian clams, American bullfrog, 

Eurasian milfoil, Brazilian elodea and hydrilla; provide reports to the 

Commission regarding any incidental observations that rise to the level of 

needing follow-up management actions, and add California DFW and the 

Water Board to the entities invited to consult on revisions to the plan.

Terrestrial Resources

 Develop a protection plan for special-status bats after consultation with 

BLM, FWS, California DFW, and the Water Board to protect bats roosting 

at project facilities. The plan would include specific details about agencyrecommended measures and proposed measures to document all known 

bat roosts at project facilities, the type and design of exclusion devices, 

and define appropriate metrics to evaluate the effectiveness of the 

measures.

 Modify the proposed Bald Eagle Management Plan to:

– include educational information about bald eagle roost sites in public 

information; 

– describe activities that would be considered emergencies, and define 

why these activities would supersede bald eagle protection;

– protect winter roost trees from vegetation management and future 

construction activities to reduce potential for degrading these areas; and

– revise all protocols and methodologies to be consistent with the FWS

National Bald Eagle Management Guidelines.
xxxvi

 Modify the Invasive Species Management Plan on federal land to:

– stipulate that the measures in the plan apply to all land within the project 

boundary, including treatment measures for the existing population of 

perennial pepperweed on Merced ID land; 

– provide details about specific BMPs that would be implemented as part 

of the plan;

– include notification to agencies of planned pesticide use; and

– include descriptions of unexpected outbreaks that would not require 

notification prior to use of pesticides.

 Modify the Vegetation Management Plan on federal land to:

– provide details about specific BMPs that would be implemented as part 

of the plan; 

– include maps in section 3.0 to show locations of elderberry plants and 

identify which plants show signs of occupancy by the valley elderberry 

longhorn beetle; and

– include consultation with BLM, California DFW, and FWS during the 

planning phases for any new disturbance such as any potential future 

construction of new facilities and other project operation and 

maintenance activities that could disturb vegetation resources through

excavation, grading, topsoil stripping, or other similar activities, to 

identify the need for pre-disturbance surveys and develop protection 

measures for any sensitive species in the disturbance area.

 Develop a protection plan for western pond turtles, including the proposed 

monitoring and reporting measures to protect western pond turtles from 

project effects such as water level fluctuations, traffic associated with 

project maintenance and recreation, and maintenance activities such as 

pesticide applications.

 Modify the Limestone Salamanders Sensitive Areas Management Plan to:

– provide details about the specific BMPs that would be implemented as 

part of the plan; and

– site new hiking trails or modifications to existing hiking trails outside of 

limestone salamander habitat. 

Threatened and Endangered Species

 Develop a protection plan for the San Joaquin kit fox, including surveys 

and the development of protection and mitigation measures to minimize 

project-related effects (i.e., effects of rodenticides, potential effects on 

dispersal).
xxxvii

 Develop a protection plan for the vernal pool fairy shrimp and its habitat to 

reduce project effects (i.e., long-term habitat degradation).

 Develop a protection plan for federally listed plants potentially occurring 

in the project area to minimize project effects (i.e., project maintenance 

activities, recreation) on these plant species.

 Develop a protection plan for the California red-legged frog, foothills 

yellow-legged frog, and western spadefoot to reduce project effects (i.e., 

changes in water temperature, increases in the populations of predators, 

and pesticide use).

 Develop a protection plan for California tiger salamanders that includes a

proposed measure to avoid use of pesticides in California tiger salamander 

habitat to protect the species from project effects (i.e., effects of 

rodenticides and burrow fumigants, vegetation maintenance, recreation 

activities, and vehicular traffic).

Recreation Resources

 Modify the proposed Recreation Facilities Plan, filed on September 22, 

2014, to:

– extend the proposed paved bicycle lane along the entire length of Lake 

McClure Road (7.8 miles) between County Road J16 and the proposed 

parking area from the McSwain shoreline trailhead;

– remove the provision for a host site at the project’s Horseshoe Bend 

recreation area campground;

– identify the location of the three floating restrooms provided on Lake 

McClure, and include an operation and maintenance schedule and 

construction and rehabilitation measures (if needed) for each restroom; 

and

– revise the implementation schedule to: begin construction no earlier 

than Labor Day and no later than Memorial Day to avoid the prime 

recreation season; begin construction at Bagby recreation area within 2 

years of license issuance; begin construction of the project’s nonmotorized trails within 3 years of license issuance; begin rehabilitation 

planning at each campground within 3 years of license issuance (to be 

completed within 6 years of license issuance: and include a mid-license 

term rehabilitation assessment in the implementation schedule that 

would identify any facilities and or water systems in need of 

rehabilitation. 
xxxviii

 Develop and implement a fish stocking plan that includes the type, size, 

and amount of fish to be stocked in Lake McClure and McSwain reservoir

based on recreational use, angling demand, and state fish stocking 

management targets and an implementation schedule to ensure appropriate 

recreational fish stocking levels at the project for the license term. 

Land Use

 Modify the Transportation Management Plan, filed on September 22, 

2014, to include an inventory of all project roads and current road 

conditions, a detailed schedule of maintenance based on that inventory, 

relevant BMPs that would be implemented, a schedule for monitoring 

project road use over the term of the license, and a schedule for 

consultation with BLM and the California Department of Forestry and Fire 

Protection.

Aesthetics

 Modify the Visual Resource Plan, filed on September 22, 2014, such that it 

applies to all lands within the project boundary.

Staff Alternative—Merced Falls Project

Under the staff alternative, the project would be operated and maintained as 

proposed by PG&E with the modifications and additional measures described below. 

Our recommended modifications and additional environmental measures include, or are 

based on, recommendations and conditions made by federal and state resource agencies 

and Conservation Groups that have an interest in resources that may be affected by the 

operation of the proposed project.

Under the staff alternative, the project would include most of PG&E’s proposed 

measures, as outlined above with the exception of PG&E’s proposed modification to 

remove 4.8 acres from the project boundary (75.6 to 70.8 acres) at the northeastern 

shoreline of the Merced Falls impoundment. Under the staff alternative, the project

would also include most of the Water Board’s mandatory water quality certification 

conditions with the exception of the following due to cost and project nexus 

considerations: (1) a gravel augmentation plan for Merced Falls reach; (2) a fish passage 

plan; and (3) a review of federally listed and special-status species lists. 

Under the staff alternative, the project would also include the following additional 

measures and modifications: 

Aquatic Resources

 Participate in a Merced River technical advisory committee in conjunction 

with Merced ID to inform and coordinate the implementation of 

environmental measures.
xxxix

 Develop a coordinated operation plan, in conjunction with Merced ID, for 

the Merced River and Merced Falls Projects in consultation with the 

technical advisory committee.

 Develop a LWD management plan in consultation with the technical 

advisory committee to provide habitat enhancement for aquatic species.

 Develop an annual fish monitoring plan in the reach of the Merced River 

downstream of Merced Falls dam and upstream of Crocker-Huffman dam 

(Merced Falls reach) in consultation with the technical advisory 

committee.

Terrestrial Resources

 Develop a control plan for noxious weeds and invasive plants, with a 

component for pest management and pesticide use.

 Develop and implement a management plan for bald eagles in consultation 

with BLM, FWS, California DFW, and the Water Board.

Threatened and Endangered Species

 Develop a protection plan for the valley elderberry longhorn beetle to 

minimize project effects on the valley elderberry longhorn beetle and its 

habitat.

 Develop a protection plan for the San Joaquin kit fox to reduce projectrelated and cumulative effects on the San Joaquin kit fox.

 Develop a protection plan for the California red-legged frog, foothills 

yellow-legged frog, and western spadefoot to reduce project effects on 

these species.

Recreation

 Operate and maintain all recreation facilities at the Merced Falls Fishing 

Access area, including one sign, restroom, parking area, and car-top boat 

launch, the informal angler trail along the northern shoreline, the two 

informal parking areas on either side of Hornitos Road County Bridge, and 

the informal canoe portage trail at the south end of Merced Falls dam.

Project Boundary

 Modify the project boundary to include the informal canoe trail on the 

south side of Merced Falls dam.
xl

Staff Alternative with Mandatory Conditions

BLM filed preliminary conditions for the Merced River Project pursuant to section 

4(e) of the FPA by letter dated July 22, 2014. The Water Board issued preliminary WQC 

conditions for the Merced River and Merced Falls Projects pursuant to section 401 of the 

Clean Water Act by letters dated July 22, 2014. We recognize that the Commission is 

required to include valid section 4(e) conditions and section 401 conditions in any 

licenses issued for the projects. The staff alternative with mandatory conditions includes 

the staff-recommended measures noted above as well as the mandatory conditions filed 

by BLM and the Water Board.

Public Involvement and Areas of Concern

Both Merced ID and PG&E used the Commission’s Integrated Licensing Process 

to prepare their license applications. The intent of the Commission’s pre-filing process 

under the Integrated Licensing Process is to initiate public involvement early in the 

project planning process and to encourage citizens, governmental entities, tribes, and 

other interested parties to identify and resolve issues prior to an application being 

formally filed with the Commission. 

Merced River Project 

As part of the pre-filing process, we distributed a scoping document (SD1) to 

interested parties on January 2, 2009, soliciting comments, recommendations, and 

information on the project. Scoping meetings were held in Merced, California, on 

January 28, 2009. We conducted a site visit on January 29, 2009. Based on discussions 

during the site visit and written comments filed with the Commission, we issued a second 

scoping document (SD2) on April 17, 2009. On March 24, 2014, we issued a notice that 

Merced ID’s application to relicense the Merced River Project was ready for 

environmental analysis and requested conditions and recommendations.

The primary issues associated with relicensing the project are flow quantity and 

timing in the lower Merced River; the availability and enhancement of Chinook salmon 

and O. mykiss spawning and rearing habitat in the lower Merced River; water quality; 

protection and management for federally listed and special-status species; vegetation 

management; management of noxious weeds and invasive plants, including pest 

management and pesticide use; recreation access; maintenance of recreation sites; and 

maintenance of project roads.

Merced Falls Project 

As part of the pre-filing process, we distributed SD1 to interested parties on April 

24, 2009, soliciting comments, recommendations, and information on the project. Based 

written comments filed with the Commission, we issued SD2 on August 6, 2009. On 

March 24, 2014, we issued a notice that the application was ready for environmental 

analysis and requested conditions and recommendations. 
xli

The primary issues associated with relicensing the project are coordination with 

Merced ID on project operation and the implementation of environmental measures; the 

incremental contribution of the project on water temperature and availability of fish 

habitat in the lower Merced River; protection and management of federally listed and 

special-status species; management of noxious weeds and invasive plants, including pest 

management and pesticide use; recreation access; and maintenance of recreation sites.

Staff Alternative Discussion

Merced River Project

Aquatic Resources

Implementation of the proposed site-specific and general erosion control and 

restoration plans and construction and non-routine maintenance hazardous materials spill 

prevention, control, and countermeasure plans with the additional staff-recommended 

elements would ensure that BMPs are in place and that project waters would be protected 

from sedimentation and contaminants during construction and non-routine maintenance 

that entails ground-disturbing activities. 

Current and proposed minimum flows provide minimal habitat in the lower 

Merced River for Chinook salmon and O.mykiss. Under the staff alternative, the

minimum flow regime would enhance habitat in the lower Merced River for Chinook 

salmon and O. mykiss while balancing Lake McClure water storage for irrigation and 

water temperature enhancements.

Spring pulse flows do no occur under existing conditions, nor does Merced ID 

propose spring pulse flows. Under the staff alternative, the implementation of spring 

pulse flows would inundate riparian floodplains during most water year types, providing 

young anadromous salmonids with access to additional cover and foraging habitat, 

thereby enhancing anadromous fish populations. Spring pulse flows would also stimulate 

riparian forest growth that could provide shade to the river channel and additional 

temperature enhancement for salmonids. During all water year types, a spring pulse flow 

would stimulate outmigration of rearing anadromous salmonids prior to the onset of harsh 

low flow, high temperature summer conditions. 

Merced ID does not propose any fall pulse flow releases. Under the staff 

alternative, fall pulse flow releases would serve to attract adult anadromous salmonids to 

the mouth of the Merced River and stimulate upstream migration to the primary 

spawning area between Crocker-Huffman diversion dam and Shaffer Bridge. 

The staff-recommended minimum flows and pulse flows downstream of CrockerHuffman diversion dam would result in the diversion of less water for irrigation purposes, 

which could adversely affect agricultural interests served by Merced ID.

The project would continue to contribute to a lack of LWD/LWM in the lower 

Merced River. LWD/LWM provides important habitat for aquatic organisms. 
xlii

Implementation of the proposed LWD/LWM management plan, with staff-recommended 

elements, would enhance physical habitat and other ecological conditions for Chinook 

salmon, O. mykiss, and other aquatic organisms that may provide forage for anadromous 

fish in the lower Merced River. 

The project would continue to contribute to a lack of sediment, required by 

salmonids for spawning, in the lower Merced River. The staff-recommended gravel 

augmentation plan would enhance salmonid populations by introducing spawning-sized 

gravel to areas of the lower Merced River and would ensure that gravel harvest sites 

would be regraded after harvest to mitigate for any aesthetic impacts and reestablish a 

more natural floodplain topography at the harvest sites. 

The proposed monitoring of anadromous fish and water temperature, with 

additional staff-recommended elements, would allow stakeholders to evaluate the 

effectiveness of environmental measures, such as minimum flow and pulse flow 

prescriptions. Additionally, monitoring would serve to trigger the need for additional

protective measures if water temperatures become unusually stressful when anadromous 

fish are present. 

Terrestrial Resources

Project operation, maintenance, and recreation activities would cause noise 

resulting in disturbance to nesting and roosting bald eagles, and vegetation management 

activities could also result in the removal of nest trees or roost trees. Under the staff 

alternative, the proposed Bald Eagle Management Plan would be revised to include a 

public education component and to be consistent with FWS guidelines for eagle 

management. Operation and maintenance of the project and construction of any new 

facilities could disturb vegetation resources through excavation, grading, topsoil 

stripping, or other similar activities, could contribute to the spread and establishment of 

invasive plants. Project maintenance activities, such as vegetation maintenance and 

pesticide applications, could adversely affect sensitive plants and wildlife. Under the 

staff alternative: (1) the Invasive Species Management Plan would be modified to 

require advance notification to agencies regarding planned pest management and 

pesticide use; (2) the Vegetation Management Plan would be modified to (i) provide 

details about specific BMPs that would be implemented as part of the plan, (ii) include 

maps showing locations of elderberry plants with signs of occupancy by the valley 

elderberry longhorn beetle, (iii) require consultation with BLM, California DFW, and 

FWS during the planning phases for any new disturbance to identify the need for predisturbance surveys and (iv) develop protection measures for any sensitive species in the 

disturbance area; and (3) the Limestone Salamander Monitoring Plan would be modified 

to site new hiking trails outside of limestone salamander habitat. Because special-status 

bat species roosting in project facilities could be disturbed by human presence, the staff 

alternative would include a protection plan for special-status bats. The staff alternative 

would also include a protection plan for western pond turtles to conserve western pond 

turtles observed on project lands.
xliii

Threatened and Endangered Species

The Central Valley steelhead, federally listed as threatened, occurs within the San 

Joaquin River and likely occurs in the Merced River downstream of Crocker-Huffman 

diversion dam. Staff-recommended measures, including increased minimum flows, fall 

and spring pulse flows, and gravel augmentation would enhance (1) fall attraction flows 

for adult steelhead; (2) spawning substrate; (3) water temperature during spring rearing 

and smoltification; (4) off-channel habitat, floodplain connectivity, and juvenile 

emigration triggers with spring pulse flows; and (5) physical habitat. With these 

measures, continued operation of the Merced River Project is not likely to adversely 

affect the Central Valley steelhead.

Five federally listed animal species and five federally listed plant species occur or 

potentially occur in the project area: San Joaquin kit fox (Vulpes macrotis mutica), 

California red-legged frog (Rana aurora draytonii), California tiger salamander 

(Ambystoma californiense), valley elderberry longhorn beetle (Desmocerus californicus 

dimorphus), and vernal pool fairy shrimp (Branchinecta lynchi); Keck’s checkerbloom 

(Sidalcea keckii), Layne’s ragwort (Packera layneae), Chinese Camp brodiaea (Brodiaea 

pallida), Mariposa pussypaws (Calyptridium pulchellum), and California vervain 

(Verbena californica). The project area overlaps with about 1 acre of critical habitat for 

the vernal pool fairy shrimp, and also with one recovery unit identified for the California 

red-legged frog.

Project operation supports habitat for bullfrogs and predatory fishes, which would 

adversely affect California red-legged frogs through increased predation. Herbicide 

applications also could adversely affect this species. The use of rodenticides and burrow 

fumigants to control rodents on project lands would adversely affect the San Joaquin kit 

fox and California tiger salamander. The California tiger salamander also could be 

adversely affected by vehicular traffic and foot traffic from recreation and vegetation 

maintenance. Project maintenance activities, such as pesticide use and vegetation 

maintenance, would adversely affect Keck’s checkerbloom, Layne’s ragwort, Chinese 

Camp brodiaea, Mariposa pussypaws, and California vervain, in addition to the valley 

elderberry longhorn beetle by affecting its obligatory host plant, the elderberry shrub. 

Project maintenance activities and vehicular traffic would adversely affect vernal pool 

fairy shrimp and could modify adjacent habitats by causing long-term habitat 

degradation. With the development and implementation of the various staffrecommended plans, the Merced River Project is not likely to adversely affect San 

Joaquin kit fox, California red-legged frog, California tiger salamander, valley elderberry 

longhorn beetle, vernal pool fairy shrimp, Keck’s checkerbloom, Layne’s ragwort, 

Chinese Camp brodiaea, Mariposa pussypaws, and California vervain. 
xliv

Recreation, Land Use, and Aesthetics

Numerous recreational opportunities exist at the Merced River Project. 

Implementing Merced ID’s proposed Recreation Facilities Plan with the staffrecommended modifications would enhance recreation opportunities further and ensure 

operation and adequate maintenance of existing and proposed recreational facilities at the 

project. Implementing Merced ID’s proposed measures to implement off-road vehicle 

(ORV) road closures, improve existing trails, and provide more trail access at the project 

would ensure safe, reliable access over the term of the license. Development and 

implementation of the staff-recommended fish stocking plan would ensure that fish 

stocking continues at the project reservoirs and would allow for changes in stocking 

numbers based on recreational use and state stocking targets.

Implementation of the proposed Transportation Management Plan, Fire Prevention 

and Response Plan, and Visual Resource Plan would ensure that project roads are 

maintained to applicable standards; improve the prevention, management, and 

coordination of potential wildfires; and improve overall visual quality at the project.

Merced Falls Project 

Aquatic Resources

The project is located immediately downstream of Merced ID’s Merced River 

Project and would continue to operate run-of-river, thus maintaining its operational 

dependence on the upstream Merced River Project. Under the staff alternative, PG&E 

would develop a coordinated operations plan that would ensure effective cooperation 

between Merced ID and PG&E in the implementation of any operational scenarios, such 

as flow releases to the lower Merced River, or maintenance-related reservoir drawdowns. 

Additionally, PG&E would participate in a technical advisory committee in conjunction 

with Merced ID, which would ensure coordination between the licensees for the Merced 

River and Merced Falls Projects and adaptively manage resources during the term of the 

licenses. PG&E’s current LWD management practices do not effectively document the 

quantity or timing of LWD removal from the project intake and do not address the 

biological significance of its placement back into the Merced River channel. Under the 

staff alternative, PG&E would develop a LWD management plan to more effectively 

manage the removal and subsequent placement of LWD for the benefit of aquatic species 

in the project area.

Terrestrial Resources

Project maintenance activities and recreation could adversely affect sensitive 

plants and wildlife occurring in the project area. Vegetation maintenance, such as 

trimming, clearing, and herbicide applications, and recreation could adversely affect 

sensitive plants, and the use of rodenticides and insecticides in the project area could

affect sensitive wildlife. Under the staff alternative, a control plan for noxious weeds and 

invasive plants integrated with pest management and pesticide use would reduce effects 
xlv

on sensitive plants and wildlife. Project maintenance activities and recreation activities 

could disturb bald eagles nesting and roosting in the project area. Under the staff 

alternative, a bald eagle protection plan would be developed, which would minimize the 

effects of project maintenance and recreation activities on nesting and roosting bald 

eagles.

Threatened and Endangered Species

The Central Valley steelhead, federally listed as threatened, occurs within the San 

Joaquin River and likely occurs in the Merced River downstream of Crocker-Huffman 

diversion dam. The proposed project with staff-recommended measures would have 

minimal incremental effects on downstream environmental variables because the project 

would continue to operate run-of-river. Therefore, we conclude that the Merced Falls 

Project as proposed with staff-recommended measures, is not likely to adversely affect 

the Central Valley steelhead.

Three federally listed terrestrial species have the potential to occur in the project 

area: the endangered San Joaquin kit fox; the threatened California red-legged frog; and 

the threatened valley elderberry longhorn beetle. The project reservoir may be a dispersal 

barrier for the San Joaquin kit fox and the opening of the dam for fish passage, per FWS’

recommendation, may also affect kit fox dispersal. Project operations that increase 

bullfrogs and predatory fishes would adversely affect California red-legged frogs 

dispersing to the project area by increasing predation. Project maintenance activities (i.e., 

herbicide applications) could also affect California red-legged frogs dispersing to the 

project area. Project maintenance and recreation activities may affect habitat for the 

valley elderberry longhorn beetle. Developing and implementing the various staffrecommended plans would protect these three species, as well as other threatened and 

endangered species potentially occurring within the project area. Thus, we conclude that 

the Merced Falls Project as proposed with staff-recommended measures is not likely to 

adversely affect the California red-legged frog or the threatened valley elderberry 

longhorn beetle.

Recreation 

Although there are only a few recreational facilities located at the Merced Falls 

impoundment, operating and maintaining these facilities would ensure public access to 

recreational opportunities at the project over the term of the license. Additionally, 

providing public access and maintaining the informal canoe trail on the south side of 

Merced Falls dam would eliminate potential trespassing issues and create additional 

recreational boating access at the project. 

No-Action Alternative

Under the no-action alternative, Merced ID and PG&E would continue to operate 

under the terms and conditions of the existing licenses, and no new environmental 

protection, mitigation, or enhancement measures would be implemented.
xlvi

Conclusions

Based on our analysis, we recommend licensing the project as proposed by 

Merced ID and PG&E with some staff modifications and additional measures. 

In section 4.2 of the EIS, we estimate the likely cost of alternative power for each 

of the three alternatives identified above. For the Merced River Project, our analysis 

shows that during the first year of operation under the no-action alternative, project 

power would cost $12,527,000, or $32.4 per megawatt-hour (MWh) less than the likely 

alternative cost of power. Under the proposed action alternative, project power would 

cost $1,795,000 or $4.6/MWh less than the likely alternative cost of power. Under the 

staff alternative, project power would cost $1,077,000 or $2.9/MWh more than the likely 

alternative cost of power.

For the Merced Falls Project, our analysis shows that during the first year of 

operation under the no-action alternative, project power would cost $596,000 or 

$41.41/MWh more than the likely alternative cost of power. Under the proposed action 

alternative, project power would cost $621,000 or $43.1/MWh more than the likely 

alternative cost of power. Under the staff alternative, project power would cost 

$655,000,000 or $45.4/MWh more than the likely alternative cost of power.

We chose the staff alternative as the preferred alternative because: (1) the projects 

would provide a dependable source of electrical energy for the region; (2) the generation 

comes from a renewable resource that does not contribute to atmospheric pollution, 

including greenhouse gases; and (3) the recommended environmental measures proposed 

by Merced ID and PG&E, as modified by staff, would adequately protect and enhance 

environmental resources affected by the projects. The overall benefits of the staff 

alternatives would be worth the cost of the environmental measures.

We conclude that issuing new licenses for the Merced River and Merced Falls 

Projects, with the environmental measures we recommend, would not be major federal 

actions significantly affecting the quality of the human environment.
1

DRAFT ENVIRONMENTAL IMPACT STATEMENT 

Federal Energy Regulatory Commission 

Office of Energy Projects 

Division of Hydropower Licensing

Washington, D.C.

Merced River Hydroelectric Project 

FERC Project No. 2179-043—California

Merced Falls Hydroelectric Project 

FERC Project No. 2467-020—California

1.0 INTRODUCTION 

1.1 APPLICATION 

1.1.1 Merced River Project 

On February 26, 2012, Merced Irrigation District (Merced ID) filed an application 

for new license with the Federal Energy Regulatory Commission (Commission). The 

Merced Hydroelectric Project is located on the main stem of the Merced River in 

Mariposa County, about 23 miles northeast of the city of Merced, California (figures 1-1 

and 1-2). The two Merced ID reservoirs (McClure and McSwain) are capable of 

impounding about 1,029,497 acre-feet of usable storage. The two powerhouses (New 

Exchequer and McSwain) have an authorized installed capacity of 101.25 megawatts 

(MW) of power. The Merced River Project occupies 3,154.9 acres of federal land 

administered by the U.S. Department of the Interior, Bureau of Land Management 

(BLM). It generates an average of about 387 gigawatt-hours (GWh) of energy annually. 

Merced ID proposes no new capacity and no new construction. 

1.1.2 Merced Falls Project 

On February 8, 2012, Pacific Gas and Electric Company (PG&E) filed an 

application for new license with the Commission. The 3.4-MW Merced Falls 

Hydroelectric Project is located on the Merced River on the border of Merced and 

Mariposa Counties, California (figures 1-2, 1-3, and 1-4). The project occupies 1.0 acre 

of federal land administered by BLM. It generates an average of about 14.4 GWh of 

energy annually. PG&E proposes no new capacity and no new construction. 

The existing licenses for both the Merced River and Merced Falls Projects expired 

on February 28, 2014. 
2

Figure 1-1. Location of Merced River Hydroelectric Project (Source: Merced ID, 2012a, as modified by staff).
3

Figure 1-2. Merced River and Merced Falls Hydroelectric Projects and vicinity (Source: Merced ID, 2012a, as modified 

by staff).
4

Figure 1-3. Location of the Merced Falls Hydroelectric Project (Source: PG&E, 2012).
5

Figure 1-4. Merced Falls Hydroelectric Project (Source: PG&E, 2012).
6

1.2 PURPOSE OF ACTION AND NEED FOR POWER

1.2.1 Purpose of Action

The purpose of both the Merced River and Merced Falls Projects is to continue to 

provide a source of hydroelectric power and provide irrigation and domestic water to the 

local communities. Therefore, under the provisions of the Federal Power Act (FPA), the 

Commission must decide whether to issue a license to Merced ID for the Merced River

Project and to PG&E for the Merced Falls Project, and what conditions should be placed 

on any licenses issued. In deciding whether to issue a license for a hydroelectric project, 

the Commission must determine that the project will be best adapted to a comprehensive 

plan for improving or developing a waterway. In addition to the power and 

developmental purposes for which licenses are issued (such as flood control, irrigation, or 

water supply), the Commission must give equal consideration to the purposes of: 

(1) energy conservation; (2) the protection of, mitigation of damage to, and enhancement 

of fish and wildlife resources; (3) the protection of recreational opportunities; and (4) the 

preservation of other aspects of environmental quality.

Issuing new licenses for the Merced River and Merced Falls Projects would allow 

Merced ID and PG&E, respectively, to generate electricity at the projects for the term of 

the new licenses, making electric power from a renewable resource available to 

their customers. 

This draft environmental impact statement (EIS) assesses the effects associated 

with operation of the projects and alternatives to the proposed projects. It also includes

recommendations to the Commission on whether to issue new licenses, and if so, 

includes the recommended terms and conditions to become a part of any licenses issued. 

In this draft EIS, we assess the environmental and economic effects of continuing 

to operate the projects: (1) as proposed by the applicant, and (2) with our recommended 

measures. We also consider the effects of the no-action alternative. Important issues for 

the Merced River Project that are addressed include: establishing an appropriate flow 

regime in the Merced River, including downstream of Crocker-Huffman diversion dam;

the need to modify releases from New Exchequer powerhouse to enhance downstream 

water temperatures; the need to enhance anadromous fish habitat and provide upstream 

and downstream fish passage; protection of wildlife from project-related effects; control 

of invasive species; the need for new or enhanced existing recreational facilities; and 

protection of cultural resources. Important issues for the Merced Falls Project that are 

addressed include: coordination of operations and environmental measures with the 

upstream Merced River Project; the need to enhance fish habitat and provide upstream 

fish passage; protection of wildlife from project-related effects; the need for new or 

enhanced existing recreational facilities; and protection of cultural resources.
7

1.2.2 Need for Power

The Merced River and Merced Falls Projects would provide hydroelectric 

generation to meet part of California’s power requirements, resource diversity, and 

capacity needs. The Merced River Project has an authorized installed capacity of 

101.25 MW and would generate approximately 387 GWh per year. The Merced Falls 

Project has an authorized installed capacity of 3.4 MW and would generate 

approximately 14.4 GWh per year.

The North American Electric Reliability Corporation (NERC) annually forecasts 

electrical supply and demand nationally and regionally for a 10-year period. The Merced 

River and Merced Falls Projects are located in the Western Electricity Coordinating 

Council region, California/Mexico subregion, of the NERC. According to NERC’s 2014

forecast, net internal summer and winter demand requirements for the California/Mexico

subregion are projected to grow at rates of 0.25 percent and 0.37 percent, respectively, 

from 2015 through 2024 (NERC, 2014). NERC projects that resource summer capacity 

margins (generating capacity in excess of demand) will range between 15.31 percent in 

2015 and 20.95 percent in 2024, including planned new capacity additions. NERC 

projects that winter capacity margins will range between 34.61 percent in winter 

2013/2014 and 29.15 percent in winter 2024/2025. 

We conclude that power from the Merced River and Merced Falls Projects would 

help meet the need for power in the California\Mexico subregion in both the short and 

long term. The projects provide low-cost power that displaces generation from nonrenewable sources. Displacing the operation of non-renewable facilities may avoid some

power plant emissions, thus creating an environmental benefit. 

1.3 STATUTORY AND REGULATORY REQUIREMENTS

Licenses for the Merced River and Merced Falls Projects are subject to numerous 

requirements under the FPA and other applicable statutes. We describe the major 

regulatory requirements for both projects below. 

1.3.1 Merced River Project

1.3.1.1 Federal Power Act

Section 18 Fishway Prescriptions

Section 18 of the FPA states that the Commission is to require construction, 

operation, and maintenance by a licensee of such fishways as may be prescribed by the 

Secretaries of Commerce or the U.S. Department of the Interior. Interior and the 

National Marine Fisheries Service (NMFS), by letters dated July 22, 2014, request that a 

reservation of authority to prescribe fishways under section 18 be included in any license 

issued for the project. 
8

Section 4(e) Conditions

Section 4(e) of the FPA provides that any license issued by the Commission for a 

project within a federal reservation will be subject to and contain such conditions as the 

Secretary of the responsible federal land management agency deems necessary for the 

adequate protection and use of the reservation. BLM filed preliminary conditions by 

letter dated July 22, 2014, pursuant to section 4(e) of the FPA. These conditions are 

described under section 2.2.1.5, Modifications to Applicant’s Proposal—Mandatory 

Conditions.

Alternative Section 4(e) Conditions under the Energy Policy Act of 2005

The Energy Policy Act of 2005 provides parties to this licensing proceeding the 

opportunity to propose alternatives to preliminary conditions. On August 21, 2014, the 

Commission received a copy of Merced ID’s filing to BLM proposing alternative 4(e) 

conditions in response to BLM preliminary section 4(e) conditions. Merced ID’s 26 

alternative 4(e) conditions are divided into five groups: (1) conditions that have no nexus 

to BLM-managed land (four conditions); (2) conditions that require Merced ID to 

develop plans for which little, if any, detail or guidance regarding the plan to be 

developed is provided (six conditions); (3) conditions that require Merced ID to develop 

plans, for which some level of detail regarding the plan to be developed is provided (four 

conditions); (4) conditions that require Merced ID to develop a plan and for which 

BLM’s condition included a plan (three conditions); and (5) conditions that are unrelated 

to plans (nine conditions). The Merced ID alternative conditions that pertain to 

environmental effects are analyzed within the corresponding resource areas in section 

3.0, Environmental Analysis, and section 5.1, Comprehensive Development and 

Recommended Alternative.

Section 10(j) Recommendations

Under section 10(j) of the FPA, each hydroelectric license issued by the 

Commission must include conditions based on recommendations provided by federal and 

state fish and wildlife agencies for the protection, mitigation, or enhancement of fish and 

wildlife resources affected by the project. The Commission is required to include these 

conditions unless it determines that they are inconsistent with the purposes and 

requirements of the FPA or other applicable law. Before rejecting or modifying an 

agency recommendation, the Commission is required to attempt to resolve any such 

inconsistency with the agency, giving due weight to the recommendations, expertise, and 

statutory responsibilities of such agency.

California Department of Fish and Wildlife (California DFW) timely filed on July 

21, 2014, and NMFS and the U.S. Fish and Wildlife Service (FWS) timely filed, on July 

22, 2014, recommendations under section 10(j), as summarized in table 5-5, in section 

5.3.1, Fish and Wildlife Agency Recommendations. On October 22, 2014, California 

DFW filed an amendment to its 10(j) recommendations. In section 5.3, we also discuss 

how we address the agency recommendations and comply with section 10(j).
9

1.3.1.2 Clean Water Act

Under section 401 of the Clean Water Act (CWA), a license applicant must obtain 

certification from the appropriate state pollution control agency verifying compliance 

with the CWA. On May 21, 2014, Merced ID applied to the California State Water 

Resources Control Board (Water Board) for 401 water quality certification (WQC) for 

the Merced River Project. The Water Board received this request on May 21, 2014. The 

Water Board has not yet acted on the request although it filed preliminary WQC 

conditions on July 22, 2014. The WQC is due by May 20, 2015.

1.3.1.3 Endangered Species Act

Section 7 of the Endangered Species Act (ESA) requires federal agencies to ensure 

that their actions are not likely to jeopardize the continued existence of endangered or 

threatened species or result in the destruction or adverse modification of the critical 

habitat of such species. Our analyses of project impacts on threatened and endangered 

species are presented in section 3.3.1, Aquatic Resources (for Central Valley steelhead) 

and section 3.3.3, Threatened and Endangered Species, and our recommendations in 

section 5.1, Comprehensive Development and Recommended Alternative.

The Central Valley steelhead, federally listed as threatened, occurs within the San 

Joaquin River and likely occurs in the Merced River downstream of Crocker-Huffman 

diversion dam. Designated critical habitat for this species includes the Merced River 

downstream of the diversion dam, San Joaquin River, and the Sacramento-San Joaquin 

Delta (letter from S. Edmondson, FERC Hydropower Branch Supervisor, NMFS, 

Sacramento, California, to K.D. Bose, Secretary, FERC, Washington, D.C., July 22, 

2014). Compared to existing conditions, the proposed project with staff-recommended 

measures would enhance (1) fall attraction flows for adult steelhead; (2) spawning 

substrate; (3) water temperature during spring rearing and smoltification; (4) off-channel 

habitat, floodplain connectivity, and juvenile emigration triggers with spring pulse flows; 

and (5) physical habitat with increased minimum instream flows. Consequently, we 

conclude that the Merced River Project as proposed with staff-recommended measures, is 

not likely to adversely affect the Central Valley steelhead. We will request NMFS 

concurrence with our conclusion.

Five federally listed animal species and five federally listed plant species occur or 

potentially occur in the project area: San Joaquin kit fox (Vulpes macrotis mutica), 

California red-legged frog (Rana aurora draytonii), California tiger salamander 

(Ambystoma californiense), valley elderberry longhorn beetle (Desmocerus californicus 

dimorphus), and vernal pool fairy shrimp (Branchinecta lynchi); Keck’s checkerbloom 

(Sidalcea keckii), Layne’s ragwort (Packera layneae), Chinese Camp brodiaea (Brodiaea 

pallida), Mariposa pussypaws (Calyptridium pulchellum), and California vervain 

(Verbena californica). The project area overlaps with about 1 acre of critical habitat for 

the vernal pool fairy shrimp and with one recovery unit identified for the California red-
10

legged frog (letter from P. Sanderson Port, U.S. Department of Interior, San Francisco, 

CA, to K.D. Bose, Secretary, FERC, Washington, D.C., July 22, 2014). 

We conclude that relicensing of the Merced River Project, as proposed with staffrecommended measures, is not likely to adversely affect the San Joaquin kit fox,

California red-legged frog, California tiger salamander, valley elderberry longhorn beetle,

vernal pool fairy shrimp, Keck’s checkerbloom, Layne’s ragwort, Chinese Camp 

brodiaea, Mariposa pussypaws, and California vervain. We will seek concurrence from 

FWS with issuance of this draft EIS. 

1.3.1.4 Coastal Zone Management Act

Under section 307(c)(3)(A) of the Coastal Zone Management Act (CZMA), 16 

U.S.C. § 1456(3)(A), the Commission cannot issue a license for a project within or 

affecting a state’s coastal zone unless the state CZMA agency concurs with the license 

applicant’s certification of consistency with the state’s CZMA program, or the agency’s 

concurrence is conclusively presumed by its failure to act within 180 days of its receipt of 

the applicant’s certification.

The project is not located within the state-designated Coastal Management Zone

boundary, which extends from a few city blocks to 5 miles inland from the sea and it 

would not affect California’s coastal resources. Therefore, the project is not subject to 

California’s coastal zone program review, and no consistency certification is needed for 

the action. 

1.3.1.5 National Historic Preservation Act

Section 106 of the National Historic Preservation Act (NHPA) requires that every 

federal agency “take into account” how each of its undertakings could affect historic 

properties. Historic properties are districts, sites, buildings, structures, traditional cultural 

properties (TCPs), and objects significant in American history, architecture, engineering, 

and culture that are eligible for inclusion in the National Register of Historic Places 

(National Register). 

To meet the requirements of section 106, the Commission intends to execute a 

Programmatic Agreement (PA) with the California State Historic Preservation Officer 

(California SHPO) for the protection of historic properties from the effects of operation 

and maintenance of the Merced River Project. The terms of the PA would ensure that 

Merced ID addresses and treats all historic properties identified within the project’s area 

of potential effects (APE) through the implementation of a final Historic Properties 

Management Plan (HPMP) expected to be filed with the Commission by the end of 

December 2014, with staff modifications, if needed. Compliance with the executed PA 

would be a condition of any order issuing a license. 
11

1.3.1.6 Wild and Scenic Rivers Act

Section 7(a) of the Wild and Scenic Rivers Act requires federal agencies to make a 

determination as to whether the operation of the Merced River Project under a new 

license would invade the area or unreasonably diminish the scenic, recreational, and fish 

and wildlife values present in the designated river corridor. Public Law 102-432

(October 23, 1992) designated the segments of the Merced River as a Wild and Scenic 

River, which extend from the main stem of the Merced River from its sources (including 

Red Peak Fork, Merced Peak Fork, Triple Peak Fork, and Lyell Fork on the south side of 

Mount Lyell) in Yosemite National Park downstream to the normal maximum water 

surface elevation (NMWSE) of Lake McClure (elevation 867 feet National Geodetic 

Vertical Datum of 192911), and the South Fork Merced River from its source near Triple 

Divide Peak in Yosemite National Park to the confluence with the main stem of the 

Merced River. The Wild and Scenic River is managed by BLM; U.S. Department of the 

Interior, National Park Service (Park Service); and the U.S. Department of Agriculture, 

Forest Service (Forest Service) to protect and enhance the free-flowing condition, water 

quality, and outstanding remarkable values for which the river was designated while 

providing for public recreation and resource uses that do not adversely affect or degrade 

those values. The project would not affect any segments of the Merced River designated

under the Wild and Scenic Rivers Act because none occur downstream of the project.

1.3.1.7 Magnuson-Stevens Fishery Conservation and Management Act

The Magnuson-Stevens Fishery Conservation and Management Act requires 

federal agencies to consult with National Oceanic and Atmospheric Administration

Fisheries on all actions that may adversely affect Essential Fish Habitat (EFH). No EFH

has been designated within the Merced River Project boundary. However, the extent of 

potential existing project effects on EFH (the EFH action area) includes the lowermost 52 

miles of the Merced River (i.e., downstream of Crocker-Huffman diversion dam) and 118 

miles of the San Joaquin River from the Merced River confluence downstream to 

Vernalis (Pacific Fisheries Management Council, 1999). EFH in the lower Merced River 

is designated for Chinook salmon spawning, rearing, and migration, and EFH in the San 

Joaquin River is designated for Chinook salmon migration. Our analyses of project 

impacts on Chinook salmon EFH is presented in section 3.3.1, Aquatic Resources (for 

Central Valley steelhead) and our recommendations in section 5.1, Comprehensive 

Development and Recommended Alternative. 

 

11 All elevations in this EIS are in National Geodetic Vertical Datum of 1929

unless otherwise noted.
12

Compared to existing conditions, the proposed project with staff-recommended 

measures would enhance: (1) fall attraction flows for adult Chinook salmon; 

(2) spawning substrate; (3) water temperature during spring rearing and smoltification; 

(4) off-channel habitat, floodplain connectivity, and juvenile emigration triggers with 

spring pulse flows; and (5) physical habitat with increased minimum instream flows. 

Consequently, we conclude that the Merced River Project, as proposed with staffrecommended measures, would not adversely affect EFH. As such, no consultation is 

required with NMFS. 

1.3.2 Merced Falls Project

1.3.2.1 Federal Power Act

Section 18 Fishway Prescriptions

Section 18 of the FPA states that the Commission is to require construction, 

operation, and maintenance by a licensee of such fishways as may be prescribed by the 

Secretaries of Commerce or the U.S. Department of the Interior. NMFS and FWS, by 

letters dated July 22, 2014, request that a reservation of authority to prescribe fishways 

under section 18 be included in any license issued for the project. 

Section 10(j) Recommendations

Under section 10(j) of the FPA, each hydroelectric license issued by the 

Commission must include conditions based on recommendations provided by federal and 

state fish and wildlife agencies for the protection, mitigation, or enhancement of fish and 

wildlife resources affected by the project. The Commission is required to include these 

conditions unless it determines that they are inconsistent with the purposes and 

requirements of the FPA or other applicable law. Before rejecting or modifying an 

agency recommendation, the Commission is required to attempt to resolve any such 

inconsistency with the agency, giving due weight to the recommendations, expertise, and 

statutory responsibilities of such agency.

California DFW, timely filed on July 21, 2014, and NMFS and FWS timely filed, 

on July 22, 2014, recommendations under section 10(j), as summarized in table 5-6, in 

section 5.3.1, Fish and Wildlife Agency Recommendations. In section 5.3, we also 

discuss how we address the agency recommendations and comply with section 10(j). 

1.3.2.2 Clean Water Act

Under section 401 of the CWA, a license applicant must obtain certification from 

the appropriate state pollution control agency verifying compliance with the CWA. 

PG&E applied to the Water Board for 401 WQC for the Merced Falls Project. The Water 

Board received this request on May 20, 2014. The Water Board has not yet acted on the 

request although it filed preliminary WQC conditions on July 22, 2014. The WQC is due 

by May 20, 2015. 
13

1.3.2.3 Endangered Species Act

Section 7 of the ESA requires federal agencies to ensure that their actions are not 

likely to jeopardize the continued existence of endangered or threatened species or result 

in the destruction or adverse modification of the critical habitat of such species. Our 

analyses of project impacts on threatened and endangered species are presented in section 

3.3.1, Aquatic Resources, and section 3.3.3, Threatened and Endangered Species, and our 

recommendations in section 5.1, Comprehensive Development and Recommended 

Alternative.

As described above, for the Merced River Project in section 1.3.1.3, Endangered 

Species Act, the Central Valley steelhead, federally listed as threatened, occurs within the 

San Joaquin River and likely occurs in the Merced River downstream of CrockerHuffman diversion dam. The proposed project with staff-recommended measures would 

have minimal incremental effects on downstream environmental variables. 

Consequently, we conclude that the Merced Falls Project as proposed with staffrecommended measures, is not likely to adversely affect the Central Valley steelhead. 

We will request NMFS concurrence with our conclusion.

Three federally listed animal species occur or potentially occur in the project area: 

San Joaquin kit fox, California red-legged frog, and valley elderberry longhorn beetle. 

No critical habitat for these species occurs in the immediate vicinity of the project. 

We conclude that relicensing of the Merced Falls Project, as proposed with staffrecommended measures, is not likely to adversely affect the San Joaquin kit fox, 

California red-legged frog, and valley elderberry longhorn beetle. We will seek 

concurrence from FWS with issuance of this draft EIS.

1.3.2.4 Coastal Zone Management Act

Similar to the Merced River Project, the Merced Falls Project is not located within 

the state-designated Coastal Management Zone boundary, which extends from a few city 

blocks to 5 miles inland from the sea, and the project would not affect California’s 

coastal resources. Therefore, the project is not subject to California’s coastal zone 

program review, and no consistency certification is needed for the action.

1.3.2.5 National Historic Preservation Act

Section 106 of the NHPA requires that every federal agency “take into account” 

how each of its undertakings could affect historic properties. Historic properties are 

districts, sites, buildings, structures, TCPs, and objects significant in American history, 

architecture, engineering, and culture that are eligible for inclusion in the National 

Register. 

To meet the requirements of section 106, the Commission intends to execute a PA

with the California SHPO for the protection of historic properties from the effects of

operation and maintenance of the Merced Falls Project. The terms of the PA would 
14

ensure that PG&E addresses and treats all historic properties identified within the 

project’s APE through implementation of a HPMP filed on October 6, 2014, with staff 

modifications, if needed. Compliance with the executed PA would be a condition of any 

order issuing a license. 

1.3.2.6 Wild and Scenic Rivers Act

Section 7(a) of the Wild and Scenic Rivers Act requires federal agencies to make a 

determination as to whether the operation of the Merced Falls Project under a new license 

would invade the area or unreasonably diminish the scenic, recreational, and fish and 

wildlife values present in the designated river corridor. As noted above, segments of the 

Merced River have been designated wild and scenic. However, similar to the Merced 

River Project, the Merced Falls Project would not affect any segments of the Merced 

River designated under the Wild and Scenic Rivers Act because none occur downstream 

of the project.

1.3.2.7 Magnuson-Stevens Fishery Conservation and Management Act

The Magnuson-Stevens Fisheries Conservation and Management Act requires 

federal agencies to consult with NMFS on all actions that may adversely affect EFH. In 

the case of the Merced Falls Project, EFH has not been officially designated within the 

project area. In section 1.3.1.7, Magnuson-Stevens Fishery Conservation and 

Management Act, we describe the extent of Chinook salmon EFH in the lower Merced 

River. Our analyses of Merced River Project impacts on Chinook salmon EFH in the 

lower Merced River is presented in section 3.3.1, Aquatic Resources (for Central Valley 

steelhead) and our recommendations in section 5.1, Comprehensive Development and 

Recommended Alternative.

1.4 PUBLIC REVIEW AND COMMENT

The Commission’s regulations (18 Code of Federal Regulations [CFR], sections

5.1–5.16) require that applicants consult with appropriate resource agencies, tribes, and 

other entities before filing an application for a license. This consultation is the first step 

in complying with the Fish and Wildlife Coordination Act, the ESA, the NHPA, and 

other federal statutes. Pre-filing consultation must be complete and documented 

according to the Commission’s regulations.

1.4.1 Merced River Project

1.4.1.1 Scoping

Before preparing this EIS, we conducted scoping to determine what issues and 

alternatives should be addressed. A scoping document (SD1) was distributed to 

interested agencies and others on January 2, 2009. Two scoping meetings, both 

advertised in the local newspaper, were held on January 28, 2009, in Merced, California, 

to request oral comments on the project. A court reporter recorded all comments and 
15

statements made at the scoping meetings, and these are part of the Commission’s public 

record for the project. In addition to comments provided at the scoping meetings, the 

following entities provided written comments:

Commenting Entity Date Filed

Park Service February 27, 2009

Water Board March 2, 2009

Merced River Conservation Committee -

Ralph Mendershausen

March 2, 2009

Mariposa County March 2, 2009

Rick W. Jones March 3, 3009

Golden West Women Flyfishers March 3, 2009

Merced ID March 3, 2009

Friends of the River March 3, 2009

Merced River Conservation Committee March 3, 2009

California Sportfishing Protection 

Alliance

March 3, 2009

BLM March 4, 2009

NMFS March 4, 2009

A revised scoping document (SD2), addressing these comments, was issued on 

April 17, 2009.

1.4.1.2 Interventions

On March 24, 2014, the Commission issued a notice that Merced ID’s application 

to relicense the Merced River Project was ready for environmental analysis. The 

Commission set May 23, 2014, as the deadline for filing protests and motions to 

intervene. On April 24, 2014, the Commission granted a 60-day extension of time, until 

July 22, 2014, for filing protests and motions to intervene. In response to the notice, the 

following entities filed motions to intervene:

Intervenor Date Filed

PG&E May 30, 2012

Water Board April 14, 2014

California DFW April 29, 2014

Conservation Groups May 22, 2014

U.S. Department of the Interior May 22, 2014
16

1.4.1.3 Comments on the Application

A notice requesting conditions and recommendations was issued on March 24, 

2014. The following entities commented: 

Commenting Agency and Other Entity Date Filed

California DFW July 21, 2014

FWS July 22, 2014

Conservation Groups July 22, 2014

BLM July 22, 2014

NMFS July 22, 2014

Water Board July 29, 2014

City of Merced September 3, 2014

The applicant filed reply comments on September 5, 2014, and amendments to its 

application on September 22, 2014. In addition to the above comments 243 comment 

letters from members of the public were filed in response to the notice. A list of the 

commenters and the filing date of their letters are provided in appendix C.

1.4.2 Merced Falls Project

1.4.2.1 Scoping

Before preparing this EIS, we conducted scoping to determine what issues and 

alternatives should be addressed. SD1 was distributed to interested agencies and others 

on April 24, 2009. It was noticed in the Federal Register (FR) on April 24, 2009. The 

following entities provided written comments:

Commenting Entity Date Filed

Merced River Conservation Committee June 22, 2009

PG&E June 22, 2009

NMFS June 22, 2009

Water Board June 22, 2009

A revised scoping document (SD2), addressing these comments, was issued on 

August 6, 2009.

1.4.2.2 Interventions

On March 24, 2014, the Commission issued a notice that PG&E’s application to 

relicense the Merced Falls Project was ready for environmental analysis. The 

Commission set May 23, 2014, as the deadline for filing protests and motions to 
17

intervene. On April 24, 2014, the Commission granted a 60-day extension of time, until 

July 22, 2014, for filing protests and motions to intervene. In response to the notice, the 

following entities filed motions to intervene:

Intervenor Date Filed

Water Board April 14, 2014

California DFW April 29, 2014

Merced ID May 20, 2014

Conservation Groups May 22, 2014

U.S. Department of Interior May 22, 2014

1.4.2.3 Comments on the Application

A notice requesting conditions and recommendations was issued on March 24, 

2014. The following entities commented: 

Commenting Agency and Other Entity Date Filed

FWS July 22, 2014

NMFS July 22, 2014

Conservation Groups July 22, 2014

California DFW July 22, 2014

Water Board July 22, 2014

The applicant filed reply comments on September 5, 2014.
18

This page intentionally left blank.
19

2.0 PROPOSED ACTION AND ALTERNATIVES

2.1 NO-ACTION ALTERNATIVE

The no-action alternative is the baseline from which to compare the proposed 

action and all action alternatives that are assessed in the environmental document. Under 

the no-action alternative, the projects would continue to operate under the terms and 

conditions of their current licenses. 

2.1.1 Merced River Project

The Merced River Project was constructed from 1964 to 1967 and placed in 

service in 1966. Merced ID owns and operates the project, consisting of two 

developments located in Mariposa County, California, within the Merced River drainage. 

The project’s reservoirs—Lake McClure and McSwain reservoir—are capable of 

impounding 1,029,497 acre-feet of usable storage. The two powerhouses have an 

authorized installed capacity of 101.25 MW of power. The project includes no 

transmission lines. The project includes five recreational areas.

2.1.1.1 Existing Project Facilities

The Merced River Project includes two developments—New Exchequer 

Development and McSwain Development. Reservoir and powerhouse characteristics are 

shown in tables 2-1 and 2-2, below.

Table 2-1. Water storage characteristics of Merced River Hydropower Project 

reservoirs (Source: Merced ID, 2012a, as modified by staff).

Characteristics Lake McClure McSwain Reservoir

Drainage area (square miles) 1,035 1,055

Normal maximum/minimum water 

surface elevation (feet)

867.0/630.0 399.0/391.5

Gross storage at NMWSE (acre-feet) 1,024,600 9,730

Usable storage at NMWSE(acre-feet) 1,021,600 7,897

Surface area at NMWSE (acres) 7,110 310

Length (miles) 19.0 6.3

Maximum width (miles) 1.8 0.2

Maximum depth (feet) 427 66

Shoreline length (miles) 82.0 12.5

Note: NMWSE – normal maximum water surface elevation
20

Table 2-2. Characteristics of powerhouses associated with the Merced River 

Hydropower Project (Source: Merced ID, 2012a, as modified by staff).

Reservoir Name

Powerhouse 

Capacity 

(MW)

Number 

of Units Type of Units

Minimum/ 

Maximum 

Discharge 

(cfs)

Lake McClure 94.5 1 Vertical Francis 200/3,200

McSwain reservoir 9.0 1 Vertical Kaplan 600/2,700

Note: cfs – cubic feet per second, MW – megawatt

New Exchequer Development

The New Exchequer development is the upstream facility and consists of: 

(1) New Exchequer dam—a rock structure with a reinforced concrete upstream face, 

490 feet high and 1,220 feet long that impounds Lake McClure; (2) an ogee-type, 

concrete spillway with a 1,080-foot-long, ungated section and a 240-foot-long, gated 

section with six radial gates that are 40 feet wide and 30 feet high; (3) an earth-and-rock 

dike that is 62 feet high and 1,500 feet long; (4) an intake structure located upstream of 

the dam in Lake McClure; (5) a concrete-lined power tunnel that is 383 feet long and 

18 feet in diameter; (6) a concrete-encased, steel penstock that is 982 feet long and 16 

feet in diameter; (7) an above-ground concrete powerhouse that is 75 feet by 91 feet and 

discharges directly to the Merced River; (8) a low-level outlet, consisting of a 945.5-foot 

long, 108-inch-diameter powerhouse bypass (a steel pipe) that runs from the New 

Exchequer power tunnel to McSwain reservoir north of the New Exchequer powerhouse 

with a 108-inch-diameter Howell-Bunger valve; and (9) an interconnection to the grid at 

the step-up transformer in the powerhouse switchyard. The development is located on 

Merced ID (7,577.5 acres), BLM (3,134.7 acres), and private (13.2 acres) land (Merced 

ID, 2012b). 

Merced ID maintains four recreation areas at Lake McClure: (1) McClure Point, 

which includes a campground, picnic area, swim beach, marina, and boat ramp; 

(2) Barrett Cove, which includes a campground, swim beach, marina with two boat 

ramps, and overflow parking; (3) Horseshoe Bend, which includes a campground, swim 

beach, and boat ramp; and (4) Bagby, which includes a campground, boat ramp, and 

Shepherd’s Point primitive area (considered part of the Bagby recreation area). See table 

3-22 in section 3.3.4, Recreation Resources, for a listing of the amenities provided at 

these sites.

McSwain Development

McSwain development is the downstream facility, consisting of: (1) McSwain 

dam—an embankment structure with a central impervious core of rolled fill between 

shoulders of cobbles or crushed rock—that is 80 feet high and 1,620 feet long and 
21

impounds McSwain reservoir; (2) an ungated concrete overflow spillway that is 802 feet 

long; (3) an intake structure that is integral with the dam; (4) a concrete-lined power 

tunnel that is 160 feet long and 15 feet in diameter that leads to; (5) a steel penstock that 

is 160 feet long and 15 feet in diameter; (6) an above-ground, concrete powerhouse that is 

72 feet by 72 feet and discharges directly into the Merced River; and (7) a low-level 

outlet, consisting of a 360-foot-long, 9-foot diameter powerhouse bypass pipe that runs 

from the McSwain power tunnel to Merced Falls reservoir with a fixed wheel gate at the 

upstream end of the bypass and an 8-foot-diameter Howell-Bunger valve on its 

downstream end. There is no transmission line associated with the project. The project 

connects to PG&E’s interconnected system at the step-up transformer in the powerhouse 

switchyard. The development is located on Merced ID (907.5 acres) and BLM (20.2 

acres) land (Merced ID, 2012b). 

Merced ID maintains the McSwain recreation area at this development, which 

includes a campground, picnic area, group picnic area, informal day use area, swim 

beach, marina, and boat ramp. See table 3-22 in section 3.3.4, Recreation Resources, for 

a listing of the amenities provided at this site.

Crocker-Huffman Diversion Dam

Crocker-Huffman diversion dam is located 4.3 miles downstream of Merced ID’s 

McSwain dam and 3.0 miles downstream of PG&E’s Merced Falls dam. Merced ID

owns Crocker-Huffman diversion dam and operates it as part of Merced ID’s water 

delivery system, but the dam is not included as part of the Merced River Project. The 

concrete gravity dam is approximately 725 feet long and 22 feet high (Vogel, 2007), and 

diverts approximately 2,000 cubic feet per second (cfs) of water into Merced ID’s Main 

Canal (irrigation canal). 

Refuge Water Delivery Facilities

Article 45 of the existing license requires that Merced ID provide to FWS up to 

15,000 acre-feet of project water and return flow to the Merced National Wildlife Refuge

(NWR). The refuge, located about 30 miles southeast of McSwain dam, is part of the 

San Luis National Wildlife Refuge Complex (see figures 1-1 and 1-2). It encompasses 

10,262 acres of wetlands, native grasslands, vernal pools, and riparian areas and was 

established in 1951 under the federal Lea Act12 to attract wintering waterfowl from 

adjacent farmland where their foraging was causing crop damage.

To provide this water, in the early 1990s, Merced ID made eight modifications, 

each of which was incorporated into the project license (but not included in the project 

boundary), to Merced ID’s existing Benedict lateral canal, which is part of Merced ID’s 

 

12 16 USC §695–695c; 62 Stat. 238.
22

water supply delivery system, composed of non-project facilities. The eight 

modifications, from upstream to downstream, include:

 Benedict lateral headworks,

 Benedict lateral duck slough crossing,

 Benedict lateral Rahilly Road crossing,

 Benedict lateral Farm Road crossing,

 Benedict lateral to Deadman Creek connection,

 Deadman Creek dam and flashboard risers (Station 77+73),

 Deadman Creek dam and flashboard risers (Station 142+00), and

 a measurement weir.

2.1.1.2 Existing Project Boundary

The project boundary encompasses the two project reservoirs and project roads, 

infrastructure, and recreation areas. Along the reservoir shorelines, most of the project 

boundary consists of a metes and bounds survey line that generally follows an elevation 

contour above the maximum water surface elevation. The project boundary location 

around the reservoirs provides a buffer of at least 50 horizontal feet from the maximum 

water surface elevation at all but about 0.75 mile of the 114-mile project boundary (letter 

from B. Kelly, Deputy General Manager, Water Resources, Merced ID, to the 

Commission, filed on September 13, 2013). The project boundary encompasses a 100-

foot corridor of land along portions of project roads that extend beyond the larger 

contiguous project footprint (e.g., Lake McClure Road near its intersection with County 

Road J16). The recreational facilities located within the project boundary include the 

McClure Point, Barrett Cove, Horseshoe Bend, and Bagby recreation areas on Lake 

McClure and the McSwain recreation area on McSwain reservoir.

The New Exchequer development includes 7,577.5 acres of Merced ID land, 

3,134.8 acres of public land managed by BLM, and 13.2 acres of private land. The 

McSwain development includes 927.5 acres of Merced ID land. Overall, the project 

includes 8,505.3 acres of Merced ID land, 3,134.8 acres of public land managed by BLM, 

and 13.2 acres of private land (Merced ID, 2012b, Merced ID, 2014b).

2.1.1.3 Project Safety

The project has been operating for more than 46 years under the existing license, 

and during this time, Commission staff has conducted operational inspections focusing on 

the continued safety of the structures, identification of unauthorized modifications, 

efficiency and safety of operations, compliance with the terms of the license, and proper 

maintenance. In addition, an independent consultant has inspected and evaluated the 

project every 5 years, and a consultant’s safety report has been filed for Commission 
23

review. As part of the relicensing process, the Commission staff would evaluate the 

continued adequacy of the proposed project facilities under a new license. Special 

articles would be included in any license issued, as appropriate. Commission staff would 

continue to inspect the project during the new license term to ensure continued adherence 

to Commission-approved plans and specifications, special license articles related to 

construction (if any), operation and maintenance, and accepted engineering practices and 

procedures.

2.1.1.4 Existing Project Operation

Historically, Merced ID has operated Lake McClure to retain snowmelt from 

springtime runoff for flood control, water supply, recreation, hydropower, and 

environmental purposes. During winter storms, the project attenuates high flows (e.g., 

those in excess of about 3,200 cfs) that would otherwise pass downstream of the project 

and stores this water in Lake McClure. During the drier months of July through 

November, the project augments flows in the lower Merced River compared to those that 

would occur without the project. In spring and summer, water levels are maintained 

relatively high for recreation at Lake McClure. From March through October, Merced ID

releases water primarily for downstream water supply. These releases are also used for 

hydropower generation at New Exchequer and McSwain powerhouses. The normal 

maximum and minimum reservoir elevations for Lake McClure are 867 feet and 630 feet,

but, typically, the reservoir is operated within a range of 842 feet to 780 feet.

In September and October, Merced ID releases water from storage when necessary 

to achieve a level of storage that allows for the required flood space, and storage is 

maintained at or below this level through mid-March. In the spring, depending on the 

snowpack and runoff forecasts, Merced ID begins to refill Lake McClure with the 

snowmelt runoff. During drier years and drier periods, water levels may consistently stay 

below the required flood-space level because water supply and recreation needs drive 

reservoir storage more than flood control requirements.

McSwain reservoir is typically operated as a re-regulating afterbay13 for flows 

released from Lake McClure. This operation allows the New Exchequer powerhouse to 

be used to meet peak power demands or perform load-following functions while still 

maintaining a steady flow release to the lower Merced River. The normal maximum and 

minimum reservoir elevations for McSwain reservoir are 399.0 feet and 391.5 feet. 

Water surface elevation excursions below the normal minimum reservoir elevation do 

occur, but they are generally due to atypical operating conditions, such as unplanned 

outages, inspections, or work on the dam.

 

13 The term afterbay as used here is a reservoir of a hydroelectric power plant at 

the outlet of the turbines.
24

Historically, Merced ID has operated New Exchequer and McSwain powerhouses 

as base-load plants with seasonal peaking capabilities; these peaking capabilities were 

primarily exercised at New Exchequer powerhouse. McSwain powerhouse is operated to 

re-regulate flows released by the New Exchequer powerhouse by providing flows that are 

more indicative of inflows to Lake McClure with releases dependent on the requirements 

for downstream water supply at, and downstream of, Crocker-Huffman diversion dam. 

Both project powerhouses are operated on-site by Merced ID from a centralized control 

center at New Exchequer dam and powerhouse, and have Automatic Generation Control 

capability.

The New Exchequer development diverts all flows from Lake McClure through 

the intake, power tunnel, penstock, and powerhouse and then directly releases the flows 

to McSwain reservoir. The McSwain development diverts all flows from McSwain 

reservoir through the intake, power tunnel, penstock, and powerhouse and then directly to 

the Merced River and to Merced Falls reservoir.

2.1.1.5 Existing Environmental Measures

Merced ID currently provides environmental measures and implements plans and 

agreements at the Merced River Project.

FERC License Requirements

 Operate the project in full compliance with the U.S. Army Corps of 

Engineers’ (Corps) document entitled: New Exchequer Dam and 

Reservoir, Merced River, California; Water Control Manual; Appendix 

VII to Master Water Control Manual, San Joaquin River Basin, 

California, dated October 1981, adhering to the year-round flood control 

limits in Lake McClure for rain flood space and to the March through July 

flood control limits for snow melt flood space, or conditional space (as 

required by license article 39).

 In an agreement with the Corps, provide for the operation of the project for 

flood control in accordance with rules and regulations prescribed by the 

Secretary of the Army (license article 39).

 Provide minimum streamflows in the Merced River downstream from the 

project reservoirs according to the following schedule (license article 40):

– Downstream from New Exchequer dam, maintain a minimum flow of 

25 cfs at all times.

– At Shaffer Bridge (River Mile [RM] 32.8), 23.8 miles downstream from 

New Exchequer dam, maintain a minimum streamflow, as follows:
25

Period

Normal Year 

(cfs)

Dry Years 

(cfs)

June 1 through October 15 25 15

October 16 through October 31 75 60

November 1 through December 31 100 75

January 1 through May 31 75 60

 To the extent possible from November 1 through December 31, regulate 

the Merced River streamflow downstream from the New Exchequer 

development between 100 and 200 cfs, except during dry years when the 

streamflow is maintained between 75 and 150 cfs, as measured at Shaffer 

Bridge (license article 41).

 Operate the power plants to avoid rapid fluctuation of the Merced River. 

At Crocker-Huffman diversion, restrict the rate of change of release during 

any 1-hour period to no more than double nor less than one-half the 

amount of release as the start of the change, and during emergency 

periods, endeavor to make releases in a manner that is not detrimental to 

fish (license article 42).

 From October 16 through December 31, make all releases at New 

Exchequer dam, from the outlets at or below elevation 485 feet insofar as 

physically possible (license article 43).

 Maintain the water surface elevation of New Exchequer reservoir (Lake 

McClure) as high as possible from April through October consistent with 

the primary purposes of the reservoir and maintain a minimum pool of no 

less than 115,000 acre-feet in Lake McClure, except when a drawdown is 

needed to maintain minimum streamflow as required by license article 40 

(license article 44).

 Cooperate with the Bureau of Sport Fisheries and Wildlife of FWS to 

determine means of providing up to 15,000 acre-feet of project water and 

return flow waters to the Merced NWR (license article 45).

 Within 1 year from the effective date of the license, prepare and file with 

the Commission for approval a proposed recreational use plan that 

includes recreational improvements, which may be provided by others in 

addition to the improvements that Merced ID plans to provide (license 

article 47). Exhibit R drawings (filed in 1963 and most recently revised in 

2007) depict four recreation areas at Lake McClure (Horseshoe, Bagby, 

McClure, and Barrett Cove) and the McSwain recreation area at McSwain 

reservoir. The recreation areas include campgrounds, boat launches, 

picnic areas, swimming areas, and parking.
26

Measures in Other Agreements and Contracts

In addition to the current license requirements (noted above), four agreements and 

contracts include various streamflow-related requirements. These agreements and 

contracts, and the terms and conditions in the agreements and contracts, which are not 

part of the existing license, include the following:

 California Department of Fish and Game (now California DFW) 

Memorandum of Understanding—Merced ID is required to supplement 

flows in the Merced River in October by providing 12,500 acre-feet of 

water in addition to the project’s minimum flow requirement in that 

month. 

 Water supply deliveries in Lake McClure (no expiration date)—Merced ID

makes three small diversions from Lake McClure for water supply: 

(1) Lake Don Pedro Community Service District withdraws from a 

location just north of Barrett Cove Marina up to about 5,000 acre-feet of 

water annually for water supply; (2) the Merced ID recreation facilities 

annually withdraw less than 1,000 acre-feet of water at three locations 

along Lake McClure; and (3) the McClure Boat Club, a small development 

adjacent to the project, diverts about 25 acre-feet at a point near the 

development. (The diversions are so minor that they do not affect project 

operations, and Merced ID anticipates that the diversions will continue 

unchanged.)

 Cowell Agreement (no expiration date)—Merced ID provides releases 

from Crocker-Huffman diversion dam up to the following flows for use by 

the Cowell Agreement diverters at 11 locations: 100 cfs in March; 175 cfs 

in April; 225 cfs in May; 250 cfs from the first day in June until the natural 

flow of the Merced River falls below 1,200 cfs; 225 cfs flow for the next 

31 days; 175 cfs flow for the next 31 days; 150 cfs for the next 30 days; 

and 50 cfs thereafter or the natural inflow into Lake McClure, whichever is 

less, through the last day of February.

 Davis-Grunsky Agreement with the State of California (expires December 

31, 2017)—Merced ID provides a continuous flow of between 180 cfs and 

220 cfs in the Merced River between Crocker-Huffman diversion dam and 

Shaffer Bridge.

2.1.2 Merced Falls Project

2.1.2.1 Existing Project Facilities

The existing Merced Falls Project consists of: (1) a concrete gravity dam with a 

structural height of 34 feet and a crest length of 575 feet; (2) three radial gates, each 

20 feet long and 13.5 feet high; (3) a 1-mile-long project impoundment with

approximately 900 acre-feet of storage capacity, a useable storage capacity of 
27

approximately 579 acre-feet, a total surface area of approximately 65 acres, and a normal 

impoundment elevation of 344 feet above mean sea level (msl); (4) powerhouse facilities 

consisting of a steel building housing a 3.4- MW turbine/generator unit and a vertical 

Kaplan-type four-blade turbine; (5) a 1,000-foot-long earthen levee with a crest width of 

8 feet; (6) an adjacent intake structure with a debris rack; and (7) a non-operable fish 

ladder. 

The project has a dependable capacity of 1.7 MW and an annual average 

generation of approximately 14.4 GWh. 

2.1.2.2 Existing Project Boundary

The project boundary includes about 75.6 acres. The project boundary generally 

follows the shoreline of the impoundment at the 344-foot msl elevation contour line and 

encloses lands on which the powerhouse and switchyard are located. On the northeast 

edge of the Merced Falls impoundment, the project boundary rises above the 344-foot 

msl elevation contour to include a small strip (approximately 4.8 acres) of reservoir 

shoreline that encompasses a fishing access site owned and operated by Merced ID. 

PG&E owns 20.5 acres of land within the project boundary that includes lands around the 

project dam, powerhouse, and the Merced Falls fishing access site. Merced ID owns a 

majority of the remaining acreage on which PG&E possesses flowage rights. 

Approximately 1 acre of federal lands administered by BLM is within the project 

boundary. 

2.1.2.3 Project Safety

The project has been operating for more than 46 years under the existing license 

and during this time, Commission staff has conducted operational inspections focusing on 

the continued safety of the structures, identification of unauthorized modifications, 

efficiency and safety of operations, compliance with the terms of the license, and proper 

maintenance. In addition, the project has been inspected and evaluated every 5 years by 

an independent consultant and a consultant’s safety report has been submitted for 

Commission review. As part of the relicensing process, Commission staff would 

evaluate the continued adequacy of the proposed project facilities under a new license. 

Special articles would be included in any license issued, as appropriate. Commission 

staff would continue to inspect the project during the new license term to assure 

continued adherence to Commission-approved plans and specifications, special license 

articles relating to construction (if any), operation and maintenance, and accepted 

engineering practices and procedures.

2.1.2.4 Existing Project Operation

The Merced Falls Project is operated in a run-of-river mode dependent on water 

outflow from Merced ID’s upstream Merced River Project. Inflow to the project passes 

through the impoundment, which is kept at a constant water elevation and then flows 

either through the powerhouse or the dam’s radial gates. Flows of up to approximately 
28

1,750 cfs are diverted through the powerhouse, and then discharged to the Merced River 

via the tailrace. When water inflows exceed 2,200 cfs, the project spills water through 

the radial gates. The main section of the dam, approximately 535.5 feet long, is topped 

with needle beams. During flood events with flows greater than 12,250 cfs, the needle 

beams can be dropped, allowing the 575-foot-long concrete section of the dam to act as a 

spillway.

2.1.2.5 Existing Environmental Measures

FERC License Requirements

 Minimize soil erosion and siltation on lands adjacent to the stream

resulting from construction and operation of the project (license article 

14).

 Construct, maintain, and operate such recreational facilities as prescribed 

by the Commission or upon the recommendation of the Secretary of the 

Interior or other interested state or federal agency (license articles 12, 39,

and 40). 

 Allow free public access, to a reasonable extent, to project waters and 

adjacent project lands owned by the licensee for the purposes of navigation 

and recreation. The licensee may also permit construction by others of 

wharves, access roads, landings, and other facilities, subject to the 

payment of reasonable rent (license article 13).

Voluntary Measures

 Under license article 28, the licensee is required to install stream gages as

deemed necessary by the Commission. However, no stream gaging has 

been specifically required by the Commission. Nevertheless, PG&E has 

installed gaging instruments above and below the dam.

2.2 APPLICANT’S PROPOSAL

2.2.1 Merced River Project

2.2.1.1 Proposed Project Facilities

Generating Facilities

Merced ID does not propose to add any new generating facilities or to modify 

existing generating facilities. 

Water Delivery Facilities

Merced ID proposes to remove the eight facilities associated with the delivery of 

water to the Merced NWR from the project but retain them in operation outside of the 
29

license. Merced ID proposes to continue to provide water to the Merced NWR under the 

new license but believes the minor facilities that were constructed in the early 1990s are 

not needed as part of the license because Merced ID now has a number of alternative 

water delivery options to the refuge and the facilities now also provide water to Merced 

ID’s water customers. Merced ID states that providing water to the refuge is no longer 

the sole purpose of the facilities and that the original facilities added for this purpose are 

no longer the primary method of delivering water to the refuge.

Recreation Facilities

In addition to operating and maintaining the existing recreation facilities and 

reconstructing the existing and proposed recreation facilities at the end of their useful 

lives, Merced ID proposes the following modifications to the existing recreational 

facilities, construction of one new recreation area, and construction of one new access 

point to the lower Merced River.

 Reconstruct existing recreation development components (e.g., campsites, 

restrooms, and parking areas) to comply with accessibility guidelines.

 Provide at McClure Point recreation area:

– concrete boat launch ramp, restroom, and paved parking area at the 

existing informal boat launch;

– aerator in the swimming area;

– up to 10 park model cabins with picnic tables and pedestal grills; 

– group day use area with shelter, picnic tables, pedestal grills, and 

restroom;

– additional sand at the existing swimming area and up to 10 additional 

picnic tables and pedestal grills; and

– up to two floating swim platforms.

 Provide at Barrett Cove recreation area:

– aerator in the swimming area;

– additional sand at the existing swimming area and up to 15 additional 

picnic tables and pedestal grills;

– sand lot volleyball court and playground at the swimming area; and

– up to 12 park model cabins with picnic tables and pedestal grills.

 Provide at Horseshoe Bend recreation area:

– 1-mile-long, non-motorized loop trail and information board;

– aerator in the swimming area;
30

– additional sand at the existing swimming area and up to 10 additional 

picnic tables and pedestal grills;

– swim platform;

– sand lot volleyball court and playground at the swimming area;

– host site at the campground with septic system, power, and water; and

– up to 10 park model cabins with picnic tables and pedestal grills.

 Provide at Bagby recreation area:

– interpretive and educational displays at the boat launch parking area and 

campground.

 Provide at Shepherd’s Point primitive area:

– gravel parking area with 10 spaces, including at least 2 trailer spaces;

– two-unit vault restroom; and

– take-out trail or path from the reservoir/river to the parking area.

 Construct upstream takeout facility at Sherlock Creek recreation area:14

– gravel parking area with 10 spaces;

– two-unit vault restroom; and

– take-out trail or path from reservoir/river to the parking area.

 Provide at McSwain recreation area:

– non-motorized shoreline trail between the day use area and New 

Exchequer dam (about 4.1 miles, native surfaced);

– information board at existing, native-surfaced parking areas and 

directional signs on Lake McClure Road;

– up to 12 park model cabins; 

– paved bicycle lane (about 5 miles) on Lake McClure Road from County 

Road J16 to near New Exchequer dam;

– additional sand at the existing swimming area and extend beach to the 

east by up to 50 percent; and

– up to two swim platforms.

 

14 Merced ID proposes to develop an upstream take-out facility at Sherlock Creek 

only if BLM is able to secure public access to Mosher Road and ensures the road 

condition is suitable for vans/buses with trailers.
31

 Construct the new Mack Island non-motorized recreation area:

– non-motorized trails (paved and unpaved) for bicycle and pedestrian 

use;

– trailhead parking area with restroom;

– pedestrian bridge to Mack Island;

– up to 10 primitive campsites on Mack Island with shoreline trail access;

– up to two swim platforms; and

– watercraft restriction area between west shore of Mack Island and 

reservoir shoreline to the west.

 Maintain existing Merced River Trail from the project boundary to the 

Bagby trailhead and provide:

– interpretive and educational display at Bagby trailhead;

– pedestrian bridge over Merced River near Sherlock Creek; and

– new trail segment on the south side of Merced River to the Bagby 

recreation area.15

 Construct a parking area with an unspecified capacity and install river 

access directional signage at the existing gravel-surfaced parking area at 

Merced Falls Road near Crocker-Huffman diversion dam (proposed as part 

of Merced ID measure RR2).

2.2.1.2 Proposed Project Boundary

Merced ID proposes the following changes to lands within the project boundary:

 Add 215.59 acres of land that would encompass the proposed Mack Island 

non-motorized recreation area at Lake McClure (New Exchequer 

development). Merced ID owns the land to be added to the project 

boundary.

 Add 1.06 acres of land that would encompass the main access road for the 

McSwain powerhouse (McSwain development). Merced ID owns the land 

to be added to the project boundary.

 

15 Merced ID proposes to construct and maintain the pedestrian bridge and south 

side trail only if all lands necessary have legal access through ownership or easements to 

allow public access to Bagby recreation area and BLM agrees to construct a bridge across 

the North Fork of the Merced River to allow safe public crossing during spring snow melt 

off and storm events.
32

 Remove 22.60 acres of McSwain development land that overlaps with 

PG&E’s Merced Falls Project boundary because this land is not necessary 

for the continued operation and maintenance of the Merced River Project 

and is already under Commission jurisdiction of the Merced Falls Project. 

Merced ID owns the land to be removed from the project boundary.

 Remove 8.04 acres of McSwain development land that is not necessary for 

encompassing the extent of the McSwain reservoir spillway channel 

because this land is not necessary for the continued operation and 

maintenance of the McSwain reservoir spillway and spillway channel. 

Merced ID owns the land to be removed from the project boundary.

After these modifications to the project area, the New Exchequer development 

would include 7,793.09 acres of Merced ID land (a net increase of 215.59 acres). The 

McSwain development would include 877.92 acres of Merced ID land (a net reduction of 

29.58 acres). The proposed project would include a total of 8,671.01 acres of Merced ID

land, 3,154.9 acres of land managed by BLM, and 13.2 acres of private land.

2.2.1.3 Proposed Project Operation 

Merced ID proposes to continue to operate the project as it has for the past 10 

years, including making no changes to existing minimum flow release conditions.

2.2.1.4 Proposed Environmental Measures

Merced ID proposes the following environmental measures (Merced ID

designations for proposed measures are in parenthesis):

General Measures (could apply to more than one resource area)

 Consult annually (at a minimum) with BLM regarding measures needed to 

ensure protection and use of resources on federal land administered by 

BLM and affected by the project (GEN1).

 Consult with BLM regarding potential future new facilities on federal land 

(GEN5).

 Consult with BLM regarding potential future new ground-disturbing 

activities on or directly affecting BLM lands that were not specifically 

addressed in the Commission’s National Environmental Policy Act

(NEPA) process (GEN4).

Aquatic Resources

 Develop a plan to coordinate operation with the downstream, run-of-river 

Merced Falls Project to assure implementation of flow-related measures at 

the two projects (GEN6).
33

 Develop an erosion control and restoration plan at least 90 days in advance 

of initiating construction of project facilities on BLM-managed land

(G&S1).

 Develop a recreation facilities construction hazardous material spill 

prevention, control, and countermeasures plan at least 90 days in advance 

of initiating construction of recreation facilities (WR1).

 Deliver 15,000 acre-feet of water to Merced NWR at a single delivery 

point during Merced ID’s irrigation season (WR2).

 Operate the project for flood control in accordance with the rules and 

regulations specified by the Corps (WR3).

 Provide minimum flows (from 40 to 180 cfs as measured at Shaffer Bridge 

depending on time of year and water year type) (AQR1, parts 1 and 4).

 Provide target flows (from 50 to 225 cfs as measured at Shaffer Bridge, 

depending on time of year and water year type) (AQR1, parts 1 and 4).

 Limit all controllable flow rate changes above a base flow of 200 cfs 

during any 1-hour period to not more than double or less than half the 

amount of the controlled release from McSwain dam at the start of the 

change (AQR1, part 2).

 Determine water year type as currently determined (AQR1, part 3).

 Notify the Water Board, BLM, FWS, NMFS, and California DFW by 

March 10 of the second or subsequent dry/critically dry water year if 

Merced ID has drought concerns (i.e., if there may not be sufficient water 

to meet both environmental and irrigation demands). By May 1 of these 

same years (i.e., the second or subsequent dry/critically dry water year), 

consult with these same agencies to discuss the project’s operational plans 

to manage the drought conditions and file a drought plan with the 

Commission with a request for expedited approval (AQR1, part 5). 

Implement the drought plan unless notified otherwise by the Commission.

 Maintain the Lake McClure minimum pool of 115,000 acre-feet 

(approximate elevation 640 feet) and the minimum pool of McSwain 

reservoir at or above elevation 388 feet, unless further drawdowns are 

needed to maintain required minimum flows (AQR2).

 Operate four water temperature monitoring recorders at suitable sites in the 

Merced River downstream of Crocker-Huffman diversion dam, as selected 

by a technical advisory committee (T&E1).

 Continuously monitor anadromous fish migrating into the Merced River at 

an Alaskan weir or similar device to be installed and operated from 

October 1 through December 31, using a VAKI RiverwaterTM system, and 
34

identify the time and direction of migration, size, sex, marks, and other 

attributes. Monitor juvenile anadromous fish outmigration from the 

Merced River from January 1 through May 31 with a rotary screw trap 

(RST) and document the total number and, for a representative subsample 

of the catch, size, weight, and life stage (T&E2).

 Establish a Merced River anadromous fish committee that would meet four 

times a year and invite NMFS, FWS, California DFW, the Water Board, 

and a representative of a non-governmental organization selected by 

Merced ID to join the committee. The purpose of the committee would be 

to facilitate Merced ID’s implementation of license conditions that pertain 

to monitoring anadromous fish. An annual report would be filed with the 

Commission by January 1 of each year documenting the activities of the 

committee during the previous calendar year (T&E3, mislabeled T&E2 by 

Merced ID).

 Implement the amended Aquatic Invasive Species Management Plan filed 

with the Commission on April 23, 2014, and supplemented on September 

5, 2014 to provide guidance for the prevention of aquatic invasive species 

in project reservoirs (AQR4).

 Develop a large woody debris (LWD) management plan that excludes 

BLM-managed land from any stockpiling activities to provide LWD to the 

Merced River downstream of Crocker-Huffman diversion dam for the 

purpose of enhancing habitat for aquatic organisms (G&S2).

Terrestrial Resources

 Implement the Invasive Species Management Plan on federal land, filed 

with the final license application and amended on September 22, 2014

(TR1).

 Implement the Vegetation Management Plan on federal land, filed with the 

final license application, as amended, to protect special-status plants and 

minimize project effects on sensitive habitats (TR2).

 Avoid the use of pesticides and herbicides on land administered by BLM 

to control undesirable woody and herbaceous vegetation, aquatic plants, 

insects, rodents, and undesirable fish without the prior written approval of 

BLM (TR3).

 Implement the Bald Eagle Management Plan, filed the final license 

application (TR4).

 Document all known bat roosts at project facilities, and if bats could be 

subject to human disturbance, install exclusion devices (TR5).
35

 Implement the Limestone Salamanders Sensitive Areas Management Plan, 

filed with the final license application (TR6).

 Record the incidental observations of western pond turtles.

Threatened and Endangered Species

 Provide annual employee training regarding the identification of specialstatus, non-native species, and sensitive areas that are known to occur in 

the project area and their locations in the project boundary (GEN2).

 Review special-status species lists annually and assess new species on 

federal land, and if necessary, consult with agencies to develop and 

implement protection measures (GEN3).

 Avoid the use of burrow fumigants and rodenticides in habitat of the 

California tiger salamander and the San Joaquin kit fox.

Recreation Resources

 Implement the Recreation Facilities Plan, amended on September 22, 

2014.

 Provide real-time recreation information on the California Data Exchange 

Center (California DEC) (RR2), including:

– flow information for the Merced River below Merced Falls, Dry Creek 

near the city of Snelling, the Merced River near the cities of Snelling, 

Cressey, and Stevinson (existing measure);

– elevations for Lake McClure and McSwain reservoir (existing measure); 

and

– flow information for the Merced River at Shaffer Bridge (U.S. 

Department of the Interior, Geological Survey [USGS] gage no. 

11271290).

 Construct a parking area and install river access directional signage at the 

existing gravel-surfaced parking area at Merced Falls Road near CrockerHuffman diversion dam (RR2).

 Develop a conceptual plan to align the existing Merced River Trail to a 

new trail segment that would follow along the shoreline of Lake McClure 

and McSwain reservoir.

 Annually stock rainbow trout, fingerling kokanee, and Chinook salmon in 

Lake McClure and McSwain reservoir for recreational fishing (AQR3).
36

Land Use

 Implement the Transportation Management Plan, filed on September 22, 

2014, to ensure project roads are adequately maintained.

 Implement the Fire Prevention and Response Plan, revised on September 

22, 2014, to provide for management, reporting, and the prevention of 

wildfires at the project.

Cultural Resources

 Implement the HPMP upon filing to manage project effects on properties 

eligible for listing on the National Register (CR1).

Aesthetic Resources

 Implement the Visual Resource Plan, filed on September 22, 2014, to 

ensure visual quality objectives are met at the project through monitoring 

and consultation.

2.2.1.5 Modifications to Applicant’s Proposal—Mandatory Conditions

The following mandatory conditions have been provided and are evaluated as part 

of the applicant’s proposal.

Section 4(e) Land Management Conditions 

The following preliminary mandatory conditions have been provided by BLM 

under section 4(e) and are included in appendix D. We consider preliminary conditions 7 

and 27 through 50 to be administrative and therefore not analyzed in our EIS. The 

remaining conditions are resource-specific and analyzed in this EIS. 

 Condition 1: Consult annually with BLM and other interested agencies 

regarding status of implementation of license conditions affecting 

BLM-managed land including, monitoring results, review of any nonroutine maintenance, foreseeable changes to the project, discussion of 

needed protection for newly listed sensitive species, upcoming 

maintenance, and any planned pesticide use.

 Condition 2: Establish a consultation group to provide a forum for Merced 

ID to consult with resource agencies and other interested parties on topics 

not addressed in condition 1, including development of plans that may be 

included in a new license and proposed temporary or permanent 

modifications to license conditions. The consultation group would 

establish mutually agreeable process guidelines for conducting effective 

and efficient meetings that would occur at least four times a year.
37

 Condition 3: Annually perform employee awareness training to 

familiarize Merced ID operations and maintenance staff with special-status 

species, non-native invasive plants, and sensitive areas known to occur 

within or adjacent to the project boundary.

 Condition 4: Develop a coordinated operations plan with the licensee of 

the Merced Falls Project and with resource agencies to assure 

implementation of flow-related measures in the two project licenses.

 Condition 5: Develop an erosion control and restoration plan for actions 

affecting BLM-managed land within or adjacent to the project boundary 

for BLM approval and file the plan with the Commission at least 90-days 

in advance of initiating construction of recreation or other project 

facilities.

 Condition 6: Develop a large woody material (LWM) management plan in 

consultation with BLM, California DFW, FWS, NMFS, and the Water 

Board that: (1) addresses the location of LWM collection in Lake 

McClure and McSwain reservoir; (2) describes potential options for

moving LWM to locations downstream of Crocker-Huffman diversion 

dam; and (3) identifies suitable locations downstream of Crocker-Huffman 

diversion dam where LWM can be placed within the active channel and be 

passively mobilized by 2 to 5 year high flow events or where it would be 

appropriate to anchor LWM in the active channel and floodplain.

 Condition 8: Develop an aquatic invasive species management and 

monitoring plan for BLM approval after consultation with California 

DFW, FWS, and the Water Board that initially addresses zebra and quagga 

mussels, New Zealand mudsnail, Eurasian milfoil, hydrilla, didymo, and 

Asian clams. The plan should include provisions for: (1) a public 

education program; (2) developing best management practices (BMPs) for 

individual operation and maintenance activities that have the potential to 

introduce aquatic invasive species into a project reservoir; (3) conducting a 

specific monitoring program for quagga and zebra mussels, including 

surface surveys, veliger sampling, and artificial substrate monitoring; and 

(4) incidental observation monitoring of quagga and zebra mussels, New 

Zealand mudsnail, Asian clams, Eurasian milfoil, hydrilla, didymo, and 

American bullfrog. 

 Condition 13: Develop and implement a management plan for the 

California red-legged frog in the Piney Creek core area after consultation 

with California DFW, FWS, and the Water Board that addresses 

conservation and habitat needs for the red-legged frog. The plan should 

include provisions to: (1) identify sites where deleterious non‐native 

predators are present; (2) prioritize where control efforts should take place; 
38

(3) control/eliminate deleterious non‐native species/predators (plants, 

vertebrates) for all known occurrences of the California red-legged frog on 

BLM land, using methods that are determined to be the most effective; and 

4) identify suitable habitat within watersheds that includes a mosaic of 

breeding habitat interspersed with a matrix of barrier-free dispersal habitat. 

 Condition 14: Develop and implement a management plan for the foothill 

yellow-legged frog after consultation with California DFW, FWS, and the 

Water Board to address water temperatures and potential temperature 

effects on foothill yellow-legged frogs at the confluence of Sherlock Creek 

and the Merced River. Monitoring should be conducted once in each 

water year type for first 10 years and once every 5 years thereafter.

 Condition 17: Develop and implement a riparian vegetation monitoring 

plan for BLM approval after consultation with California DFW, FWS, and 

the Water Board that addresses the conservation and restoration of riparian 

habitats and ensures proper functioning and advanced ecological status of 

riparian vegetation and associated stream channels and floodplains. 

 Condition 19: Coordinate an annual recreation meeting with interested 

resource groups (at minimum, BLM) to discuss the management, public 

safety, protection, and utilization of project recreation facilities and 

resources.

 Condition 20: Develop and implement a Merced River Trail conceptual 

plan after consultation with BLM for the Merced River Trail from 

McSwain dam to the Bagby recreation area.

 Condition 21: Enter into an agreement to provide annual funding to BLM 

for the operation, maintenance, management, and administration costs of 

BLM-administered lands in and around the Merced River Project.

 Condition 22: Develop and implement, upon BLM approval, a recreation 

facilities plan for the Merced River Project for the operation, maintenance, 

and monitoring of recreation use at the project.

 Condition 23: Close off illegal off road vehicle (ORV) access at Piney 

Creek to prevent illegal ORV use on project lands.

 Condition 24: Implement a HPMP, upon BLM and Commission approval.

 Condition 25: Implement a fire prevention and response plan, upon BLM 

approval, to protect project resources and facilities, provide public safety, 

and develop fire response protocols.

 Condition 26: Implement a visual resource plan, upon BLM approval, 

addressing procedures to address visual resources impacted by the project.
39

Water Quality Certification Conditions

The following preliminary mandatory WQC conditions have been provided by the 

Water Board, and are included in appendix E. We consider preliminary conditions 22 

and 30 through 49 to be administrative and therefore not analyzed in our EIS. The 

remaining conditions are resource-specific and analyzed in this EIS.

 Condition 1: Organize a Merced River anadromous fish committee 

comprising Merced ID, PG&E, NMFS, FWS, California DFW, the Water 

Board, and a non-governmental organization.

 Condition 2: The Water Board reserves the right to condition the project 

with minimum instream flows in light of the whole record.

 Condition 3: Consult with the relevant resource agencies for any activity 

not addressed in the NEPA or California Environmental Quality Act

document or WQC document that may adversely affect water quality to 

determine if supplemental NEPA or California Environmental Quality Act

documents and/or a WQC amendment are required.

 Condition 4: Develop a gravel augmentation plan in consultation with the 

committee specified in condition 1 that provides for augmentation 

consistent with the annual gravel amount trapped behind New Exchequer 

and McSwain dams.

 Condition 5: Develop, within 1 year of license issuance in consultation 

with FWS and California DFW, a monitoring plan for bald and golden 

eagles. 

 Condition 6: Develop, within 1 year of license issuance, a monitoring and 

conservation plan for vernal pool fairy shrimp. 

 Condition 7: Develop, within 1 year of license issuance, a monitoring and 

conservation plan for California tiger salamanders. 

 Condition 8: Develop, in consultation with the committee specified in 

condition 1, a fish passage or habitat restoration plan that would result in 

fish passage over Crocker-Huffman, McSwain, and New Exchequer dams 

or decreasing water temperature in and downstream of the project.

 Condition 9: Develop a drought plan, in consultation with the committee 

specified in condition 1 that provides overarching guidance for operations 

during an emergency drought and/or multiple critically dry years and 

specifies license or WQC variances the Merced ID may request.

 Condition 10: Develop, within 1 year of license issuance, a monitoring 

and conservation plan for the California red-legged frog, foothill yellowlegged frog, and western spadefoot toad. 
40

 Condition 11: Develop, within 1 year of license issuance, a monitoring 

and conservation plan for the valley elderberry longhorn beetle.

 Condition 12: Consult annually with BLM, the committee specified in 

condition 1, and the Park Service regarding the status of implementation of 

license conditions, including study and monitoring results; review of any 

non-routine maintenance; foreseeable changes to the project and associated 

resource plans; discussion of needed protection for newly listed sensitive 

species; and upcoming operation and maintenance plans.

 Condition 13: Consult with BLM, the Park Service, and the Water Board 

within 3 months of license issuance and annually for the term of the 

license to conduct an annual review of endangered and special-status 

species lists to determine if any species added to the lists would be 

adversely affected by the project, and if so, develop and implement a 

species-specific study plan. 

 Condition 14: Develop a LWM plan in consultation with the committee 

specified in condition 1.

 Condition 15: The Water Board reserves the right to condition the project 

with a new value for the minimum pool requirement in Lake McClure in 

light of the whole record.

 Condition 16: Develop a fish stocking plan in consultation with the 

committee specified in condition 1. Beginning the first year after license,

annually stock fish in Lake McClure with a minimum of 32,000 to 70,000 

of catchable sized fish and 39,000 to 95,000 fingerlings. Annually stock 

fish in McSwain reservoir with 1,000 to 2,000 catchable-sized rainbow 

trout.

 Condition 17: Develop, in consultation with California DFW, an aquatic 

invasive species management plan that includes: (1) a statement of goals 

and objectives; (2) a description of proposed monitoring protocols; (3) a 

detailed monitoring and reporting schedule; (4) a plan for corrective 

measures and timetable for implementation if data indicate the presence of 

aquatic invasive species; and (5) protective measures that would prevent 

introduction of aquatic invasive species in the project area.

 Condition 18: Develop a pesticide use plan within 6 months of license 

issuance. 

 Condition 19: Develop, in consultation with the committee specified in 

condition 1, a water temperature monitoring plan that includes: (1) a 

statement of goals and objectives; (2) a description of proposed monitoring 

protocols at four to eight monitoring locations; (3) a comprehensive 

description of factors that may affect water temperature and whether those 
41

factors are associated with project operations; (4) a detailed monitoring 

and reporting schedule; and (5) a plan for corrective measures and a 

timetable for implementation if data indicate that the project may be 

increasing water temperature and/or adversely affecting water quality.

 Condition 20: Develop, in consultation with the committee specified in 

condition 1, an anadromous fish monitoring plan that includes: (1) a 

statement of goals and objectives; (2) a description of proposed monitoring 

protocols; (3) a comprehensive description of factors that may adversely 

affect state or federally listed anadromous fish and whether those factors 

are associated with project operations; (4) a detailed monitoring and 

reporting schedule; (5) a plan for corrective measures and a timetable for 

implementation if data indicate that the project may be affecting 

anadromous fish or their habitat; and (6) protective measures.

 Condition 21: A) Develop a transportation management plan that 

includes: (1) a map and inventory roads associated with the project using 

a geographic information system (GIS); and (2) a road inventory and 

B) Conduct road monitoring and maintenance, including at least annual 

monitoring and inspection of project road conditions, as well as inspection 

of drainage structures and runoff patterns after major storm events. 

 Condition 23: Implement measures to control erosion, excessive 

sedimentation, and turbidity prior to the commencement of and through 

any ground-clearing activities, excavation, or any other project activities 

that could result in erosion or sediment discharges to surface waters.

 Condition 24: Keep waters free from changes in turbidity due to project 

activities that cause nuisance or adversely affect beneficial uses.

 Condition 25: Pre-wash all imported riprap, rocks, and gravels used for 

construction within or adjacent to any water sources.

 Condition 26: Prevent construction material, debris, spoils, soil, silt, sand, 

bark, slash, sawdust, rubbish, steel, or other inorganic, organic, or earthen 

material, and any other substances from any project-related activity from 

entering surface waters.

 Condition 27: Prevent unset cement, concrete, grout, damaged concrete, 

concrete spoils, or water used to clean concrete surfaces from contacting or 

entering surface waters.

 Condition 28: Wash all equipment prior to transport to the project site and 

keep it be free of sediments, debris, and foreign matter. Steam-clean any 

equipment used in direct contact with surface water prior to use. Inspect 

all equipment using gas, oil, hydraulic fluid, or other petroleum products 

for leaks prior to use and monitor them for leakage. Position stationary 
42

equipment over drip pans or other types of containment. Maintain spill 

and containment equipment onsite at all locations where such equipment is 

used or staged.

 Condition 29: Keep onsite containment for storage of chemicals classified 

as hazardous away from watercourses and include secondary containment 

and appropriate management as specified in California regulations.

2.2.2 Merced Falls Project

2.2.2.1 Proposed Project Facilities

PG&E is not proposing any new or upgraded facilities or structural changes to the 

project.

2.2.2.2 Proposed Project Boundary

PG&E proposes to modify the project boundary by removing approximately 4.8 

acres of PG&E-owned lands, which it indicates are not needed for project purposes. The 

proposed 4.8-acre reduction in land encompassed by the project boundary is the result of 

PG&E redrawing the boundary along the north side of the project impoundment, east of 

the county highway bridge, to match the impoundment’s high water mark; this results in 

the removal from the project of a strip of PG&E-owned land adjacent to the 

impoundment and facilities owned, operated, and maintained by Merced ID (parking lot, 

restrooms) within the Merced Falls Fishing Access area.

2.2.2.3 Proposed Project Operation

PG&E is not proposing any changes to project operation. The Merced Falls 

Project would continue to operate in run-of-river mode dependent on water outflow from 

Merced ID’s upstream Merced River Project.

2.2.2.4 Proposed Environmental Measures

Aquatic Resources

 Conduct annual fall fish sampling in the reach of the Merced River 

downstream of Merced Falls dam and upstream of Crocker-Huffman dam 

(Merced Falls reach) to monitor fish populations (new proposal from 

September 5, 2014, response to comments).

 Continue to periodically rake the project’s intake racks to clear them of 

LWD, and place the removed material on the debris chute at the dam to 

mobilize downstream.
43

Water Resources

 Develop and implement a long-term water quality monitoring program in 

the Merced River downstream of Merced Falls dam and upstream of 

Crocker-Huffman diversion dam to monitor dissolved oxygen (DO) and 

temperature.

Recreation

 Continue to operate and maintain existing recreation facilities at the 

Merced Falls impoundment area, including the River’s Edge Fishing 

Access area and the car-top boat launch at Merced Falls Fishing Access 

area.

 Develop and post directional and safety signage at the informal canoe 

portage trail.

 Develop a fish stocking plan in consultation with California DFW that 

includes stocking 11,000 adult-sized rainbow trout at the Merced Falls 

impoundment for the first 2 years following license issuance and a plan for 

stocking (schedule and type and amount of fish) for the rest of the license 

term.

Cultural Resources

 Implement the HPMP, filed on October 6, 2014.

2.2.2.5 Modifications to Applicant’s Proposal—Mandatory Conditions

The following mandatory conditions have been provided and are evaluated as part 

of the applicant’s proposal. 

Water Quality Preliminary Certification Conditions

The following preliminary mandatory WQC conditions have been provided by the 

Water Board, and are included as appendix F. We consider preliminary conditions 10 

through 36 to be administrative conditions and standard conditions to protect water 

quality and beneficial uses, and therefore not analyzed in our EIS. The remaining 

conditions [preliminary conditions 2 through 9] are project-specific, and specify the 

following conditions for the licensee:

 Condition 2: Develop a pesticide use plan, within 6 months of license 

issuance, in consultation with California DFW, FWS, NMFS, and the 

Water Board.

 Condition 3: Submit a gravel augmentation plan within 1 year of license 

issuance, in consultation with California DFW, FWS, and NMFS. The 

amount of gravel augmented should be consistent with the amount of 

gravel trapped annually behind Merced Falls dam.
44

 Condition 4: Submit a fish passage plan if:

– Fish passage resumes at Crocker-Huffman diversion dam; and

– Resumption of fish passage at Merced Falls dam is recommended after 

consultation with NMFS, California DFW, and FWS.

 Condition 5: Submit an eagle monitoring and conservation plan within 1 

year of license issuance, developed in consultation with FWS, California 

DFW, and BLM.

 Condition 6: Develop a monitoring and conservation plan, within 6 

months of license issuance in consultation with FWS, California DFW, 

and BLM, for the valley elderberry longhorn beetle.

 Condition 7: Review lists of endangered and special-status species within 

6 months of license issuance, and every 5 years thereafter. For any newly 

added species in the project area that could be adversely affected by the 

project, consult with FWS, California DFW, Water Board, and NMFS to 

develop a species-specific study plan. 

 Condition 8: Hold a meeting, beginning 1 year after license issuance, every 

5 years with resource agencies, and open to tribes and the public to provide 

updates to all monitoring and data required by the WQC.

 Condition 9: Develop and implement a plan to monitor and identify 

locations of the California red-legged frog, foothill yellow-legged frog, and 

western spadefoot toad within 1 year of license issuance. 

2.3 STAFF ALTERNATIVE

2.3.1 Merced River Project

Under the staff alternative, the project would include the following revisions to the 

proposed project or additional measures.

Aquatic Resources

 Expand the scope of the proposed technical advisory committee beyond 

measures that pertain only to anadromous fish downstream of CrockerHuffman diversion dam (i.e., topics that pertain to resident fish, aquatic 

and terrestrial monitoring results, and actions that could affect BLMmanaged land, including Lake McClure water level management); 

establish guidelines for conducting meetings that provide ground rules for 

decision making; and add BLM and the Park Service to the entities invited 

to participate on the committee.
45

 Add the Water Board, BLM, FWS, California DFW, NMFS, and the Park 

Service to the entities invited to consult on the coordinated operations plan 

for the Merced River and Merced Falls Projects.

 Add the Water Board, California DFW, and FWS to the entities invited to 

consult on site-specific erosion control and restoration plans and expand 

the plans to apply to all construction on all land within the project 

boundary.

 Include, at a minimum, the following elements in the proposed erosion 

control and restoration plans: (1) a description of BMPs that would be 

applied in specific circumstances, (2) provisions for inspecting erosion 

control measures while they are in place, (3) emergency protocols for 

erosion and sedimentation control, (4) site stabilization techniques that 

would be used once construction is completed, and (5) a description of 

when and what type of water quality monitoring of surface waters would 

occur during and after ground-disturbing activities. Identifying such 

measures and protocols in the erosion control and restoration plans would 

assure that erosion does not unacceptably degrade water quality adjacent to 

construction and other ground-disturbance sites.

 In addition to monitoring ramping rates associated with releases from 

McSwain dam, monitor flows and stage at 1-hour intervals at the existing 

gage immediately downstream of Crocker-Huffman diversion dam and 

provide annual reports to the Commission from both gages after review by 

the technical advisory committee. Monitoring flows at both locations 

would document compliance with the recommended ramping rate at 

McSwain dam and to establish a relationship of ramping rates at McSwain 

dam to the ramping rates downstream of Crocker-Huffman diversion dam 

to provide data on whether or not the ramping rate protocol should be 

adjusted in the future.

 Include, at a minimum, the following elements in the construction and 

non-routine maintenance hazardous material spill prevention, control, and 

countermeasure plans: (1) a description of the BMPs for contaminant 

control that would be applied in specific circumstances, (2) emergency 

protocols for spill containment and remediation, (3) the location of 

emergency cleanup equipment in the event of contaminant release,

(4) identification of entities to be contacted in the event of a spill,

(5) designated equipment refueling and maintenance areas, (6) provisions 

requiring equipment to be cleaned and inspected prior to entering a 

construction site, (7) post-spill water quality monitoring protocols, and 

(8) a listing of applicable local, state, and federal regulations that pertain to 

prevention of spills and protection of water quality. Identifying such 

measures and protocols in the hazardous materials spill prevention, 
46

control, and countermeasure plans would assure that surface water and 

groundwater are protected from contaminants.

 Use the Hughes method to determine water year type rather than the 

proposed Merced 60-20-20 Index16 to better designate water year types 

based on both forecasted and observed runoff that would avoid biased 

water year designations to below normal conditions.

 Release the staff-recommended instantaneous minimum flows as measured 

at Shaffer Bridge and shown in table 5-2 rather than the proposed 

minimum and target flows.

 Maintain a minimum flow of 25 cfs at all times from New Exchequer dam 

to ensure that the channel is not dewatered.

 Develop a water temperature monitoring plan in consultation with the 

technical advisory committee and monitor water temperature at four to 

eight sites (rather than limiting the number of sites to four) from CrockerHuffman diversion dam, downstream to Shaffer Bridge.

 Release a fall pulse flow of 1,000 cfs, as measured at Shaffer Bridge, 

during October or November until a total volume of 12,500 acre-feet is 

released to attract adult anadromous salmonids to the mouth of the Merced 

River and stimulate upstream migration to the primary spawning area 

between Crocker-Huffman diversion dam and Shaffer Bridge. The timing 

of the beginning of the release would be determined by the technical 

advisory committee.

 Release a spring pulse flow of 30,000 acre-feet during wet, above normal, 

and below normal water years that would consist of flows equal to or 

above 1,000 cfs, as measured at Shaffer Bridge, for 9 days and peak flows 

that hold for 2 or 3 days, with a gradually ascending and descending 

hydrograph. 

– During dry and critically dry water years, release a spring pulse flow of 

10,000 acre-feet. 

 

16 Merced ID established a five-level water year classification system for the 

Merced River. The 60-20-20 Index is based on the unregulated inflow to Lake McClure. 

The five-water year classifications are: wet, above normal, below normal, dry, and 

critical and are calculated as 60 percent of the current year’s April through July inflow 

plus 20 percent of the current year’s October through March inflow plus 20 percent of the 

previous year’s index.
47

– After a minimum of two dry or critically dry water years, consult with 

the technical advisory committee and make recommendations to the 

Commission regarding whether anadromous fish outmigration data 

supports changing the 10,000 acre-feet pulse flow release. 

– The timing of the onset of the spring pulse flow release would be 

determined by the technical advisory committee.

 Annually report Lake McClure stage and acre-feet of storage to the 

Commission to document compliance with water management measures 

and, when applicable, drought management plans.

 File the drought plans developed after two or more consecutive dry or 

critically dry water years as proposed with the Commission for approval.

 Develop a general drought management plan in consultation with the 

technical advisory committee that identifies the measures that would be 

considered to address droughts when they occur, decision paths regarding 

how management options for a specific drought would be decided, and a 

listing of Commission, BLM, and WQC license conditions that would 

require variances with drought management options. Approval of this plan 

would expedite approval of the drought-specific plan, which would be 

time-sensitive.

 Develop a Merced NWR water delivery plan in consultation with FWS 

and California DFW to ensure to the extent reasonably practical, the 

delivery of 15,000 acre-feet of water to the refuge during times of the year 

when this water would provide the most benefit to wildlife.

 Develop, in consultation with the technical advisory committee, an 

anadromous fish monitoring plan that includes that includes the attributes 

Merced ID proposes to monitor. Include in the plan the proposed 

monitoring station locations, the rationale for selecting those locations, and 

corrective actions that could be taken, including assisting with fish rescue 

efforts, if monitoring shows the project is adversely affecting anadromous 

fish.

 Add the technical advisory committee and California Department of 

Transportation to the entities invited to consult on the LWM management 

plan.

 Develop a gravel augmentation plan in consultation with the technical 

advisory committee that (1) provides for the annual placement of 2,600 

cubic yards of gravel in the lower Merced River; (2) identifies the range of 

particle sizes to be used for augmentation; (3) identifies gravel harvesting 

sites; (4) includes provisions for restoring harvest sites to contours 

expected in a natural riparian floodplain forest to mitigate for any aesthetic 
48

or ecological impact associated with gravel harvesting; (5) includes the 

protocol for selecting augmentation sites between Merced Falls dam and 

Shaffer Bridge; (6) provides for monitoring and mapping augmented 

gravel; and (7) provides for annual reporting.

 Modify the amended Aquatic Invasive Species Management Plan to 

include provisions to document incidental observations of quagga and 

zebra mussels, New Zealand mudsnails, Asian clams, American bullfrog, 

Eurasian milfoil, Brazilian elodea, and hydrilla; provide reports regarding 

any incidental observation that rise to the level of needing follow-up 

management actions, to the Commission. Add California DFW and the 

Water Board to the entities invited to consult on revisions to the plan.

Terrestrial Resources

 Develop a protection plan for special-status bats after consultation with 

BLM, FWS, California DFW, and the Water Board to protect bats roosting 

at project facilities. The plan would include specific details about agencyrecommended measures and proposed measures to document all known 

bat roosts at project facilities, the type and design of exclusion devices, 

and would define appropriate metrics to evaluate the effectiveness of the 

measures.

 Modify the Bald Eagle Management Plan to:

– include educational information about bald eagle roost sites in public 

information; 

– describe activities that would be considered emergencies, and define 

why these activities would supersede bald eagle protection;

– protect winter roost trees from vegetation management and future 

construction activities to reduce potential for degrading these areas; and

– revise all protocols and methodologies to be consistent with the FWS 

National Bald Eagle Management Guidelines.

 Modify the Invasive Species Management Plan on federal to:

– stipulate that the measures in the plan apply to all land within the project 

boundary, including treatment measures for the existing population of 

perennial pepperweed on Merced ID land;

– provide details about specific BMPs that would be implemented as part 

of the plan;

– include notification to agencies of planned pesticide use; and

– include descriptions of unexpected outbreaks that would not require 

notification prior to use.
49

 Modify the Vegetation Management Plan on federal land (TR2, as 

amended) to:

– provide details about specific BMPs that would be implemented as part 

of the plan; 

– include maps in section 3.0 to show locations of elderberry plants and 

identify which plants show signs of occupancy by the valley elderberry 

longhorn beetle; and

– include consultation with BLM, California DFW, and FWS during the 

planning phases for any new disturbance such as any potential future 

construction of new facilities and other project operation and 

maintenance activities that could disturb vegetation resources through

excavation, grading, topsoil stripping, or other similar activities, to 

identify the need for pre-disturbance surveys and develop protection 

measures for any sensitive species in the disturbance area.

 Develop a protection plan for western pond turtles, including the proposed 

monitoring and reporting measures to protect western pond turtles from 

project effects such as water level fluctuations, traffic associated with 

project maintenance and recreation, and maintenance activities such as 

pesticide applications.

 Modify the Limestone Salamanders Sensitive Areas Management Plan to:

– provide details about specific BMPs that would be implemented as part 

of the plan 

– site new hiking trails or modifications to existing hiking trails outside of 

limestone salamander habitat. 

Threatened and Endangered Species

 Develop a protection plan for the San Joaquin kit fox, including surveys 

and the development of protection and mitigation measures to minimize 

project-related and cumulative effects (i.e., effects of rodenticides, 

potential effects on dispersal).

 Develop a protection plan for vernal pool fairy shrimp and its habitat to 

reduce project effects on fairy shrimp and its associated habitat (i.e., longterm habitat degradation).

 Develop a protection plan for federally listed plants potentially occurring 

in the project area to minimize project effects (i.e., project maintenance 

activities, recreation) on these plant species.
50

 Develop a protection plan for the California red-legged frog, foothills 

yellow-legged frog, and western spadefoot to reduce project effects such as 

changes in water temperature, increases in the populations of predators, 

and pesticide use.

 Develop a protection plan for California tiger salamanders that includes a

proposed measure to avoid use of pesticides in California tiger salamander 

habitat to protect the species from project effects (i.e., effects of 

rodenticides and burrow fumigants, vegetation maintenance, recreation 

activities, and vehicular traffic).

Recreation Resources

 Modify the Recreation Facilities Plan, filed on September 22, 2014, to:

– extend the proposed paved bicycle lane along the entire length of Lake 

McClure Road (7.8 miles) between County Road J16 and the proposed 

parking area from the McSwain shoreline trailhead;

– remove the provision for a host site at the project’s Horseshoe Bend 

recreation area campground;

– identify the location of the three floating restrooms provided on Lake 

McClure and include the operation and maintenance schedule and 

construction and rehabilitation measures (if needed) for each restroom; 

and

– revise the implementation schedule to: begin construction no earlier 

than Labor Day and no later than Memorial Day to avoid the prime 

recreation season; begin construction at Bagby recreation area within 2 

years of license issuance; begin construction of the project’s 

non-motorized trails within 3 years of license issuance; begin 

rehabilitation planning at each campground within 3 years of license 

issuance (to be completed within 6 years of license issuance); and 

include a mid-license term rehabilitation assessment in the 

implementation schedule that would identify any facilities and or water 

systems in need of rehabilitation.

 Develop and implement a fish stocking plan that includes the type, size, 

and amount of fish to be stocked in Lake McClure and McSwain reservoir

based on recreational use, angling demand, and state fish stocking 

management targets and an implementation schedule to ensure appropriate 

recreational fish stocking levels at the project for the license term.
51

Land Use

 Modify the Transportation Management Plan, filed on September 22, 

2014, to include an inventory of all project roads and current road 

conditions, a detailed schedule of maintenance based on that inventory, 

relevant BMPs that would be implemented, a schedule for monitoring 

project road use over the term of the license, and a schedule for 

consultation with BLM and the California Department of Forestry and Fire 

Protection.

Aesthetics

 Modify the Visual Resource Plan, filed on September 22, 2014, such that it 

applies to all lands within the project boundary.

2.3.2 Merced Falls Project

Under the staff alternative, the project would include the following revisions to the 

proposed project or additional measures:

Aquatic Resources

 Participate in a Merced River technical advisory committee in conjunction 

with Merced ID to inform and coordinate the implementation of 

environmental measures.

 Develop a coordinated operation plan in conjunction with Merced ID for 

the Merced River and Merced Falls Projects in consultation with the 

technical advisory committee.

 Develop a LWD management plan in consultation with the technical 

advisory committee to provide habitat enhancement for aquatic species.

 Develop an annual fish monitoring plan in the Merced Falls reach in 

consultation with the technical advisory committee.

Terrestrial Resources

 Develop a control plan for noxious weeds and invasive plants, integrated 

with pest management and pesticide use.

 Develop and implement a management plan for bald eagles in consultation 

with FWS, California DFW, and the Water Board.
52

Threatened and Endangered Species

 Develop a protection plan for the valley elderberry longhorn beetle to

minimize project effects on the valley elderberry longhorn beetle and its 

habitat.

 Develop a protection plan for the San Joaquin kit fox to reduce projectrelated and cumulative effects on the San Joaquin kit fox.

 Develop a protection plan for the California red-legged frog, foothills 

yellow-legged frog, and western spadefoot.

Recreation

 Operate and maintain all recreation facilities at the Merced Falls Fishing 

Access area, including one sign, restroom, parking area, and car-top boat 

launch, the informal angler trail along the northern shoreline, the two 

informal parking areas on either side of Hornitos Road County Bridge

(Hornitos Bridge), and the informal canoe portage trail at the south end of 

Merced Falls dam.

Project Boundary

 Modify the project boundary to include the informal canoe trail on the 

south side of Merced Falls dam.

2.4 STAFF ALTERNATIVE WITH MANDATORY CONDITIONS

We recognize that the Commission is required to include valid section 4(e) 

conditions and section 401 conditions in any license issued for the project. 

2.4.1 Merced River Project

The staff alternative with mandatory conditions includes staff-recommended 

measures along with the mandatory conditions that we did not include in the staff 

alternative: (1) provide annual funding in a contributed funds account to offset operation, 

maintenance, management, and administration costs incurred by the BLM; (2) annual 

consultation to review the project status and plans, results of studies, necessary 

modifications to plans, and protection measures for newly listed species; (3) a fish 

passage or habitat restoration plan that would result in fish passage over CrockerHuffman, McSwain, and New Exchequer dams or decrease water temperature in and 

downstream of the project; and (4) review the lists of federally listed and special-status 

species and evaluate potential project effects on newly listed species.
53

2.4.2 Merced Falls Project

The staff alternative with mandatory conditions includes staff-recommended 

measures along with the mandatory conditions that we did not include in the staff 

alternative: (1) gravel augmentation in the Merced Falls reach; (2) a fish passage plan; 

and (3) annual consultation to review the project status and plans, results of studies, 

necessary modifications to plans, and protection measures for newly listed species. 

2.5 ALTERNATIVES CONSIDERED BUT ELIMINATED FROM DETAILED 

ANALYSIS

We considered several alternatives to the applicant’s proposals, but eliminated 

them from further analysis because they are not reasonable in the circumstances of either

case. They are: (1) issuing a non-power license; (2) federal government takeover of the 

projects; and (3) retiring the projects.

2.5.1 Issuing a Non-Power License

A non-power license is a temporary license that the Commission will terminate 

when it determines that another governmental agency will assume regulatory authority 

and supervision over the lands and facilities covered by the non-power license. At this 

point, no agency has suggested a willingness or ability to do so. No party has sought a 

non-power license and we have no basis for concluding that the project should no longer 

be used to produce power. Thus, we do not consider issuing a non-power license to 

either the Merced River Project or the Merced Falls Project a realistic alternative to 

relicensing in these circumstances.

2.5.2 Federal Government Takeover of the Projects

We do not consider federal takeover to be a reasonable alternative. Federal 

takeover and operation of the projects would require Congressional approval. While that 

fact alone would not preclude further consideration of this alternative, there is no 

evidence to indicate that federal takeover should be recommended to Congress. No party 

has suggested federal takeover would be appropriate, and no federal agency has 

expressed an interest in operating the projects.

2.5.3 Retiring the Projects

Project retirement could be accomplished with or without dam removal. Either 

alterative would involve denial of the relicense application and surrender or termination 

of the existing license with appropriate conditions. No participant has suggested that dam 

removal would be appropriate in either case, and we have no basis for recommending it. 

The New Exchequer, McSwain, and Merced Falls dams and associated reservoirs 

serve other important purposes including recreation, irrigation, and flood control, 

regardless of whether power is produced. Thus, dam removal is not a reasonable 
54

alternative to relicensing the Merced River Project or the Merced Falls Project with 

appropriate protection and enhancement measures. 

The second project retirement alternative would involve retaining the dams and 

disabling or removing equipment used to generate power. Project works would remain in 

place and could be used for historic or other purposes. This would require us to identify 

another government agency with authority to assume regulatory control and supervision 

of the remaining facilities. No agency has stepped forward, and no participant has 

advocated this alternative. Nor have we any basis for recommending it. Because the 

power supplied by the projects is needed, a source of replacement power would have to 

be identified. In these circumstances, we do not consider removal of the electric 

generating equipment at the Merced River and Merced Falls Projects to be a reasonable 

alternative.
55

3.0 ENVIRONMENTAL ANALYSIS

In this section, we present: (1) a general description of the project vicinity; (2) an 

explanation of the scope of our cumulative effects analysis; and (3) our analysis of the 

proposed action and other recommended environmental measures. Sections are

organized by resource area. Under each resource area, historic and current conditions are 

first described. The existing condition is the baseline against which the environmental 

effects of the proposed action and alternatives are compared, including an assessment of 

the effects of proposed mitigation, protection, and enhancement measures, and any 

potential cumulative effects of the proposed action and alternatives. Staff conclusions 

and recommended measures are discussed in section 5.1, Comprehensive Development 

and Recommended Alternative.

17

3.1 GENERAL DESCRIPTION OF THE RIVER BASIN

The main stem of the Merced River forms in Yosemite National Park at an 

elevation of approximately 8,200 feet just east of the border of Mariposa and Madera 

Counties, California, in the central Sierra Nevada, and then flows west, meandering 

through Yosemite Valley before plunging into the steep canyon of the Merced Gorge 

(figure 3-1). Upstream of Lake McClure, the Merced River Basin is steep, rugged, 

sparsely populated, and mostly occupied by conifer forests. Portions of the South Fork 

Merced River, which drains into the Merced River about 16 miles upstream of the 

project, and the main stem of the Merced River from its sources to Lake McClure at 

RM 84.5 (a total of 81 miles) are managed by BLM, the Park Service, and the Forest 

Service as a designated Wild and Scenic River corridor. The North Fork Merced River 

drains into the Merced River about 0.5 mile upstream of the Merced River Project 

boundary. Flow in the river upstream of Lake McClure is unrestricted, except that the 

Mariposa County Public Utility District withdraws for consumptive purposes up to 5,000 

acre-feet of water from Saxon Creek, located approximately 10 miles upstream of Lake 

McClure.

The Merced River at New Exchequer dam (at RM 62.4) has a drainage area of 

approximately 1,035 square miles. Lake McClure, which is formed by New Exchequer 

dam and inundates about 19 miles of the Merced River, is deep, has a retention time of 

about a year, and thermally stratifies. Lake McClure has a NMWSE of elevation 867 feet 

and a gross storage capacity of 1,024,600 acre-feet. The portion of Lake McClure just 

north of New Exchequer dam near the McClure Point recreation area is the most open 

expanse of water in the reservoir, and has two named arms—the Temperance arm and the 

Cotton arm—named for the creeks that enter the reservoir. The second open expanse of

 

17 Unless otherwise indicated, information for the Merced River and Merced Falls 

Projects is taken from the applications for license for these projects, Merced ID, 2014a 

and PG&E, 2012, respectively. 
56

Figure 3-1. Merced River Basin and subbasins (Source: Merced ID, 2012a).
57

Lake McClure is in the northeast corner of the reservoir near the Horseshoe Bend 

recreation area. The remainder of the reservoir occupying the canyon is narrow, and 

generally less than 1,000 feet across. Besides the Merced River and Temperance and 

Cotton creeks, named tributaries into Lake McClure include Maxwell, Piney, Sherlock, 

and Willow creeks.

Most of the land surrounding Lake McClure consists of oak woodland vegetation 

with grasses, oaks, chapparal, and gray pine. Very few residences occur along the 

shoreline of Lake McClure.

Downstream of New Exchequer dam and powerhouse, water flows directly into 

the 6.3-mile-long reservoir formed by McSwain dam at RM 56.1. McSwain reservoir reregulates peaking power releases from the New Exchequer powerhouse and has a 

retention time of a few days under typical operations, which allows for only weak 

thermal stratification. McSwain reservoir is a long, narrow reservoir occupying the 

western-most steep-walled canyon carved by the Merced River before the river enters the 

plains of California’s Central Valley (see figure 1-2). There are no appreciable 

diversions from the reservoir, and there are no tributaries into McSwain reservoir. The 

portion of the Merced River Basin upstream of McSwain reservoir comprises 

approximately 1,055 square miles, adding about 16.5 square miles to the drainage area 

upstream of New Exchequer dam. Land surrounding McSwain reservoir is primarily 

vegetated with chaparral and grasses.

Immediately downstream of McSwain reservoir lies Merced Falls reservoir, which 

has a storage capacity of about 579 acre-feet of water at a NMWSE of 344 feet, and 

inundates 1.1 miles of the river (see figure 1-4). The reservoir is formed by Merced Falls 

dam at RM 55.0. Merced Falls reservoir and dam, as well as the 3.6-MW Merced Falls 

powerhouse at the base of the dam, are part of PG&E’s Merced Falls Project. One 

significant withdrawal occurs from PG&E’s Merced Falls reservoir—up to 100 cfs of 

water is withdrawn at the northside canal for water supply purposes. Merced ID owns 

and operates the northside canal as part of its water supply system, but the facilities are 

not a part of either the Merced River or Merced Falls Projects (i.e., the canal is a nonjurisdictional facility).

From Merced Falls dam, water flows about 3 miles downstream to CrockerHuffman diversion dam at RM 52.0. The diversion dam forms an impoundment that is 

about 1.5 miles long, relatively shallow, and has a retention time on the order of hours or 

days, depending on flow conditions. Up to 2,000 cfs of water is withdrawn from 

Crocker-Huffman diversion dam impoundment into the Main Canal for water supply 

purposes. Water is also drawn from Crocker-Huffman diversion dam impoundment by 

California DFW’s Merced River fish hatchery and the privately owned Calaveras Trout 

Farm, Inc. The land surrounding this section is vegetated with oaks and grasses with 

scattered residences.

The Merced River flows about 19 miles from Crocker-Huffman diversion dam 

(RM 52.0) to Shaffer Bridge (RM 32.8). This section of river has been extensively 
58

affected by water withdrawals, agricultural water returns, and land use activities, most 

notably dredger mining for gold. The major water withdrawals are associated with the 

Cowell Agreement water users and riparian water users (described in section 2.1.1.5, 

Existing Environmental Measures) who have the right to divert up to approximately 

94,000 acre-feet of water annually from this section of river, and have maintained 

11 channel diversions since the mid-1800s. 

The Merced River between Shaffer Bridge and the San Joaquin River (RM 0) has 

a very simple channel shape. The lower section of the river (RM 0 to RM 8.0) is mostly 

a single, u-shaped channel that is situated between high, sandy banks. The floodplain is 

much narrower than it was before the agriculture and suburban development that now 

exists along the shoreline. From RM 8.0 to RM 19.0, the river is confined between 

levees, revetments, and bank armoring that maintain the river’s position and create a 

trapezoidal-shaped channel. The uppermost section of the river (RM 19.0 to RM 32.8) 

has been mined for aggregate, leaving deep holes next to the channel that can capture, 

slow, and warm water. Bank revetments also limit channel movement across an 

agricultural/developed floodplain.

Dry Creek, which is the only major tributary in this reach and enters the river 

downstream of Shaffer Bridge at RM 31.9, supplies large quantities of sand to the 

Merced River. The sand transported from Dry Creek combined with erosion of the sandy 

soils along the shoreline has produced a sand-bedded main stem channel downstream of 

Dry Creek.

The Merced River ultimately flows into the San Joaquin River near the Stanislaus 

County/Merced County border, just north of California DFW’s North Grasslands 

Wildlife Area. At the confluence with the San Joaquin River, the drainage area of the 

Merced River is approximately 1,328 square miles.

The Merced River Basin climate is highly varied due to the vast differences in 

topography from the headwaters of the Merced River in the central Sierra Nevada to the 

western portion of watershed in the valley floor. Project facilities lie in the foothills 

between the lowlands of California’s Central Valley and the high country of the Sierra 

Nevada. Climate in the foothills is characteristic of a mixed-elevation Mediterranean 

climate with warm, dry summer days and cool nights, and cool, wet winters with 

occasional snowfall in small amounts.

Annual mean precipitation at the National Weather Service station at New 

Exchequer dam (no. 042920) is 19.75 inches, 80 percent of which falls from November 

through March. The summer months of June through August produce less than 2 percent 

of the total annual average precipitation. The remaining 18 percent of precipitation 

occurs during April, May, September, and October. The closest National Weather 

Service air temperature monitoring station at a similar climate and elevation as the 

projects is at the Electra powerhouse on the Mokelumne River, north of the projects at 

elevation 700 feet (no. 042728). July air temperatures at this monitoring station range 

from an average high of 97.2 degrees Fahrenheit (°F) (36.2 degrees Celsius [°C]) to an 
59

average low of 56.3°F (13.5°C). The average high temperature for January is 56.9°F 

(13.8°C) while the average low temperature is 34.0°F (1.1°C). The annual average high 

and low temperatures are 76.2°F (24.5°C) and 44.6°F (7°C), respectively.

Lands within the Merced River Basin have a patchwork of ownership. Of the 

700,000 acres of the Merced River Watershed upstream of New Exchequer dam, more 

than 300,000 acres lie within Yosemite National Park. The Park Service manages the 

land within Yosemite National Park. Of the remaining Merced River Basin upstream of 

the project, more than 270,000 acres are managed by the Forest Service as a part of the 

Stanislaus and Sierra national forests, or are administered by BLM as federal lands.

The project vicinity is located at the southern end of California’s famed Mother 

Lode region, which shaped the region’s economy in the mid- to late-1800s. Since the end 

of the California gold rush, the economic base has grown to include agriculture and 

tourism with mining playing a greatly reduced role in the area’s economic viability. The 

presence of Yosemite National Park in the eastern half of Mariposa County is an 

important contributor to the area’s economy, which is based primarily on government

employment, retail sales, services, tourism, and agriculture.

3.2 SCOPE OF CUMULATIVE EFFECTS ANALYSIS

According to the Council on Environmental Quality’s regulations for 

implementing NEPA (40 CFR §1508.7), a cumulative effect is the impact on the 

environment that results from the incremental impact of the action when added to other 

past, present, and reasonably foreseeable future actions regardless of what agency 

(federal or non-federal) or person undertakes such actions. Cumulative effects can result 

from individually minor but collectively significant actions taking place over time, 

including hydropower and other land and water development activities.

Based on our review of the Merced River license application and agency and 

public comments, we identified water quantity, water quality (primarily DO, temperature, 

and total suspended solids), aquatic habitat, and Central Valley steelhead (Oncorhynchus 

mykiss), which is federally listed as threatened, as having the potential to be cumulatively 

affected by the proposed project in combination with other past, present, and foreseeable 

future activities.

Based on our review of the Merced Falls license application and agency and 

public comments, we identified water quality, aquatic habitat, and Central Valley 

steelhead (O. mykiss),18 as having the potential to be cumulatively affected by the 

proposed project in combination with other past, present, and foreseeable future 

activities.

 

18 In this draft EIS, O. mykiss refers to both the anadromous (steelhead) and 

resident (rainbow trout) form of this species.
60

We selected water quantity because water used for hydroelectric generation at the 

Merced River Project is also used for irrigation and supplies the Merced NWR through 

Merced ID’s water distribution system. Water flowing through the Merced River and 

Merced Falls Projects is also diverted by numerous other entities besides Merced ID for 

various purposes in accordance with the Cowell Agreement and other water rights. In 

addition, use of Lake McClure for flood control in accordance with the Corps’ document 

New Exchequer Dam and Reservoir, Merced River, California; Water Control Manual; 

Appendix VII to Master Water Control Manual, San Joaquin River Basin, California

(required by article 39 of the current license) shifts the timing of flow releases to river 

reaches downstream of New Exchequer dam. The amount of un-diverted water 

influences the quality of aquatic habitat and the upstream extent of saline water from the 

San Francisco Bay/Sacramento-San Joaquin Delta Estuary (Bay-Delta).

Operation of the Merced River Project, especially releases from Lake McClure, 

can affect water temperature and DO. The impoundment of water diversions, diversions 

from the river, and return of irrigation water to the river can exacerbate these effects in 

downstream reaches of the Merced River. Water quality in downstream river reaches can 

also be affected by increases in total suspended solids associated with erosion (from 

project-related and other sources), mining activities, and habitat restoration efforts.

We selected aquatic habitat as a cumulatively affected resource because various 

dams block access of migratory fish to aquatic habitat and prevent downstream transport 

of sediment and LWD, which are key components of aquatic habitat. Agricultural and 

instream mining activities have greatly altered the physical river channel, further limiting 

the diversity of available habitat for aquatic biota.

We selected Central Valley steelhead as a cumulatively affected resource because 

many historical and current factors influence the abundance of this threatened species in 

the Merced and San Joaquin Rivers. Historical factors that have influenced Central 

Valley steelhead populations include the construction of Crocker-Huffman, Merced Falls, 

McSwain, and New Exchequer dams without provisions for upstream and downstream 

fish passage, removal of spawning gravel associated with aggregate and gold mining, and 

agricultural encroachment on the river channel. Ongoing factors that potentially affect

Central Valley steelhead include numerous diversions from the Merced River at and 

downstream of Crocker-Huffman diversion dam, altered flow regimes due to upstream 

hydropower and flood control operations, predation by non-native fish such as striped 

bass, ocean growth and mortality from fishing and other factors, competition for available 

habitat by native and hatchery-reared fall Chinook salmon, and gravel augmentation and 

other lower Merced River stream enhancement initiatives.

3.2.1 Geographic Scope

The geographic scope of analysis for cumulatively affected resources defines the 

physical limits or boundaries of the effects of the proposed action on the resources. 
61

Because the proposed action can affect resources differently, the geographic scope for 

each resource may vary. 

For water quantity, we define the geographic scope of analysis as the main stem of 

the Merced River from the upstream end of Lake McClure to the confluence of the San 

Joaquin River and the San Joaquin River from the confluence of the Merced River to the 

confluence of the Sacramento River at Chipps Island, near Pittsburg, California. For 

water quality and aquatic habitat, we define the geographic scope of analysis as the main 

stem of the Merced River from the upstream end of Lake McClure to Shaffer Bridge, 

about 19 miles downstream of Crocker-Huffman diversion dam. For Central Valley 

steelhead, we define the geographic scope of analysis as the estimated 107 miles of 

habitat that was originally available to migratory anadromous fish in the Merced River, 

including 51 miles upstream of Crocker-Huffman diversion dam and 56 miles 

downstream of Crocker-Huffman diversion dam (California HSRG, 2012). We also 

include the San Joaquin River from the confluence of the Merced River to the confluence 

of the Sacramento River at Chipps Island.

3.2.2 Temporal Scope

The temporal scope of analysis includes a discussion of the past, present, and 

future actions and their effects on water quantity, water quality, aquatic habitat, and 

Central Valley steelhead. Based on the potential term of a license, the temporal scope 

looked 30 to 50 years into the future, concentrating on the effects on water, aquatic 

habitat, and Central Valley steelhead from reasonably foreseeable future actions. The 

historical discussion is limited, by necessity, to the amount of available information for 

each resource. We identified the present resource conditions based on the license 

application, agency comments on the draft license application, and comprehensive plans. 

3.3 PROPOSED ACTION AND ACTION ALTERNATIVES

In this section, we discuss the effect of the project alternatives on environmental 

resources. For each resource, we first describe the affected environment, which is the 

existing condition and baseline against which we measure effects. We then discuss and 

analyze the specific site-specific and cumulative environmental issues. 

Only the resources that would be affected, or about which comments have been 

received, are addressed in detail in this EIS. We have not identified any substantive 

issues related to socioeconomics associated with the proposed action, and, therefore, 

socioeconomics is not assessed in this EIS. Project-related construction, operation, and 

maintenance have the potential to influence erosion and sediment transport. The primary 

expected effect of erosion and sediment transport would be on water quality (e.g., 

suspended sediments and turbidity) and aquatic habitat. We therefore discuss these 

potential effects in section 3.3.1, Aquatic Resources, rather than in a separate geology and 

soils section. We present our recommendations in section 5.1, Comprehensive 

Development and Recommended Alternative. 
62

3.3.1 Aquatic Resources

3.3.1.1 Affected Environment

Water Quantity

Merced River Project

Water Storage and Hydrology—The Merced River Project includes two reservoirs 

for water storage—Lake McClure and McSwain reservoir (see figure 1-2). The two 

reservoirs are contiguous, having no free-flowing river between the two developments. 

Water from Lake McClure is released from New Exchequer powerhouse directly into 

McSwain reservoir. From McSwain reservoir, water impounded by the Merced River 

Project is released from McSwain powerhouse directly into PG&E’s Merced Falls 

reservoir. Downstream of Merced Falls reservoir, water flows about 3 miles to CrockerHuffman diversion dam. Water quantity as it pertains to the Merced Falls Project and the 

lower Merced River (downstream of Merced Falls dam) is described below in the Merced 

Falls and Lower Merced River sections, respectively. 

Lake McClure has a gross storage capacity of 1,024,600 acre-feet and a usable 

storage capacity of 1,021,600 acre-feet. McSwain reservoir has 9,730 acre-feet of gross 

storage and a usable storage capacity (for power generation) of 7,897 acre-feet. Under 

the existing license, Lake McClure has a minimum pool requirement of 115,000 acre-feet

(which equates to an elevation of about 640 feet) unless further drawdowns are needed to 

meet minimum flow requirements, but McSwain reservoir has no minimum pool 

requirement. See table 2-1 for additional details regarding the two project reservoirs. 

The project attenuates high flows in the Merced River from winter storms and 

spring runoff and stores the water in Lake McClure. Figures 3-2 through 3-7 show this 

high spring flow attenuation compared to simulated unregulated19 flows. Merced ID has 

historically operated Lake McClure to retain snowmelt from springtime runoff for flood 

control, water supply, recreation, hydropower, and environmental purposes. In spring 

and summer, water levels in Lake McClure are maintained relatively high for recreation 

purposes, with releases from March through October made for downstream water supply 

and hydropower generation at New Exchequer and McSwain powerhouses. This release 

pattern results in higher flows during the drier months of July through October compared 

to unregulated flows (see figures 3-2 through 3-7). In spring, depending on the snowpack 

and runoff forecasts, Merced ID begins to refill Lake McClure with the snowmelt runoff. 

The water surface elevation of Lake McClure fluctuates by about 58 feet in a typical wet 

water year and about 79 feet in a typical dry water year. 

 

19 We use the term unregulated to mean flows that are not controlled by dams and 

diversions from the river. Stakeholders refer to this as “unimpaired” flows.
63

Hydrology statistics for the Merced River in and downstream of the project, based 

on historical daily mean flow data, are shown in table 3-1. Merced ID defines wet, 

normal, and dry water years as roughly the 10, 50, and 90 percent exceedance values for 

the unregulated annual runoff in the Merced River at New Exchequer dam. Merced ID 

established a five level water year classification for the Merced River using the same 

methods as used for the San Joaquin Valley Water Year Hydrologic Classification, but 

for the Merced River, it is based on the unregulated inflow to Lake McClure. The five 

water year classifications are: wet, above normal, below normal, dry, and critical and are 

calculated as 60 percent of the current year’s April through July inflow plus 20 percent of 

the current year’s October through March inflow plus 20 percent of the previous year’s 

index. The numerical breakpoints (in millions of acre-feet) for the five water year 

classifications are: 

 Wet: ≥0.65

 Above Normal: >0.53 and <0.65

 Below Normal: >0.42 and ≤0.53

 Dry: >0.36 and ≤0.42

 Critical: ≤0.36
64

Figure 3-2. Mean daily releases from New Exchequer powerhouse and dam, Merced 

ID’s synthesized mean daily unregulated flow at New Exchequer dam, and 

Lake McClure daily reservoir elevations in water year 2006, a 

representative wet water year (Source: Merced ID, 2012a, as modified by 

staff).
65

Figure 3-3. Mean daily releases from McSwain powerhouse and dam, Merced ID’s 

synthesized mean daily unregulated flow at McSwain dam, and McSwain 

reservoir daily reservoir elevations in water year 2006, a representative wet 

water year (Source: Merced ID, 2012a, as modified by staff).
66

Figure 3-4. Mean daily releases from New Exchequer powerhouse and dam, Merced 

ID’s synthesized mean daily unregulated flow at New Exchequer dam, and 

Lake McClure daily reservoir elevations in water year 2000, a 

representative normal water year (Source: Merced ID, 2012a, as modified 

by staff).
67

Figure 3-5. Mean daily releases from McSwain powerhouse and dam, Merced ID’s 

synthesized mean daily unregulated flow at McSwain dam, and McSwain 

reservoir daily reservoir elevations in water year 2000, a representative 

normal water year (Source: Merced ID, 2012a, as modified by staff).
68

Figure 3-6. Mean daily releases from New Exchequer powerhouse and dam, Merced 

ID’s synthesized mean daily unregulated flow at New Exchequer dam, and 

Lake McClure daily reservoir elevations in water year 1990, a 

representative dry water year (Source: Merced ID, 2012a, as modified by 

staff).
69

Figure 3-7. Mean daily releases from McSwain powerhouse and dam, Merced ID’s 

synthesized mean daily unregulated flow at McSwain dam, and McSwain 

reservoir daily reservoir elevations in water year 1990, a representative dry

water year (Source: Merced ID, 2012a, as modified by staff).
70

Table 3-1. Hydrology for selected sites associated with the Merced River Project (Sources: Merced ID, 2010a; 

USGS, 2014, both as modified by staff).

Exceedances 

and 

Summary 

Statistics

Flow (cfs) for Water Years 1974–2006

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Annual

Inflow to Lake McClurea

20% 220 364 498 1,499 2,056 2,534 3,333 5,866 4,841 1,588 463 220 2,431

50% 95 146 199 414 741 1,634 2,564 2,715 578 200 130 87 535

80% 24 71 84 136 475 1,120 1,884 753 191 59 36 19 113

Average 160 339 630 1,408 1,674 1,998 2,591 4,095 3,062 1,143 297 175 1,462

Maximum 3,765 5,645 20,421 43,964 27,551 22,244 22,525 14,335 13,913 10,326 3,006 3,070 43,964

Minimum 16 23 38 50 106 176 412 450 87 37 18 16 16

Lake McClure Powerhouseb

20% 1,404 530 564 601 1,118 2,050 2,890 3,111 2,896 2,330 2,296 1,401 2,195

50% 707 267 273 244 235 1,040 1,698 1,987 2,002 1,821 1,364 669 1,185

80% 72 83 122 80 149 504 1,338 1,617 1,701 1,383 875 53 240

Average 911 359 538 813 998 1,299 1,969 2,426 2,375 2,157 1,764 1,334 1,414

Maximum 4,135 2,995 4,546 8,087 7,996 5,406 7,113 7,121 7,882 7,872 2,859 4,133 8,087

Minimumc 0 0 0 0 6 5 14 24 146 707 6 0 0
71

Exceedances 

and 

Summary 

Statistics

Flow (cfs) for Water Years 1974–2006

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Annual

Lake McSwain Powerhouseb

20% 1,324 500 500 500 1,100 1,999 2,799 3,122 2,899 2,251 2,313 1,324 2,224

50% 713 245 250 235 235 1,036 1,700 2,007 2,075 1,825 1,338 650 1,200

80% 150 200 200 180 200 500 1,349 1,655 1,738 1,370 890 150 235

Average 928 372 546 825 1,012 1,314 1,981 2,443 2,400 2,182 1,782 1,349 1,430

Maximum 4,139 3,049 4,499 8,090 7,998 5,498 7,187 7,198 7,998 7,998 2,949 4,139 8,090

Minimum 0 17 25 38 14 120 144 243 485 950 146 80 0

Merced River below Merced Falls Dam (USGS 11270900)

20% 1,436 508 515 502 1,100 2,060 2,784 3,090 2,822 2,200 2,220 1,432 2,180

50% 721 251 253 243 239 1,010 1,650 1,970 2,010 1,760 1,280 663 1,170

80% 140 197 195 174 198 522 1,300 1,600 1,720 1,320 860 148 239

Average 939 374 539 828 1,018 1,318 1,944 2,387 2,333 2,131 1,722 1,305 1,405

Maximum 4,100 2,950 4,490 8,020 7,920 5,340 7,040 7,100 7,820 7,830 2,800 4,020 8,020

Minimum 72 115 163 101 106 106 149 244 438 883 123 71 71
72

Exceedances 

and 

Summary 

Statistics

Flow (cfs) for Water Years 1974–2006

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Annual

Crocker-Huffman Diversion Damd

20% 811 427 448 491 873 1,864 2,031 1,602 992 396 769 808 852

50% 211 238 246 241 238 253 319 297 244 225 213 198 250

80% 115 182 185 139 164 196 228 221 188 172 129 117 173

Average 491 335 489 783 961 1,030 1,145 1,060 784 482 307 370 685

Maximum 3,185 2,337 4,588 8,345 7,965 5,136 5,340 5,304 4,752 5,898 1,155 3,212 8,345

Minimum 28 86 139 78 75 75 24 83 86 73 83 32 24

Merced River near Stevinson CA (USGS 11272500)e

20% 761 508 530 1,018 834 1,720 2,284 1,558 1,130 423 710 810 865

50% 290 252 249 304 283 277 310 290 214 214 303 300 268

80% 84 196 201 213 207 189 164 133 71 74 81 89 147

Average 517 393 523 783 730 1,103 1,238 1,106 825 455 272 394 694

Maximum 3,200 2,740 4,260 6,850 5,900 6,750 5,750 5,360 5,490 5,600 1,340 2,080 6,850

Minimum 4 15 144 57 20 67 20 26 10 1 2 7 1

a Data from Merced ID (2010a), Operations Model CD file titled 2010-12-27 Merced Ops Model_V3.xlsm.

b Data compiled from Merced ID (2012a), Operations Model CD file 2010-03-26 Calculation of Acc-Dep Terms.xls as the sum of discharge through 

powerhouse plus spill or bypass flow. The New Exchequer powerhouse has a capacity of 3,200 cfs and McSwain powerhouse has a capacity of 2,700 cfs; 

flows in excess of these values are largely due to spillage.

c Merced ID’s simulated minimum inflows to Lake McClure showed no flows during many months. To provide a more representative indication of minimum 

inflows we used actual USGS data from an historic USGS gage at Bagby. Minimum daily flow values are from USGS gage no. 11268500 Merced River at 

Bagby CA (located upstream of Lake McClure) for water years 1922–1966.

d Data from Merced ID (2010a), Operations Model CD file titled 2010-03-26 Calculation of Acc-Dep Terms.xls.

e No data available for water years 1996–2001.
73

McSwain reservoir is typically operated as a re-regulating afterbay for flows 

released from Lake McClure. This operation allows Merced ID to use the New 

Exchequer powerhouse to meet peak power demands or to perform load-following 

functions while still maintaining a steady flow release to downstream reservoirs and 

subsequently to the lower Merced River. The water surface elevation of McSwain 

reservoir typically fluctuates up to 7.5 feet during normal operations.

Pursuant to article 39 of its existing license, Merced ID operates the Merced River 

Project in compliance with the Corps’ document entitled: New Exchequer Dam and 

Reservoir, Merced River, California; Water Control Manual; Appendix VII to Master 

Water Control Manual, San Joaquin River Basin, California, dated October 1981. This 

manual sets year-round flood control limits for Lake McClure rain flood space and March 

through July flood control limits for snowmelt flood space, or conditional space (table 

3-2). During drier water years and periods, water levels in Lake McClure may be 

consistently below the required flood-space level, resulting in water supply and recreation 

considerations driving reservoir storage more than flood control requirements.

Table 3-2. Maximum end-of-month storage in Lake McClure for flood control 

(Source: Merced ID, 2012a).

Month

Rain-Flood Storage Limit

(acre-feet)

Snowmelt Flood 

(Conditional) Storage 

Limit

(acre-feet)

January

674,600

None

February

March 1–March 15 Linear reduction from 

March 16 674,600 to 624,600 –March 31

Linear increase from 674,600 to 

1,024,600

April

624,600

May 1–May 15

May 16–May 31 Linear increase from 

624,600 to 1,024,600 June 1–June 15

June 16–June 30

1,024,600

None

July

August

September Linear reduction from 1,026,600 to 

October 674,600

November/December 674,600
74

Water Withdrawals and Water Rights—Merced ID diverts water from the Merced 

River at two locations: the northside canal (at Merced Falls reservoir) and the Main 

Canal (at Crocker-Huffman diversion dam) (see figure 1-2). Merced ID owns and 

operates Crocker-Huffman diversion dam and the associated Main Canal as part of its 

water supply system, but the facilities are not part of its Merced River Project or PG&E’s 

Merced Falls Project. Annually, about 520,000 acre-feet of water, which is about half the 

usable storage in Lake McClure, is released from the project and diverted by Merced ID

at the northside and Main Canals. The diversion canals lead to a network of downstream 

canals that deliver water primarily for irrigation and also for groundwater recharge, 

municipal and industrial uses, water transfers, and environmental purposes. Irrigation 

diversions from the northside and Main Canal normally occur from March through 

October. 

Pursuant to article 45 of the existing license, operation of the Merced River Project 

currently includes a required annual diversion of up to 15,000 acre-feet of water to 

Merced NWR. The refuge is located about 30 miles southeast of McSwain dam. To 

provide this water, in the early 1990s, Merced ID made eight modifications to its water 

supply delivery system, each of which was incorporated into the project license (but not 

included in the project boundary). These modifications are listed in section 2.1.1.1, 

Existing Project Facilities. Merced ID also has a commitment to annually provide to the 

Stevenson Water District with up to 26,400 acre-feet of irrigation water, which is used to 

service both Stevenson and Merquin Water Districts. 

Merced ID has a riparian water rights claim for the natural flow of the Merced 

River at both the New Exchequer and McSwain powerhouses. These riparian claims are 

documented with the Water Board through Statements of Water Diversion and Use 

numbers 15475 and 15476. Merced ID also holds pre-1914 and adjudicated rights 

originally held by the Exchequer Gold Mine Company and the Crocker-Huffman Land 

Company, as well as post-1914 appropriative water rights obtained directly by Merced ID

for the purpose of operating the project. In addition, Merced ID has water right licenses 

2685, 6047, and 16186 (Applications 1224, 10572, and 11395, respectively) for 

irrigation, domestic use, recreational, and other purposes.

Merced Falls Project

Water Storage and Hydrology—The Merced Falls Project includes a single 

reservoir—Merced Falls reservoir (see figure 1-4), located immediately downstream of 

Merced ID’s McSwain dam. PG&E has no storage rights; therefore, the Merced Falls 

Project must operate in a run-of--river mode so that all inflow to the impoundment minus 

the water being diverted by existing irrigation withdrawals passes through the project 

either via the turbine or through the radial gates. As such, outflow from the project is 

dictated by releases from Merced ID’s upstream Merced River Project and irrigation 

withdrawals (discussed above), typically result in limited flow available for generation 

from October through mid-March.
75

The project uses outflow of between approximately 500 and 1,750 cfs provided by 

the upstream Merced River Project to generate hydroelectric power. When outflow from 

the Merced River Project is below 500 cfs, flows are spilled via the radial gates. When 

water inflows exceed the powerhouse capacity, up to 12,100 cfs, excess flow is released 

through the radial gates. Currently, flows in excess of 12,100 cfs do not occur at Merced 

Falls, because Merced ID regulates the upstream reservoirs.

The current license for the project does not directly stipulate minimum flow 

requirements. Article 38 of the current license requires PG&E to coordinate operations 

with Merced ID’s upstream Merced River Project. As a run-of-river project, the Merced 

Falls Project does not control inflow from Merced ID’s upstream operations. Currently, 

flows in excess of 12,100 cfs do not occur at Merced Falls, because Merced ID regulates 

the upstream reservoirs (figure 3-8).

Figure 3-8. Annual flow duration curve for the Merced Falls Project for the period of 

record (January 1, 1916 to September 30, 2009) (Source: PG&E, 2012, as 

modified by staff)

Lower Merced River

This section describes conditions related to water quantity in the lower Merced 

River downstream of the Merced Falls Project and Crocker-Huffman diversion dam. 

Water Storage and Hydrology—Crocker-Huffman diversion dam is located at RM 

52.0, about 3 miles downstream of Merced Falls dam. Crocker-Huffman diversion dam 

forms an impoundment that is about 1.5 miles long, relatively shallow, and has a storage 

volume of about 300 acre-feet (Vogel, 2007), which would result in a typical water 

retention time of less than a day. 

Merced ID’s existing license specifies minimum streamflow requirements in the 

Merced River downstream of Crocker-Huffman diversion dam, as measured at Shaffer 
76

Bridge. Table 3-3 shows the minimum flow requirements for Merced ID under the 

existing license. The existing license also requires Merced ID to maintain a flow within 

the range of 100 and 200 cfs, measured at Shaffer Bridge, from November 1 through 

December 31, except during dry years when a flow between 75 and 150 cfs is required. 

In addition, the existing license requires Merced ID to minimize flow fluctuations 

downstream of Crocker-Huffman diversion dam by restricting the rate of change of 

release during any 1-hour period to no more than double or no less than one-half the 

amount of release at the start of the change. During emergency periods, Merced ID must 

endeavor to make releases from Crocker-Huffman diversion dam in a manner that would 

not be detrimental to fish.

Table 3-3. Current minimum flow requirements in the Merced River downstream of 

Crocker-Huffman diversion dam, as measured at Shaffer Bridge (Source: 

Merced ID, 2012a).

Period 

Normal Years 

(cfs)

Dry Years 

(cfs)

June 1 through October 15 25 15

October 16 through October 31 75 60

November 1 through December 31 100 75

January 1 through May 31 75 60

Several other agreements outside of the existing project license also influence 

flows in the Merced River downstream of Crocker-Huffman diversion dam. These 

agreements are as follows:

 A 2002 Memorandum of Understanding with California Department of 

Fish and Game (now California DFW), as amended in 2003, requires 

Merced ID to supplement flows in the Merced River in October by 

providing 12,500 acre-feet20 of water, as measured at Shaffer Bridge, in 

addition to the project’s minimum flow requirement in that month.

 Under the Davis-Grunsky Agreement with the State of California, Merced 

ID is committed to providing a continuous flow of 180 to 220 cfs in the 

Merced River between Crocker-Huffman diversion dam and Shaffer 

 

20 This volume would correspond to a rate of about 204 cfs for every day in 

October.
77

Bridge from November through March every year. The agreement expires 

on December 31, 2017.

 The 1926 Cowell Agreement requires Merced ID to provide releases from 

Crocker-Huffman diversion dam up to the following flows for use by the 

Cowell Agreement diverters at 11 locations: 100 cfs in March; 175 cfs in 

April; 225 cfs in May; 250 cfs from the first day in June until the natural 

flow of the Merced River falls below 1,200 cfs; 225 cfs flow for the next 

31 days; 175 cfs flow for the next 31 days; 150 cfs for the next 30 days; 

and 50 cfs thereafter or the natural inflow into Lake McClure, whichever is 

less, through the last day of February.

Water Withdrawals—Up to 2,000 cfs of water is withdrawn from CrockerHuffman diversion dam impoundment into the Main Canal for water supply purposes. 

The diversion substantially reduces the flow in the Merced River from an annual mean of 

1,389 cfs in the Merced River downstream of Merced Falls dam to an annual mean of 

655 cfs in the Merced River downstream of Crocker-Huffman diversion dam. Water is 

also drawn from the Crocker-Huffman diversion dam impoundment by California DFW’s 

Merced River fish hatchery and the privately owned Calaveras Trout Farm, Inc. The 

hatchery uses, on average, about 3 cfs from February through March and 7 cfs from April 

through January, while the trout farm uses about 48 cfs year-round. The majority of the 

fish hatchery and trout farm withdrawals are returned to the Merced River. 

Downstream of Crocker-Huffman diversion dam, the Merced River flows about 

19 miles to Shaffer Bridge (RM 32.8). This section of the river contains seven main 

channel diversions, with users holding diversion rights of up to about 94,000 acre-feet of 

water annually. The diversions, most of which are unscreened, are made via small, 

annually-constructed wing dams in the main river channel. Numerous agricultural water 

returns are present in this section of river, although information regarding the rate or 

volume of the returns is not available. 

In the 32.8 river miles from Shaffer Bridge downstream to its confluence with the 

San Joaquin River, additional water withdrawals and agricultural returns affect the 

Merced River. An inventory of water diversions identified more than 100 non-project 

diversions in this section of the river, many of which are unscreened pumps used mainly 

to supply water for agricultural use. Agricultural returns in this section of the river 

include non-project canal spills that discharge excess irrigation water and storm flows 

from adjacent watersheds (e.g., the Tuolumne River) into the Merced River. Like the 

water diversions, these canal returns are ungaged and the amount of water diverted and 

returned to the Merced River has not been quantified. One major tributary, Dry Creek, 

enters the river about 1 mile downstream of Shaffer Bridge, but inflow from this creek is 

minimal except during substantial rainfall events in the Central Valley area that occur 

mainly during the winter (California DEC, 2013). 
78

Water Quality

In the Water Quality Control Plan for the Sacramento and San Joaquin Basins

(Basin Plan), the Central Valley Regional Water Board (Central Valley Water Board) 

designates existing and potential beneficial uses and water quality objectives for the 

Merced River Project, the Merced Falls Project, and the river upstream and downstream 

of the projects (Central Valley Water Board, 2011). Existing designated, beneficial uses 

of surface waters in Lake McClure and McSwain reservoir are: irrigation, hydropower 

generation, contact and non-contact recreation, warm and cold freshwater habitat, and 

wildlife habitat. Municipal and domestic water supply is designated as a potential 

beneficial use. Existing designated, beneficial uses from McSwain reservoir downstream 

to the San Joaquin River are: municipal and domestic water supply, stock watering, 

industrial process and service supply, hydropower generation, contact and non-contact 

recreation, warm and cold freshwater habitat, migration of warmwater and coldwater 

aquatic organisms, spawning of warmwater and coldwater fishes, and wildlife habitat. 

Table 3-4 shows the Basin Plan water quality objectives to support these designated 

beneficial uses.

Table 3-4. Water quality objectives to support designated beneficial uses in the project 

area (Source: Central Valley Water Board, 2011).

Water Quality 

Objective Description

Temperature The natural receiving water temperature of interstate waters 

shall not be altered unless it can be demonstrated to the 

satisfaction of the Regional Water Quality Control Board 

that such alteration in water temperature does not adversely 

affect beneficial uses. In waters designated as cold 

freshwater habitat, increases in water temperatures must be 

less than 5.0°F above natural receiving-water temperature.

Bacteria In waters designated for contact recreation, fecal coliform 

concentration must be: (1) less than a geometric mean of 

200 per 100 milliliters water based on a minimum of five 

samples collected in any 30-day period, and (2) less than 

400 per 100 milliliters of water in at least 90 percent of all 

samples taken in a 30-day period. 

Biostimulatory 

substances

Water shall not contain biostimulatory substances that 

promote aquatic growth in concentrations that cause 

nuisance or adversely affect beneficial uses. 
79

Water Quality 

Objective Description

Chemical 

constituents

Waters shall not contain chemical constituents in 

concentrations that adversely affect beneficial uses. At 

minimum, waters designated for use as domestic or 

municipal supply shall not contain concentrations of

chemical constituents in excess of the maximum 

contaminant levels specified in Title 22 of the California 

Code of Regulations, which are incorporated by reference 

into the Basin Plan. 

Color Water shall be free of discoloration that causes a nuisance 

or adversely affects beneficial uses. 

DO The DO concentrations shall not be reduced below the 

following minimum levels at any time.

 Waters designated as warm freshwater habitat: 

5.0 mg/L

 Waters designated as cold freshwater habitat: 

7.0 mg/L

 Waters designated as spawning habitat: 7.0 mg/L

In the Merced River from Cressey (~RM 29.0) to New 

Exchequer dam, DO concentrations shall not be reduced 

below 8.0 mg/L year-round, and downstream of Cressey to 

the confluence with the San Joaquin River DO 

concentrations shall not be reduced below 7.0 mg/L yearround. The monthly median of the average daily DO 

concentration shall not fall below 85 percent of saturation 

in the main water mass, and the 95 percentile concentration 

shall not fall below 75 percent of saturation. 

Floating material Water shall not contain floating material in amounts that 

cause nuisance or adversely affect beneficial uses. 

Oil and grease Waters shall not contain oils, greases, waxes, or other 

materials in concentrations that cause nuisance, result in a 

visible film or coating on the surface of the water or on 

objects in the water, or otherwise adversely affect 

beneficial uses. 
80

Water Quality 

Objective Description

Pesticides Waters shall not contain individual pesticides or a 

combination of pesticides in concentrations that adversely 

affect beneficial uses. Waters designated for use as 

domestic or municipal supply shall not contain 

concentrations of pesticides in excess of the limiting 

concentrations set forth in Title 22 of the California Code 

of Regulations.

pH The pH of surface shall neither be depressed below 6.5 nor 

raised above 8.5.

Sediment and 

settleable material

The suspended sediment load and suspended sediment 

discharge rate of surface waters shall not be altered in such 

a manner as to cause a nuisance or adversely affect 

beneficial uses. Waters shall not contain substances in 

concentrations that result in deposition of material that 

causes nuisance or adversely affect beneficial uses.

Suspended 

material

Waters shall not contain suspended material in 

concentrations that cause a nuisance or adversely affect 

beneficial uses. 

Taste and odor Water shall not contain taste- or odor-producing substances 

in concentrations that impart undesirable tastes and odors to 

domestic or municipal water supplies, fish flesh or other

edible products of aquatic origin, or that cause nuisance or 

otherwise adversely affect beneficial uses.a

Toxicity All waters shall be maintained free of toxic substances in 

concentrations that produce detrimental physiological 

responses in human, plant, animal, or aquatic life. 

Compliance with this objective will be determined by 

analysis indicator organisms, species diversity, population 

density, growth anomalies, and biotoxicity tests as specified 

by the Regional Water Quality Control Board. 
81

Water Quality 

Objective Description

Turbidity Waters shall be free of changes in turbidity that cause 

nuisance or adversely affect beneficial uses. Increases in 

turbidity attributable to controllable water quality factors 

shall not exceed the following limits:

 Where natural turbidity is between 0 and 5 NTUs, 

increases shall not exceed 1 NTU.

 Where natural turbidity is between 5 and 50 NTUs, 

increases shall not exceed 20 percent.

 Where natural turbidity is between 50 and 100 

NTUs, increases shall not exceed 10 NTU.

 Where natural turbidity is greater than 100 NTU, 

increases shall not exceed 10 percent. 

Notes: DO – dissolved oxygen, °F – degrees Fahrenheit, °C – degrees Celsius, mg/L –

milligrams per liter, NTU – nephelometric turbidity unit

a Taste and odor limits for drinking water are provided as secondary maximum 

contaminant levels in Title 22 of the California Code of Regulations.

The Merced River, including project reservoirs and the river downstream of the 

project, is listed under section 303(d) of the CWA as water quality limited for the 

following pollutants and stressors (Water Board, 2010):

 Water temperature

 Escherichia coli (E. coli)

 Mercury

 Chlorpyrifos

 Diazinon

 Group A pesticides21

 Unknown toxicity

 

21 Group A pesticides consist of aldrin, dieldrin, chlordane, endrin, heptachlor, 

heptachlor epoxide, hexachlorocyclohexanes (including lindane), endosulfan, and 

toxaphene (Water Board, 2006a).
82

The listed sources for these pollutants are: agriculture (chlorpyrifos, diazinon, and 

Group A pesticides), resource extraction (mercury), and unknown source (water 

temperature, E. coli, and unknown toxicity).

Merced River Project

Based on California DFW water temperature and DO profile data collected from 

2004 through 2011, Lake McClure water typically stratifies throughout the year, although 

the thermocline is often weakly defined in the winter (figures 3-9 to 3-11). The 

thermocline is typically situated between 25 and 75 feet below the water surface. From 

May through September (and occasionally October), surface water temperatures (up to 50 

feet below the water surface) often exceed 20.0°C (68.0 °F), decreasing through the 

thermocline to 9.0 to 12.0oC (48.2 to 53.6°F) in bottom waters. The reservoir can fully 

mix in some years during December through February (e.g., in 2007), although often a 

weak thermocline appears during winter months in deeper waters (75 to 100 feet below 

the water surface), located just above the low-level intake (elevation 495 feet). Winter 

water temperatures in Lake McClure typically range from 10.0 to 15.0oC (50.0 to 59.0°F) 

with only slight (1 to 2oC) differences between surface and bottom water temperatures. 

Merced ID estimated the volume of usable cold water (i.e., water temperature less 

than or equal to the 15.0°C (59.0°F) isotherm and located above the intake elevation) in 

Lake McClure during a recent normal (2010), wet (2006), and dry (2008) water year 

(table 3-5). The estimated amount of usable cold water below the 15.0°C (59.0°F) 

isotherm varies by time of year, reservoir operations, and water year type, as shown in 

figures 3-9 through 3-11. 

Table 3-5. Estimated usable cold-water storage volume (acre-feet) in Lake McClure 

below the 15.0°C (59.0°F) isotherm (Source: Merced ID, 2012a).

2010 (Normal WY) 2006 (Wet WY) 2008 (Dry WY)

March August December August December August

502,641 477,581 642,196 411,263 230,942 25,810

Note: WY – water year

Unlike Lake McClure, McSwain reservoir typically stratifies during the spring 

(i.e., April through May) and mixes in the fall (i.e., October through November) (figures 

3-12 through 3-14). The McSwain reservoir thermocline can make up a substantial 

fraction of the water column, extending 10 to 30 feet down from the surface. During 

summer months, water temperatures within surface waters (0 to 15 feet) of McSwain 

reservoir are variable (12.0 to 20.0°C or 53.6 to 68.0°F) with bottom water temperatures 

ranging from 9.0 to 14.0oC (48.2 to 57.2°) throughout the year. 
83

Figure 3-9. Water temperature in Lake McClure near the dam (August 2004 through

December 2006) (Merced ID, 2011a).
84

Figure 3-10. Water temperature in Lake McClure near the dam (January 2007 through 

January 2009) (Merced ID, 2011a).
85

Figure 3-11. Water temperature in Lake McClure near the dam (March 2010 through 

February 2011) (Merced ID, 2011a).
86

Figure 3-12. Water temperature in McSwain reservoir near the dam (August 2004 

through December 2006) (Merced ID, 2011a).
87

Figure 3-13. Water temperature in McSwain reservoir near the dam (January 2007 

through January 2009) (Merced ID, 2011a).
88

Figure 3-14. Water temperature in McSwain reservoir near the dam (March 2010 

through February 2011) (Merced ID 2011a).

DO profiles in Lake McClure exhibit a complex pattern (figures 3-15 through 

3-17). DO concentrations in surface waters are typically 6 to 8 milligrams per liter 

(mg/L) year-round but can become supersaturated at times (e.g., August 2005 and May 

2006), likely the result of photosynthetic activity by phytoplankton during daylight hours. 

DO concentrations typically decrease rapidly with depth through the thermocline, 

frequently dropping as low as 2 to 4 mg/L near the bottom of the thermocline. This 

pattern suggests that a concentration of organisms (such as zooplankton) present in the 

middle to lower depths of the thermocline is decreasing DO concentrations via 

respiration. Below the thermocline, DO concentrations increase with depth, typically to 

levels between 4 and 8 mg/L at the elevation of the low level intake. At greater depths,

DO concentrations are highly variable, at times dropping to levels well below 4 mg/L 

(e.g., August 2005, July 2010, and November 2010). 
89

In the relatively shallow McSwain reservoir, DO exhibits less variation with 

depth, consistent with observed thermal stratification patterns. The highest DO 

concentrations (9 to 11 mg/L) are typically found in January through March, when the 

water is cold and generally well mixed (figures 3-18 through 3-20). The lowest DO 

concentrations typically occur in August through November, when measured values are 

typically less than 7 mg/L throughout the water column. Data collected in 2010 is the 

exception to this pattern, with most values measuring greater than 8 mg/L (see figure 

3-20).

Figure 3-15. Dissolved oxygen in Lake McClure near the dam (August 2004 through 

December 2006) (Source: Merced ID, 2011b).

400

425

450

475

500

525

550

575

600

625

650

675

700

725

750

775

800

825

850

875

900

0 2 4 6 8 10 12 Elevation (feet)

Dissolved oxygen (mg/L)

8/10/2004 9/27/2004 2/24/2005 3/29/2005 5/19/2005

6/23/2005 7/18/2005 8/31/2005 9/21/2005 10/27/2005

11/18/2005 12/16/2005 1/19/2006 2/14/2006 3/22/2006

4/13/2006 5/16/2006 6/13/2006 7/28/2006 9/1/2006

9/25/2006 10/27/2006 11/13/2006 12/13/2006

Low level intake elevation

Max water surface elevation
90

Figure 3-16. Dissolved oxygen in Lake McClure near the dam (January 2007 through 

January 2009) (Source: Merced ID, 2011b).

400

425

450

475

500

525

550

575

600

625

650

675

700

725

750

775

800

825

850

875

900

0 2 4 6 8 10 12 Elevation (feet)

Dissolved oxygen (mg/L)

1/16/2007 2/6/2007 3/16/2007 4/10/2007 5/16/2007 6/14/2007

7/12/2007 8/16/2007 9/7/2007 9/24/2007 10/5/2007 10/19/2007

11/8/2007 12/14/2007 1/15/2008 2/13/2008 3/5/2008 4/1/2008

5/20/2008 6/11/2008 7/8/2008 8/8/2008 10/6/2008 11/5/2008

12/10/2008 1/8/2009

Low level intake elevation

Max water surface elevation
91

Figure 3-17. Dissolved oxygen in Lake McClure near the dam (March 2010 through 

February 2011) (Source: Merced ID, 2011b).

400

425

450

475

500

525

550

575

600

625

650

675

700

725

750

775

800

825

850

875

900

0 2 4 6 8 10 12 Elevation (feet)

Dissolved oxygen (mg/L)

3/9/2010 5/19/2010 6/17/2010 7/22/2010 9/20/2010 8/18/2010

10/19/2010 11/16/2010 12/27/2010 1/25/2011 2/23/2011

Low level intake elevation

Max water surface elevation
92

Figure 3-18. Dissolved oxygen in McSwain reservoir near the dam (August 2004 

through December 2006) (Source: Merced ID, 2011b).

350

360

370

380

390

400

410

420

0 2 4 6 8 10 12 14 Elevation (feet)

Dissolved oxygen (mg/L)

8/10/2004 9/27/2004 2/24/2005 3/29/2005 5/19/2005

6/23/2005 7/18/2005 8/31/2005 9/21/2005 10/27/2005

12/16/2005 1/19/2006 3/22/2006 4/13/2006 5/16/2006

6/13/2006 7/28/2006 9/1/2006 9/25/2006 10/27/2006

11/13/2006 12/13/2006

Low level intake elevation

Max water surface elevation
93

Figure 3-19. Dissolved oxygen in McSwain reservoir near the dam (January 2007 

through January 2009) (Source: Merced ID, 2011b).

340

350

360

370

380

390

400

410

420

0 2 4 6 8 10 12 14 Elevation (feet)

Dissolved oxygen (mg/L)

4/10/2007 3/5/2008 5/20/2008 6/11/2008 1/8/2009

8/16/2007 3/16/2007 12/14/2007 9/7/2007 1/15/2008

2/13/2008 10/19/2007 8/8/2008 6/7/2007 9/24/2007

4/1/2008 10/3/2007 10/6/2008 2/6/2007 11/5/2008

12/10/2008 11/8/2007 1/12/2007 7/12/2007

Low level intake elevation

Max water surface elevation
94

Figure 3-20. Dissolved oxygen in McSwain reservoir near the dam (March 2010 through 

February 2011) (Source: Merced ID, 2011b).

350

360

370

380

390

400

410

420

0 2 4 6 8 10 12 Elevation (feet)

Dissolved oxygen (mg/L)

3/9/2010 4/13/2010 5/19/2010 6/17/2010

7/22/2010 8/18/2010 9/20/2010 10/19/2010

11/16/2010 12/27/2010 1/25/2011 2/23/2011

Low level intake elevation

Max water surface elevation
95

Overall, results from the 2010 and 2011 relicensing studies are consistent with 

historic studies and indicate that water quality in the project reservoirs generally 

conforms to regulatory water quality objectives and standards with the exception of DO. 

Merced ID reports that the project reservoirs are mesotrophic to oligotrophic, indicating 

moderate to low productivity, and that this condition is consistent with other lowerelevation reservoirs in the Sierra Nevada (Merced ID, 2012b). Based on data reported for 

spring and summer 2010, water samples in Lake McClure and McSwain reservoir 

exhibited moderate to high clarity and relatively low turbidity (i.e., Secchi depth 

measurements of about 7 to 20 feet [2 to 6 meters] and average turbidity readings <14 

nephelometric turbidity unit [NTU]). Combined with the DO profile data, the water 

clarity and turbidity data indicate the project reservoirs experience a moderate level of 

primary productivity, and therefore, would likely be classified as mesotrophic. No algal 

blooms were observed and nutrient concentrations were generally low, with measured 

concentrations of nitrate, nitrite, ammonia, total Kjeldahl nitrogen, orthophosphorus, and 

total phosphorus at or near the analytical method reporting limits for the majority of 

samples. No bacterial counts from samples collected near recreational sites were 

reported above water quality objectives. Most other analytes were reported as nondetectable to just above analytical reporting limit concentrations. None of the 

303(d)-listed agricultural pesticides (chlorpyrifos, diazinon and Group A pesticides) were 

detected at commercially available reporting limits. In addition to instances of DO below 

water quality objectives in the two project reservoirs, other periodic inconsistencies with 

the Basin Plan were documented for pH, metals and toxicity, as described below. 

Water quality was monitored in surface and bottom waters during spring and 

summer 2010 at two locations in Lake McClure (near the dam and head of reservoir) and 

one location in McSwain reservoir (near the dam), for a total of 12 samples. Of these, 

three samples did not meet the water quality objective for pH, including: the spring 

bottom water sample from Lake McClure at the head of the reservoir (pH = 6.08), and 

both spring and summer bottom water samples from McSwain reservoir near the dam 

(pH = 6.03 and 6.19, respectively) (Merced ID, 2012b). Additionally, one sample 

collected in the bottom waters of Lake McClure near the dam during summer 2010 

exhibited a dissolved copper concentration of 1.99 micrograms per liter (μg/L), which is 

slightly greater than the California Toxics Rule (hardness-dependent) value of 1.5 μg/L 

(40 CFR §131). The remaining 11 samples exhibited dissolved copper concentrations 

ranging from 0.32 μg/L to 1.27 μg/L (Merced ID, 2012b).

Water column total mercury concentrations were well below the primary 

maximum contaminant level for drinking water (0.002 mg/L; California DPH, 2008) at 

all spring and summer sampling locations in the project reservoirs. Methylmercury was

detected in numerous fish tissue samples from Lake McClure and McSwain reservoir

during various studies occurring from 2007 to 2010 (including one additional set of 

samples from Lake McClure in 1984) and reported to the California Office of 

Environmental Health Hazard Assessment (California OEHHA), which is the agency 

solely responsible for evaluating the potential public health risks of chemical 
96

contaminants in sport fish and issuing state advisories. California OEHHA has 

established guidelines relating to fish contaminant goals and advisory tissue levels in 

state water bodies (Klasing and Brodberg, 2008). Based on available data for Lake 

McClure and McSwain reservoir, California OEHHA determined that tissue 

concentrations exceed the threshold of 440 parts per billion (ppb) methylmercury (wetweight) for several fish species. Accordingly, California OEHHA has issued health 

advisories for consumption of spotted bass, largemouth bass, catfish, and Chinook 

salmon in Lake McClure and spotted bass and largemouth bass in McSwain reservoir, for 

women between the ages of 18 and 45 years old and children (California OEHHA, 2013, 

2012).

Merced Falls Project

Water temperature data collected from 1998 to 2008 throughout the Merced River 

by Merced ID and California DFW report average daily water temperatures in the 

Merced Falls Project impoundment ranged between 49°F and 60°F (9.4°C and 15.5°C).

From 2006 through 2008, water quality sampling conducted in the reach 

downstream of Merced Falls dam recorded DO levels ranging from 6.3 mg/L in spring of 

2007 to 12.3 mg/L in spring of 2008. Additional water quality monitoring data collected 

during August 2008, indicated that Merced Falls Project waters met or exceeded the 

stated DO objective. Continuous DO monitoring was conducted in the Merced Falls 

impoundment through deployment of a Hydrolab Datasonde 5. The Datasonde was 

deployed near the water’s surface (at a depth of 1.6 meters) at the upstream face of 

Merced Falls dam from August 17, 2011, to August 31, 2011. Results showed that DO 

levels never dropped below 8 mg/L, the Basin Plan’s numeric water quality objective for 

instantaneous measurements downstream of New Exchequer dam. The median percent 

saturation was above the monthly saturation objective of 85 percent.

Water quality in the Merced Falls impoundment surpassed state standards and 

most constituents were at non-detectable levels or just above reporting limits. 

Lower Merced River

Daily average water temperatures measured at four locations in the Merced River 

between Briceburg (RM 87.9) and the San Joaquin confluence are shown for a 

representative wet water year (2006) and dry water year (2008) in figure 3-21 and figure 

3-22, respectively. In general, temperatures at Crocker-Huffman diversion dam (RM 

52.0), the current upstream limit of anadromous fish habitat, ranged from approximately 

8.0 to 17.0°C (46.4 to 62.6°F) annually during both water year types. 
97

Figure 3-21. Daily average water temperatures recorded in the Merced River between 

Briceburg (RM 87.9) and the San Joaquin River confluence in water year 

2006, a representative wet water year (Source: Merced ID, 2012a).
98

Figure 3-22. Daily average water temperatures recorded in the Merced River between

Briceburg (RM 87.9) and the San Joaquin River confluence in water year 

2008, a representative dry water year (Source: Merced ID, 2012a).

During the 2010 and 2011 relicensing studies, DO measurements were collected at 

the following four locations in the lower Merced River: immediately downstream of 

Crocker-Huffman diversion dam (RM 52.0), downstream of Snelling Bridge (RM 46.5), 

near Shaffer Bridge (RM 32.8), and at River Road upstream of the San Joaquin 

confluence (RM 1.5). In summer 2011, all of the DO readings immediately downstream 

of Crocker-Huffman diversion dam and at Snelling Bridge met the 8 mg/L objective that 

is applicable upstream of Cressey, while 26 percent did not meet the objective at Shaffer 

Bridge and 8 percent of the readings measured at River Road did not meet the 7.0 mg/L 

objective that is applicable downstream of Cressey. In fall 2011, all of the DO readings 

met the 8 mg/L objective immediately downstream of Crocker-Huffman diversion dam, 

at Snelling Bridge, and at Shaffer Bridge. Less than 1 percent of the readings measured 

at River Road did not meet the 7.0 mg/L objective.

For fish tissue samples collected to date (2003 through 2006) from the lower 

Merced River, nearly all were below the 440 ppb (wet-weight) threshold for 

methylmercury concentrations and have not prompted California OEHHA to issue fish 

ingestion health advisories. Two adult largemouth bass samples collected in 2005 from 

Hatfield State Park (RM 2.0) exceeded the threshold (503 ppb and 944 ppb) (Merced ID, 

2012c).
99

Toxicity tests using various surface water samples collected in 2000, 2002, 2004, 

and 2006 from the lower Merced River were toxic to some of the laboratory test 

organisms. Because the toxicity response was not correlated with a specific chemical or 

other water quality parameter, the lower Merced River was included on the CWA 

§303(d) list for unknown toxicity.

Stream Geomorphology

The Merced River channel within and downstream of the Merced River and 

Merced Falls Projects has been substantially altered from its historical state due primarily 

to dredging associated with gold mining, dam and reservoir construction, and reduction in 

peak flows. Before mining and hydroelectric development began, the Merced River in 

the vicinity of the projects was a complex of multiple channels that became simplified 

over time as sediment was excavated from the streambed during mining operations and 

placed alongside in large rows, raising the floodplain and depleting the channels of 

sediment (Stillwater Sciences, 2001; URS, 2004). The dams that were constructed in the 

years following—Merced Falls dam in 1901, Crocker-Huffman dam in 1910, Old

Exchequer dam in 1926, McSwain dam in 1966, and New Exchequer dam in 1967—

collectively captured and stored a large amount of sediment, leading to downstream bed 

coarsening, narrowing, straightening, and further channel consolidation (Merced ID,

2011a).

Erosion in relationship to project roads, reservoir shorelines, or stream channel 

banks was not raised as a significant issue during project scoping (FERC, 2009).

Merced River Project

Sediment Capture in Reservoirs—Approximately 29.8 million tons of sediment 

was deposited in Lake McClure between 1967 and 2008, or 727,000 tons per year. 

Merced ID assumed 5 to 10 percent of the total sediment mass in Lake McClure was 

coarse (typically > 0.08 inch [2 millimeters (mm)] in diameter) and was transported as 

bedload. Given this assumption, about 36,000 to 73,000 tons of bedload was deposited 

annually in Lake McClure. McSwain reservoir has a sediment deposit estimated at 1.2 

million tons, or 29,000 tons per year, which is only about 4 percent of that supplied to 

Lake McClure. Assuming the same ratio of coarse-to-total sediment as at Lake McClure, 

bedload yield below McSwain dam could be up to 1,400 tons per year, an order of 

magnitude less than is supplied to Lake McClure based on sediment accumulated there 

since 1967. These values suggest that sediment supply (including gravel suitable for 

salmonid spawning) to reaches of the Merced River downstream of McSwain dam has 

been substantially reduced. The reach from New Exchequer dam downstream to Merced 

Falls dam is entirely impounded, leaving no areas of flowing channel where bank erosion 

could supply sediment to replace that captured in the reservoir.

Large Wood—Merced ID’s removal of wood from project reservoirs is not 

documented, but only low quantities appear to reach the dam. Lake McClure does not 

appear to be receiving much large wood. Large wood supplied to the reservoir may sink 
100

before reaching New Exchequer dam or it is stored on shorelines or in tributary deltas. 

Large wood pieces are similarly rare at the downstream end of McSwain reservoir—

Merced ID reports that an average of only two logs per year are pulled from the face of 

the dam and burned. 

Merced Falls

The water level of the approximate 1-mile-long Merced Falls impoundment does 

not fluctuate, the majority of the project shoreline is vegetated, and much of the shoreline 

is armored with bedrock. Therefore, erosion, as it relates to the contribution of sediment 

in the project area, is likely minimal.

Existing information indicates very little sediment in the Merced Falls 

impoundment, presumably due to sediment captured by the New Exchequer and 

McSwain dams upstream of the Merced Falls Project. Any sediment reaching the 

Merced Falls Project is likely limited to small particles (less than 1 mm in size).

Lower Merced River

Sediment Supply and Channel Substrate—The stream channel between Merced 

Falls dam and Crocker-Huffman diversion dam is only about 1.5 miles long and is the 

only area available to supply sediment to the channel via fluvial bank erosion upstream of 

Crocker-Huffman dam. Because the landscape through which this reach flows is 

relatively flat, and high-flow events have been substantially reduced in frequency and 

magnitude, very little sediment enters the channel. Crocker-Huffman diversion dam 

intercepts the majority of the limited amount of coarse sediment originating downstream 

of New Exchequer dam. The reaches downstream of Merced Falls dam and CrockerHuffman diversion dam are thus likely supplied with very little sediment. 

Surface particle sizes downstream of Crocker-Huffman diversion dam were found 

by Vogel (2007) to be relatively large, and the substrate as a whole in potential 

anadromous salmonid spawning areas is composed largely of cobbles (2.5 to 10.1 inch 

[64 to 256 mm] diameter) and boulders (> 10.1 inch [256 mm] in diameter). 

The estimated D50 (median particle size) of the bed surface in reaches downstream 

of Crocker-Huffman diversion dam ranges from 1.1 to 5.3 inches (28 to 134 mm) and D84

(value for which 84 percent of the particles are finer) from 2.7 to 10.6 inches (68 to 270 

mm) (California DWR, 1994; Vick, 1995; Stillwater Sciences, 2004, 2001). Grain sizes 

just downstream of Crocker-Huffman diversion dam were smaller than farther 

downstream, having a median of 0.9 to 1.2 inches (24 to 31 mm) (Stillwater Sciences, 

2006). To mobilize the bed downstream of Crocker-Huffman diversion dam would 

require an estimated 4,800 cfs flow—a 5-year recurrence interval flow under existing 

conditions (Stillwater Sciences, 2001).

The bed downstream of Crocker-Huffman diversion dam is bedrock or contains a 

cobble armor layer with banks of immobile dredger tailings (Stillwater Sciences, 2006, 

2001; URS, 2004). As a result, the channel bed and formerly active bars have become 
101

static, and riparian vegetation is encroaching upon them (Stillwater Sciences, 2002). 

Vick (1995) estimated that riparian encroachment had reduced channel width in the reach 

from Crocker-Huffman diversion dam to RM 15.0 by an average of 85 feet, or 33 percent

of the mean 1937 channel width. As a result, the area of aquatic habitat in the Merced 

River has been reduced, and the river channel is currently characterized by a simplified 

cross section with no active bars and no clearly defined low flow channel.

The sediment sampling results indicated that the reach downstream of Merced 

Falls dam was moderately armored, as was the reach downstream of Crocker-Huffman 

diversion dam (Merced ID, 2011c). No significant differences were found in particle size 

ratios above and below Crocker-Huffman diversion dam. Bedrock appeared to be 

limiting further channel incision in both reaches and irrigation diversions downstream of 

the dam appeared to have little influence on armoring. Local gravel augmentation 

reduced armoring in portions of the channel, but only adjacent to and just downstream of 

the augmentation sites (Merced ID, 2011c).

Large Wood—Large wood of the size capable of influencing channel morphology 

is largely absent in the lower Merced River. Large wood was surveyed in the reach 

downstream of Merced Falls dam by Merced ID as part of its Instream Flow Study 

habitat mapping efforts; no wood in the channel met the minimum diameter of 6 inches 

and the minimum length of >1/2 bankfull width of the channel for pieces to be considered 

capable of influencing channel morphology or storing sediment, but some (<10 pieces) 

meeting the criteria were found perched on the channel margin or submerged within the 

backwater formed by Crocker-Huffman diversion dam. 

Any large wood delivered to Crocker-Huffman diversion dam is a result of 

Merced River flows upstream—high flows transport fallen trees from the riparian zone 

and carry them downstream, whereas larger pieces are trapped at the dam. About once

every 3 years, Merced ID removes an average of 6 to 10 logs or branches of 8 to 16 

inches in diameter, with some pieces occasionally much larger (Merced ID, 2012a).

Fishery Resources

Fishery resources described in this section include reservoir and stream fish 

populations in and downstream of project reservoirs. The federally listed Central Valley 

steelhead is listed as threatened or endangered under the federal ESA are discussed 

separately in section 3.3.3, Threatened and Endangered Species.

Merced River Project

Merced ID performed a study of reservoir fish populations in 2010 to supplement 

existing information on fish in Lake McClure and McSwain reservoir. The study 

documented reservoir fish captured by electrofishing and gillnetting and those reported 

caught by anglers. The reservoir fish study also assessed fish passage from the reservoirs 

into tributaries, risk of fish entrainment, bass nesting habitat, and spawning habitat. This
102

information is based on the reservoir fish study and available information from other 

sources, including reservoir fish stocking reports.

Fish Populations—Fishes documented in Merced ID’s 2010 survey of Lake 

McClure included 5 native and 15 non-native (introduced) species. The native fishes 

found in Lake McClure were resident rainbow trout,22 Sacramento sucker, landlocked 

Chinook salmon, prickly sculpin, and Sacramento pikeminnow (table 3-6). Introduced 

threadfin shad and black bass (bass in the genus Micropterus, including largemouth,

spotted, and bass that could not be identified to species) dominate the warmwater fishery 

in Lake McClure. Rainbow trout, landlocked Chinook salmon, and kokanee,

23 all of 

which are annually stocked in the reservoir, dominate the coldwater fishery. Salmon and 

other fishes in Lake McClure can move upstream into the upper Merced River reach or 

into tributaries to spawn, but downstream movement out of the reservoir is limited to 

passage through the powerhouse or over the spillway during spill events. The relative 

condition factor for fish in Lake McClure, which was derived from length and weight 

data of fish captured in the reservoir by boat electrofishing, indicates that most species 

were of a healthy weight for their length. The relative condition factor provides a general 

indication of the fish condition and health, where a value greater than or equal to 1.0 

indicates fish of average or better condition (Merced ID, 2011d).

Fishes documented in Merced ID’s 2010 survey of McSwain reservoir included 6 

native and 12 non-native species. Native Sacramento sucker and rainbow trout were the 

most abundant species. The relatively cold temperature and short residence time of water 

in McSwain reservoir provides favorable habitat for these coldwater species. Rainbow 

trout are stocked annually in the reservoir. The other native species found in McSwain 

reservoir were hitch, riffle sculpin, prickly sculpin, and Sacramento pikeminnow (table 

3-7). As in Lake McClure, the relative condition factor for fish in McSwain reservoir 

indicates that the seven species with a reportable condition factor were of a healthy 

weight for their length. McSwain reservoir is bounded on the upstream end by New 

Exchequer dam and downstream by McSwain dam, neither of which has fish passage 

facilities. Movement of fish out of McSwain reservoir is, therefore, limited to small 

tributary streams flowing directly into the reservoir and downstream passage through the 

project powerhouse or over the spillway during spill events. 

 

22 Resident rainbow trout is a catchall designation for hundreds of nonanadromous 

wild rainbow trout (O. mykiss) populations that exist throughout California and are either 

derived naturally from steelhead or, more likely, are of mixed hatchery and native origin 

(Moyle, 2002).

23 Kokanee are nonanadromous sockeye salmon, which, in California, have been 

established through introduction (Moyle, 2002).
103

Table 3-6. Summary of relative abundance, length, weight, and relative to condition factor for fish species collected in 

Lake McClure in 2010 (Source: Merced ID, 2012a).

Speciesa Number

Percent of 

Catch by 

Number

Length

(millimeters)

Weight

(grams)

Mean 

Relative 

Condition 

Factor Minimum Maximum Mean Minimum Maximum Mean b

Threadfin shad 4,175 50.8 20 121 71 < 1 32 6 0.87

Spotted bass 1,655 20.1 33 548 198 < 1 3,100 231 0.96

Largemouth 

bass

691 8.4 47 572 197 1 4,600 312 0.96

Bluegill 524 6.4 31 272 84 < 1 440 15 1.01

Common carp 365 4.4 208 662 488 200 5,500 2,179 1.26

Green sunfish 255 3.1 30 123 76 < 1 38 9 1.15

Channel 

catfish

125 1.5 58 720 375 2 6,550 1,121 1.04

Black crappie 115 1.4 55 340 146 2 750 72 0.97

Rainbow troutc 108 1.3 232 470 346 110 1,080 481 1.35

Kokanee 50 0.6 210 430 362 130 960 563 1.38

Goldfish 38 0.5 202 405 363 173 5,800 1,656 1.06

White catfish 42 0.5 29 490 314 < 1 1,400 626 0.97

Sacramento 

suckerc

19 0.2 104 623 418 16 1,800 1,067 1.30

White crappie 17 0.2 50 350 206 2 650 241 0.95

Unknown bass 13 0.2 22 36 29 -- -- -- --
104

Speciesa Number

Percent of 

Catch by 

Number

Length

(millimeters)

Weight

(grams)

Mean 

Relative 

Condition 

Factor Minimum Maximum Mean Minimum Maximum Mean b

Chinook 

salmonc

11 0.1 270 500 409 270 1,660 969 0.90

Prickly 

sculpinc

8 0.1 38 71 51 < 1 4 2 --

Sacramento 

pikeminnowc

6 0.1 247 790 488 145 7,250 2,053 --

Golden shiner 2 < 0.1 103 105 104 13 14 14 --

Brown 

bullhead

1 < 0.1 330 330 330 575 575 575 --

Redear sunfish 1 < 0.1 71 71 71 7 7 7 --

Total 8,211 100 -- -- -- -- -- -- --

a Species are listed in descending order of numerical abundance in the catch.

b Species with 10 or less individuals or poor fit regressions did not have a reportable condition factor.

c This species is a native species.
105

Table 3-7. Summary of relative abundance, length, and weight of all fish species collected at McSwain reservoir in 2010 

(Source: Merced ID, 2012a).

Speciesa Number

Percent of 

Catch by 

Number

Length

(millimeters)

Weight

(grams)

Mean 

Relative 

Condition 

Factor Minimum Maximum Mean Minimum Maximum Mean b

Sacramento 

suckerc

1,235 71.1 19 556 248 0 1,900 280 1.39

Rainbow troutc 230 13.2 227 555 340 129 1,800 451 0.98

Golden shiner 75 4.3 140 278 181 36 330 95 1.24

Prickly 

sculpinc

72 4.1 34 113 70 1 19 4 0.98

Spotted bass 39 2.2 87 460 197 6 2,050 276 0.94

Channel 

catfish

24 1.4 77 650 297 5 6,400 867 0.94

Threadfin shad 21 1.2 55 140 118 1 39 27 1.95

Hitchc 10 0.6 50 212 148 1 120 62 --

Largemouth 

bass

8 0.5 75 422 235 5 1,600 494 --

Brown trout 6 0.3 412 522 463 1,000 2,050 1,423 --

Kokanee 4 0.2 180 249 215 82 190 126 --

Riffle sculpinc 4 0.2 75 91 86 5 10 8 --

Bluegill 2 0.1 112 113 113 27 32 29 --

Red shiner 2 0.1 45 47 46 1 1 1 --
106

Speciesa Number

Percent of 

Catch by 

Number

Length

(millimeters)

Weight

(grams)

Mean 

Relative 

Condition 

Factor Minimum Maximum Mean Minimum Maximum Mean b

Green sunfish 1 < 0.1 156 156 156 100 100 100 --

Black crappie 1 < 0.1 76 76 76 6 6 6 --

Sacramento 

pikeminnowc

1 < 0.1 535 535 535 1,680 1,680 1,680 --

White catfish 1 < 0.1 325 325 325 706 706 706 --

Total 1,736 100 -- -- -- -- -- -- --

a Species are listed in descending order of numerical abundance in the catch.

b Species with 10 or less individuals or poor fit regressions did not have a reportable condition factor.

c This species is a native species.
107

Prior to dam construction, anadromous fishes, including federally listed Central 

Valley steelhead and spring-run Chinook salmon, fall-run and late fall-run Chinook 

salmon, and Pacific lamprey migrated upstream to spawn in the Merced River upstream 

of the current location of the project dams and reservoirs. The extent of spawning and 

rearing habitat for steelhead and spring-run Chinook salmon, which are believed to have 

migrated upstream as far as El Portal and possibly into Yosemite National Park (NMFS, 

2014, Yoshiyama et al., 2001), has been reduced by up to 50 miles in the mainstem 

Merced River and 7 miles in the South Fork of the Merced River. The historical 

upstream extent of habitat for fall-run and late fall-run Chinook salmon and Pacific 

lamprey is unknown. Habitat for resident native species that currently occur both 

upstream and downstream of the project, such as Sacramento pikeminnow, hardhead, and 

Sacramento sucker, has been fragmented by project and non-project dams, effectively 

isolating the historical populations into disconnected sub-populations upstream and 

downstream of the dams.

Special-status Fish Species—No special-status fish species have been documented in 

Lake McClure or McSwain reservoir. However, hardhead, which is considered a species 

of special concern by California DFW, has been documented in the Merced River 

upstream of Lake McClure. Hardhead are known to occupy reservoirs in the Sierra 

Nevada foothills, and no migration barriers exist between Lake McClure and the Merced 

River upstream. However, hardhead are susceptible to predation by non-native predatory 

fish, such as black bass, which may reduce or eliminate hardhead from otherwise suitable 

reservoirs (Moyle, 2002). The Chinook salmon and rainbow trout found in Lake 

McClure and McSwain reservoir are landlocked varieties that are not considered part of 

the special-status populations of anadromous Chinook salmon and steelhead that occur in 

the lower Merced River downstream of migration barriers. 

Spawning Habitat—Merced ID conducted surveys in 2010 to assess reservoir and 

tributary spawning habitat for fish in Lake McClure. Of the 21 surveyed tributaries 

surveyed, six were found to have adequate flow and habitat to be used by streamspawning reservoir fish. These six tributaries included the Merced River and five smaller 

tributaries to Lake McClure (Cotton, Maxwell, Piney, Sherlock, and Willow Creeks). No 

passage barriers were documented in the surveyed portion of the Merced River or the five 

tributaries, and suitable spawning gravel was present in each. Warmwater fishes, 

including largemouth bass, bluegill, and green sunfish, were the most prevalent species in 

the Merced River and the five suitable spawning tributaries. Rainbow trout and other 

native species, including Sacramento sucker and sculpin, were found in low numbers. 

Water temperature and stream size appeared to be the primary factor determining species 

composition and number. Instantaneous water temperature measured in Cotton, 

Maxwell, Piney, and Willow creeks ranged from 54.0 to 61.0 °F (12.2 to 16.1°C) in 

March and April 2010 and from 66.5 to 80.5°F (19.2 to 26.9°C) in late June 2010 

(Merced ID, 2011d, Attachment 3-1F). Water temperatures in the Merced River 

upstream of Lake McClure and in Sherlock Creek, both of which were measured only 

during fish surveys in August 2010, were 72.0 to 75.0°F (22.2 to 23.8°C) in the Merced 
108

River and 77.0°F (25.0°C) in Sherlock Creek. Estimated stream discharge during fish 

sampling in summer 2010 was 215 cfs in the Merced River and 2 cfs or less in each of 

the five smaller tributaries (Merced ID, 2011d, Attachment 3-1F). Fish abundance and 

the number of species were greater in the Merced River than in the other surveyed 

tributaries. 

The reservoir spawning assessment documented black bass nests and additional 

suitable bass spawning habitat in Lake McClure. Habitat conditions (i.e., bottom 

substrate, cover, and water temperature) and typical reservoir operations (i.e., increasing 

spring water level; see figures 3-2, 3-4, and 3-6 in the Water Quantity subsection) appear 

conducive to reproductive success by black bass and other warmwater fish species in 

Lake McClure. Spawning by largemouth bass, an abundant species of black bass in Lake 

McClure, typically begins in March or April when water temperatures reach 59.0 to 

60.0°F (15.0 to 15.5°C) and may continue through June in water temperatures up to 

75.2°F (24.0°C) (Moyle, 2002). Reduced hatching success or complete brood failure can 

occur if nests are dewatered by declining water levels. The observation of black bass fry 

and threadfin shad fry during the nesting surveys further indicated that these species 

spawn successfully in Lake McClure.

Tributary and bass nest surveys were not conducted at McSwain reservoir, but 

age-0 (young-of-the-year) fish of numerous species (e.g., spotted bass, sucker, threadfin 

shad, and largemouth bass) were collected during the population surveys, indicating there 

was access to viable spawning habitat in the reservoir and/or tributaries and successful 

reproduction in 2010. Most of these fishes were warmwater species. Age-0 rainbow 

trout were not collected in McSwain reservoir, which may indicate limited or no natural 

rainbow trout reproduction in 2010. 

Upstream and Downstream Fish Passage—The project’s two dams, New 

Exchequer dam and McSwain dam, have no fish passage facilities and prevent volitional 

fish movement upstream and downstream. No upstream fish passage occurs at either 

dam, and downstream passage at the two project dams is limited to passage through the 

powerhouses, through the Howell-Bunger valve at New Exchequer dam, and over the 

spillways during spills. No data are available about how often or how many fish pass 

downstream from project reservoirs as a result of spills or entrainment, or the actual 

survival of entrained fish. However, in 2010, Merced ID assessed the potential for fish 

entrainment into both of the powerhouse intakes. Results suggest that most of the 

reservoir fish that are expected to occur in deep water near the intakes have swimming 

speeds that exceed the maximum approach velocity of water entering the intakes and 

should be able to avoid involuntary entrainment.

In Lake McClure, the powerhouse intake structure is located at the base of New 

Exchequer dam at a depth of 382 feet below the NMWSE of the reservoir. In rare events 

when the reservoir’s water surface elevation drops substantially, the intake depth can be 

as shallow as 100 to 150 feet below the surface. Based on a 10 percent discharge 

exceedance through the powerhouse of 2,912 cfs using data from 1970 to 2006, 
109

calculated approach velocities at the intake can be as great as approximately 2.1 feet per 

second. Entrainment probability is a function of proximity to the intake and a fish’s 

ability to avoid entrainment by swimming faster than the intake approach velocity. 

Gillnetting near the dam at depths up to 100 feet showed relatively low fish abundance;

only kokanee (n=12), largemouth bass (n=3), rainbow trout (n=1), and spotted bass (n=5) 

were collected in deepwater habitat near New Exchequer dam. Merced ID’s calculation 

of estimated swim speeds for kokanee, largemouth bass, and rainbow trout suggests that 

these species have sustained swimming speeds that exceed the maximum reported 

approach velocity of 2.1 feet per second and thus could avoid entrainment. The burst 

speed of all species significantly exceeded calculated approach velocities. If a fish were 

to become entrained and pass through the turbines, Merced ID’s review of literature 

describing Francis turbines similar to those used at New Exchequer powerhouse suggests 

that the potential for survival would be 81.0 to 99.6 percent. 

In McSwain reservoir, the powerhouse intake structure is located about 70 feet 

upstream of McSwain dam at a depth of 30 to 40 feet, depending on water levels. Based 

on a 10 percent discharge exceedance through the powerhouse of 2,900 cfs using data 

from 1970 to 2006, calculated approach velocities at the powerhouse intake can be as 

high as approximately 2.7 feet per second. Gillnet sampling in McSwain reservoir in 

2010 found primarily Sacramento sucker in deep water near the reservoir bottom. 

Kokanee are present in the reservoir and may occur in deep water, but they were only 

found in mid-water (50 percent of maximum depth) sampling. Although the maximum 

calculated approach velocity of 2.7 feet per second exceeds the estimated sustained 

swimming speed of 2.4 feet per second for adult Sacramento suckers, it is significantly 

less than the sucker’s estimated burst speed of 12.3 to 13.5 feet per second (Stamp and 

Golden, 2005). Other species for which swimming speed was estimated (largemouth 

bass, rainbow trout, kokanee) have sustained swimming speeds that exceed the maximum 

approach velocity at the McSwain powerhouse intake. Merced ID’s review of literature 

describing Kaplan reaction turbines similar to those used at McSwain powerhouse 

suggests that if a fish were to become entrained and pass through the turbines, the 

potential for survival would be 88.0 to 96.1 percent.

Merced Falls

Fish Populations—Fish populations in the impoundment were sampled using boat 

electrofishing and gill netting in four quarterly sampling efforts during 2010–2011. Five 

fish species were collected during July 2010, October 2010, February 2011, and April 

2011 boat electrofishing surveys: Sacramento sucker (Catostomus occidentalis), rainbow 

trout (O. mykiss), hitch (Lavinia exilicauda), prickly sculpin (Cottus asper), and Kern 

Brook lamprey (Lampetra hubbsi).

Overall, Sacramento sucker was the most abundant species collected. All Kern 

Brook lamprey collected were ammocoetes (95 to 142 mm). Only three fish species were

collected during July 2010, October 2010, February 2011, and April 2011 gill net 
110

surveys: Sacramento sucker, rainbow trout, and hitch. Again, Sacramento sucker was 

the most abundant species collected.

Although not detected during surveys, other non-native fish species that have been 

found in Lake McClure, and may also occur in the Merced Falls Project impoundment, 

include largemouth bass (Micropterus salmoides), bluegill (Lepomis macrochirus), black 

crappie (Pomoxis nigromaculatus), and white crappie (Pomoxis annularis).

Special-status Fish Species—As described in greater detail below, the Kern brook 

lamprey (Entosphenus hubbsi) is a small, non-anadromous lamprey endemic to the San 

Joaquin River Basin. It is considered a species of special concern by California DFW. 

Habitat—The Merced Falls impoundment exhibits a stable, shallow-water, lentic 

habitat, exhibiting no riverine-type geomorphic features (riffles, runs, or pools). 

Upstream and Downstream Fish Passage—A fish ladder at Merced Falls dam was 

operated to allow upstream access for anadromous species until 1971, when operation 

was discontinued after the construction of Merced ID’s McSwain dam, which eliminated 

upstream spawning resources. As described below, Crocker-Huffman diversion dam

situated downstream of the Merced Falls Project is considered the upstream limit for 

anadromous fish passage in the Merced River. 

Lower Merced River

Fish Populations—In the Merced River between Merced Falls dam and CrockerHuffman diversion dam, Sacramento sucker, sculpin, lamprey, and resident rainbow trout

(all native species) were the most abundant species found in surveys by PG&E (2011a) 

and Stillwater Sciences (2008). Lamprey observed in the reach included the Kern brook 

lamprey, which is considered a species of special concern by California DFW. More 

information on Kern brook lamprey is provided in the following subsection, Specialstatus Fish Species. 

In the lower Merced River from Crocker-Huffman diversion dam downstream to 

the San Joaquin River confluence, 29 fish species were observed during seasonal fish 

surveys conducted from summer 2006 through spring 2008. Twelve of the observed fish 

species are native to the Merced River drainage and 17 species are introduced. The most 

abundant species were the introduced western mosquitofish and spotted bass, and the 

native Sacramento sucker, hardhead, and Sacramento pikeminnow, which together 

comprised 82 percent of the fishes observed or captured (Stillwater Sciences, 2008). 

Hardhead, considered a species of special concern by California DFW, is discussed in the 

following subsection, Special-status Fish Species.

Crocker-Huffman diversion dam lacks functional fish passage facilities and is 

considered the upstream limit for anadromous fish passage in the Merced River. Three 

anadromous species were present downstream of Crocker-Huffman diversion dam at 

relatively low abundance, including the native fall‐run Chinook salmon and Pacific 

lamprey and the introduced striped bass. Fall-run Chinook salmon, considered a species 
111

of special concern by California DFW, is discussed in more detail in the following 

subsection, Special-status Fish Species. O. mykiss were also observed in the sampling 

reach immediately downstream of Crocker-Huffman diversion dam (RM 44.7 to RM 

51.3), but the sampling methods did not allow for absolute distinction between the 

anadromous form (steelhead) and the resident form (rainbow trout). Nevertheless, NMFS 

considers O. mykiss in the Merced River downstream of Crocker-Huffman diversion dam 

to be part of the Central Valley steelhead distinct population segment (DPS), which is 

listed as threatened under the ESA. Steelhead are discussed in more detail in section 

3.3.3, Threatened and Endangered Species. Three other special-status fish species were 

found in the lower Merced River during the 2006 to 2008 seasonal fish surveys: Kern 

brook lamprey, hardhead, and Sacramento splittail. Each is considered a species of 

special concern by California DFW and is discussed in more detail below.

Special-status Fish Species—Special-status fish species include those listed under 

the California ESA as endangered or threatened, those considered by California DFW to 

be species of special concern or fully protected species, and those classified as sensitive 

species by BLM. This section summarizes the most recent available information on 

populations of special-status fish species found in the project areas and in the Merced 

River downstream of the projects.

Kern brook lamprey: The Kern brook lamprey (Entosphenus hubbsi) is a small,

non-anadromous lamprey endemic to the San Joaquin River Basin. It is considered a 

species of special concern by California DFW. One ammocoete (immature life stage) of 

this species was reported in the Merced River between Merced Falls dam and CrockerHuffman diversion dam by Stillwater Sciences (2008), and an unknown number of 

ammocoetes was reported in this section of the Merced River by PG&E (2011a). A total 

of 36 adult lamprey and ammocoetes were also found in the lower Merced River between 

Crocker-Huffman diversion dam and the San Joaquin River confluence during seasonal 

sampling from 2006 to 2008 by Stillwater Sciences (2008). Specific age classes could 

not be determined for Kern brook lamprey found in the lower river, but most were larger 

individuals up to 5.9 inches (150 mm) in length. Adults spawn in spring in gravel riffles. 

Ammocoetes are found in sand and mud where water is shallow and slow-moving and 

summer water temperatures are generally less than 77.0°F (25.0°C). 

Pacific lamprey: The Pacific lamprey (Entosphenus tridentatus) is a widely 

distributed, anadromous lamprey that is considered a sensitive species by BLM. A total 

of 72 Pacific lamprey ammocoetes ranging from 2.0 to 6.9 inches (51 to 175 mm) in 

length were found in the Merced River during fish surveys conducted from 2006 to 2008. 

Of the total, five were found between Merced Falls dam and Crocker-Huffman diversion 

dam, and the rest were found downstream of Crocker-Huffman diversion dam. No adults 

were found during the surveys. Based on available data from the American River 

(Hannon and Deason, 2008), spawning in San Joaquin River tributaries, including the 

Merced River, is expected to occur between early January and late May with peak 

spawning typically occurring in early April. Spawning typically occurs in gravel riffles 

at water temperatures between 53.6 and 64.4°F (12.0 to 18.0°C), and embryos hatch in 
112

approximately 19 days at 59.0°F (15.0°C) (Moyle, 2002). Ammocoetes bury themselves 

in shallow eddies and backwaters where they rear in silt, sand, and mud. 

Chinook salmon: The Chinook salmon (Oncorhynchus tshawytscha) in the lower 

Merced River belongs to the Central Valley fall-run and late fall-run evolutionarily 

significant unit, and is considered a species of special concern by California DFW. Most 

Merced River Chinook salmon exhibit a fall-run life history with adults typically entering 

the Merced River to spawn from October through December. Fry emergence occurs from 

January through March, and fry rear in the river for a short time before moving 

downstream as juveniles or smolts from January through May.

The Merced River fall-run Chinook salmon population is supported by both 

natural in-river production and artificial production from the Merced River Hatchery, 

operated by California DFW. The hatchery, located immediately downstream of 

Crocker-Huffman diversion dam, produces an average of 972,344 fall-run Chinook 

salmon annually. Since 2000, approximately 50 percent of the production has been 

released at the hatchery, and the remainder is released at downstream locations in the San 

Joaquin and Merced Rivers, as well as other tributaries to the San Joaquin River 

(California HSRG, 2012).

The abundance of returning adults (i.e., escapement) has fluctuated since 1970 

with peaks in the early 1980s and early 2000s and a downward trend between 2000 and 

2010 (figure 3-23). During the most recent period of peak abundance (2000 to 2002), the 

percentage of hatchery-origin fish in the total escapement is estimated to have ranged 

from 65 percent to greater than 95 percent (Mesick, 2010). Annual captures of 

outmigrant fry using RSTs have ranged from 12,964 in 2004 (86 days of trapping) to 

127,632 in 2001 (153 days of trapping). The mean daily catch was 151 fish/day in 2004 

and 834 fish/day in 2001.

Fall-run Chinook salmon historically migrated upstream to spawn in the Merced 

River at least as far as the vicinity of present-day Lake McClure (Yoshiyama et al., 

2001). Currently, Crocker-Huffman diversion dam is the downstream-most migration 

barrier to Chinook salmon. Merced Falls dam, McSwain dam, and New Exchequer dam 

are also fish migration barriers and their reservoirs inundate former riverine habitat that 

Chinook salmon historically used (Yoshiyama et al., 2001, 1998).

Chinook salmon spawning and most juvenile rearing in the lower Merced River 

currently is restricted to the 10-mile-long reach downstream of Crocker-Huffman 

diversion dam (RM 42.0 to RM 52.0). Chinook salmon spawning does not occur in the 

lower Merced River downstream of the Highway 59 bridge (RM 42.0) or in the lower 

San Joaquin River downstream of the Merced River confluence. The lowermost 42 miles 

of the Merced River and the San Joaquin River from the Merced River confluence 

downstream to the delta function primarily as a migration corridor for adult and juvenile 

Chinook salmon. Results of California DFW redd surveys conducted from 2001 through 

2004 indicate that approximately 45 to 80 percent of redds observed in the Merced River 
113

occurred between RM 45.2 and RM 52.0. Additional habitat characteristics for Chinook 

salmon in the lower Merced River are described later in the Fish Habitat subsection.

Figure 3-23. Estimated fall-run Chinook salmon escapement in the Merced River from 

1970 through 2010, showing fish of natural and hatchery origin for years 

1981through 2007. The dashed line shows the estimated percentage of 

hatchery-origin fish in the aggregate escapement, as estimated by Mesick 

(2010) (Source: California HSRG, 2012).

The Pacific Fisheries Management Council has designated the Merced River 

downstream of Crocker-Huffman diversion dam as EFH for Chinook salmon spawning, 

rearing, and migration. 

Hardhead: The hardhead (Mylopharodon conocephalus) is a large member of the 

minnow family that is native to California. It is generally found in larger low- to middleelevation streams in the Sacramento and San Joaquin Watersheds. California DFW 

considers it a species of special concern. The hardhead has been documented in the 

Merced River upstream of Lake McClure and downstream of Crocker-Huffman diversion 

dam (Stillwater Sciences, 2008). It inhabits deep pools and runs with slow velocities and 

prefers water temperatures between 75.2 and 82.4°F (24.0 to 28.0°C) (Moyle, 2002). 

This species can tolerate warmer water temperatures than salmonids, and it occupies a 

transitional zone where distribution overlaps with both warmwater and coldwater fish 

species (Moyle, 2002). Moyle (2002) reports that the hardhead has relatively poor 

swimming ability at low temperatures, which keeps it from surmounting velocity barriers 

that are passable by salmonids. It spawns primarily in April and May, but spawning may 
114

extend into August in some streams (Moyle, 2002). Spawning behavior has not been 

documented and water temperature tolerances for spawning adults, eggs, and larvae are 

unknown. In the 2006 to 2008 fish surveys, the hardhead was relatively abundant both 

upstream and downstream of the project, comprising 7.8 percent and 8.3 percent of the 

total fish abundance in the upper Merced River and lower Merced River, respectively. 

Hardhead observed in the lower Merced River surveys ranged from young-of-the-year to 

approximately age 2+. 

Sacramento splittail: The Sacramento splittail (Pogonichthys macrolepidotus) is a 

native minnow found in estuarine habitats and low-elevation rivers in the SacramentoSan Joaquin River systems. California DFW considers it a species of special concern. 

During periods of high spring river flow, adult splittail can migrate long distances 

upstream from the Sacramento-San Joaquin Delta to spawn on inundated floodplains, 

including those in the lower reaches of San Joaquin River tributaries. Adults migrate 

upstream during winter and spring, and most spawning occurs in March and April in 

areas of flooded vegetation. The Sacramento splittail is tolerant of high salinity (up to 29 

parts per thousand) and low DO (less than 1 mg/L), and it is typically found in water 

temperatures ranging from 41 to 75°F (5.0 to 23.8°C) (Moyle, 2002). This species was 

observed in the lower Merced River during spring fish surveys in 2007 and 2008 between 

the San Joaquin River confluence and RM 26.6 (Stillwater Sciences, 2008). Sacramento 

splittail observed in the lower Merced River surveys ranged from 7.9 to 14.8 inches (201 

to 375 mm) in length and were likely adult fish in the 2+ through 5+ age classes, 

according to the age/length relationships from Moyle (2002).

Fish Habitat—Aquatic habitat conditions in the Merced River between Merced 

Falls dam and Crocker-Huffman diversion dam and in the reaches downstream of 

Crocker-Huffman diversion dam are heavily influenced by the upstream dams and by 

water withdrawals at and downstream of Crocker-Huffman diversion dam. The river 

between Merced Falls dam and Crocker-Huffman diversion dam is deep and confined 

between its banks with highly variable flows (100 cfs to 10,000 cfs), resulting in highly 

variable aquatic habitat conditions and a relatively low fish species diversity. 

Downstream of Crocker-Huffman diversion dam, reduced instream flows, land use 

activities such as mining and agriculture, instream dredging, and other factors have 

degraded spawning, rearing, and migratory habitat for anadromous salmonids in the 

Merced River and migratory habitat in the San Joaquin River. The combined effects of 

gold dredging, flow regulation, elimination of coarse sediment supply by dams, and land 

use developments have converted the Merced River’s primary spawning reach (RM 42.0 

to RM 52.0) from a historically complex, multiple-channel system to a simplified, singlethread system with a narrow floodplain adjacent to the channel. Lack of coarse sediment 

supply caused by instream mining and capture in upstream reservoirs has produced a 

channel characterized by long deep pools that are scoured to bedrock or to a coarse, 

armored cobble layer. Resulting conditions include reduced riparian vegetation, 

increased sedimentation from adjacent land uses, reduced spawning gravel recruitment, 

and degraded water quality. In and downstream of the primary spawning reach, habitat 
115

alterations have reduced habitat suitability for salmonids and other native fishes while 

creating a hospitable environment for introduced fishes, including predatory fish such as 

black bass. Numerous habitat restoration and gravel augmentation projects have been 

implemented in the primary spawning reach to restore and enhance spawning and rearing 

conditions for salmonids and reduce habitat suitability for introduced fish. Between 1990 

and 2010, approximately 11,706 tons of gravel were added to the main augmentation site 

immediately downstream of Crocker-Huffman diversion dam.

Suitable habitat for salmonids and many other native fish species is currently

concentrated in the reach extending from Crocker-Huffman diversion dam downstream to 

approximately RM 45.0. Surveys conducted in 2003 and 2004 identified approximately 

19 percent of the total wetted main and secondary channel areas in this reach as likely 

high quality salmonid rearing habitat (Stillwater Sciences, 2006). Backwaters and riffle 

margins provide complex habitat and velocity refuge for rearing salmon in this reach, and 

instream rooted aquatic vegetation provides cover for rearing salmonids. Small woody 

debris and overhanging vegetation, as well as cobble, boulders, and small amounts of 

large woody provide rearing cover. 

Merced ID evaluated the relationships between flow and fish habitat (1) in the 

Merced River from Merced Falls dam to Crocker-Huffman diversion dam, and (2) from 

Crocker-Huffman diversion dam (RM 52.0) to Shaffer Bridge (RM 32.8) using the onedimensional Physical Habitat Simulation Model (PHABSIM). Merced ID evaluated 

habitat suitability at several flows for a suite of species in each study reach using existing 

criteria or criteria developed for the study. 

In the reach between Merced Falls dam and Crocker-Huffman diversion dam, 

habitat conditions were measured at four flows (265 cfs, 780 cfs, 2,120 cfs, and 3,150 

cfs) at 19 transects in the 1.26-mile riverine (i.e., flowing) section immediately 

downstream of Merced Falls dam and 6 transects in the 1.74-mile impoundment section 

located in the slow-flowing portion of the reach immediately upstream of CrockerHuffman diversion dam. Four of the six fish species documented in the reach were 

divided into two guilds based on habitat preference: a lamprey guild (Pacific lamprey 

and Kern brook lamprey) and a sculpin guild (riffle sculpin and prickly sculpin). The 

other two study species in the reach were rainbow trout and Sacramento sucker. 

Species in the riverine sub-reach between Merced Falls dam and Crocker-Huffman 

diversion dam displayed a typical trend in weighted usable area (WUA) for all life stages 

where habitat suitability is lowest at very low flows, rises to a peak, and then decreases 

gradually or flattens out as flows increase. For fry, juvenile, and adult rainbow trout 

(figure 3-24) and juvenile Sacramento sucker (figure 3-25), habitat continues to gradually 

increase at very high flows. This second rise in habitat may be a result of flow 

overtopping low banks at certain transects and recruiting new habitat, or it may be an 

artifact of the model, in which modeled low velocities along the stream margin are 

unrealistically propagated as flows increase. The WUA trends are a direct function of the 
116

channel forms (i.e., low floodplain elevations) and vegetated stream margins (i.e., low 

margin velocities) measured in this section of the Merced River. 

Figure 3-24. Habitat suitability (weighted usable area) for all rainbow trout life stages in 

the riverine sub-reach downstream of Merced Falls dam (Source: Merced 

ID, 2014a).
117

Figure 3-25. Habitat suitability (weighted usable area) for the lamprey guild, Sacramento 

sucker, and sculpin guild in the riverine sub-reach downstream of Merced 

Falls dam (Source: Merced ID, 2014a).

In the impoundment sub-reach between Merced Falls dam and Crocker-Huffman 

diversion dam, the WUA trend for many species’ life stages is atypical, remaining 

relatively flat as flows increase. Adult and juvenile rainbow trout, lamprey ammocoete, 

and the sculpin guild are the exceptions. The habitat area for adult and juvenile rainbow 

trout is greatest from 500 to 1,500 cfs and declines at higher flows (figure 3-26). The 

habitat area for lamprey ammocoetes is greatest at the lowest flow modeled (194 cfs), 

declines until flows reach 2,750 cfs, then stabilizes and remains relatively constant at 

higher flows (figure 3-27). The habitat area for the sculpin guild rises to a peak at 1,750 

cfs and decreases gradually thereafter. At approximately 3,000 cfs, water overtops the 

banks in the lower portion of the impoundment and additional shallow, low-velocity 

habitat becomes available. As a result, the habitat area shows an increase at high flows 

for rainbow trout fry and juvenile, lamprey ammocoete, and Sacramento sucker juvenile 

life stages. However, Merced ID states that the observed increase in habitat for these life 

stages at very high flows could also be an artifact and limitation of the model, in which 

modeled low velocities along the stream margin are unrealistically propagated as flows 

increase.
118

Figure 3-26. Habitat suitability (weighted usable area) for rainbow trout, in the 

impoundment sub-reach downstream of Merced Falls dam (Source: 

Merced ID, 2014a). 
119

Figure 3-27. Habitat suitability (weighted usable area) for lamprey ammocoete, 

Sacramento sucker juvenile and adult, and sculpin guild juvenile and adult 

in the impoundment sub-reach downstream of Merced Falls dam (Source: 

Merced ID, 2014a).

Downstream of Crocker-Huffman diversion dam, the study area included three 

sub-reaches from Crocker-Huffman diversion dam (RM 52.0) downstream to Shaffer 

Bridge (RM 32.8) with a total of 65 PHABSIM transects. Sub-reach 1extends from 

RM 32.8 to 42.0, sub-reach 2 extends from RM 42.0 to 46.4, and sub-reach 3 extends 

from RM 46.4 to 52.0. Hydraulic simulations were conducted for flows ranging from 74 

to 5,823 cfs (Merced ID, 2013a). The study included (1) a 1-dimensional PHABSIM 

analysis of flow-habitat relationships for steelhead, fall-run Chinook salmon, hardhead, 

and Sacramento splittail, (2) an analysis incorporating the PHABSIM and water 

temperature modeling results, and (3) an evaluation of the relationship between river 

discharge and hydraulic connectivity with off-channel areas that provide habitat for 

predatory black bass (Merced ID, 2013a). 

For most species and life stages, WUA results downstream of Crocker-Huffman 

diversion dam showed a bimodal pattern with distinct maxima in the amount of usable 

habitat at flows within active channel discharges and at much higher flows that overtop 

the banks and inundate floodplains (Merced ID, 2013a). For example, the peak habitat 
120

area for steelhead and Chinook salmon generally occur at flows < 500 cfs and > 3,000 cfs 

with some variations depending on life stage and sub-reach (figures 3-28 through 3-36). 

For lower flows in the range of the active channel discharge, reach-averaged discharges 

that produce the maximum amount of habitat ranged from approximately 90 cfs (i.e., 

steelhead and Chinook fry) to greater than 520 cfs (i.e., steelhead spawning). Merced ID 

surmised that the bimodal character of the WUA functions was likely caused by a 

significant increase in habitat recruitment when flows inundated the vegetated riparian 

zones, and in sub-reach 2 (RM 42.0 to RM 46.4) when flows inundated the expansive 

engineered floodplain (figures 3-28 and 3-29). On inundated floodplains in particular, 

water velocities stay low and depths often do not exceed suitability criteria.

Figure 3-28. Habitat suitability (weighted usable area) for steelhead in sub-reach 1 

downstream of Crocker-Huffman diversion dam (Source: Merced ID, 

2014a).
121

Figure 3-29. Habitat suitability (weighted usable area) for Chinook salmon in sub-reach 

1 downstream of Crocker-Huffman diversion dam (Source: Merced ID, 

2014a).
122

Figure 3-30. Habitat suitability (weighted usable area) for hardhead and Sacramento 

splittail in sub-reach 1 downstream of Crocker-Huffman diversion dam

(Source: Merced ID, 2014a).

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

80,000

90,000

100,000

0 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 5500 6000 WUA per 1000 linear feet

Discharge (cfs)

Merced River Sub-Reach 1

Hardhead and Splittail - DRAFT

Hardhead Adult Hardhead Juvenile Splittail Juvenile Splittail Adult Spawning
123

Figure 3-31. Habitat suitability (weighted usable area) for steelhead in sub-reach 2 

downstream of Crocker-Huffman diversion dam (Source: Merced ID, 

2014a).
124

Figure 3-32. Habitat suitability (weighted usable area) for Chinook salmon in sub-reach 

2 downstream of Crocker-Huffman diversion dam (Source: Merced ID, 

2014a).
125

Figure 3-33. Habitat suitability (weighted usable area) for hardhead and Sacramento 

splittail in sub-reach 2 downstream of Crocker-Huffman diversion dam

(Source: Merced ID, 2014a).

0

20,000

40,000

60,000

80,000

100,000

120,000

140,000

160,000

180,000

200,000

0 500 1,000 1,500 2,000 2,500 3,000 3,500 4,000 4,500 5,000 5,500 6,000

WUA per 1000 linear feet

Discharge (cfs)

Hardhead Adult Hardhead Juvenile Sacramento Splittail Juvenile Splittail Adult Spawning
126

Figure 3-34. Habitat suitability (weighted usable area) for steelhead in sub-reach 3 

downstream of Crocker-Huffman diversion dam (Source: Merced ID, 

2014a).
127

Figure 3-35. Habitat suitability (weighted usable area A) for Chinook salmon in subreach 3 downstream of Crocker-Huffman diversion dam (Source: Merced 

ID, 2014a).
128

Figure 3-36. Habitat suitability (weighted usable area) for hardhead and splittail in subreach 1 downstream of Crocker-Huffman diversion dam (Source: Merced 

ID, 2014a).

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

80,000

0 500 1,000 1,500 2,000 2,500 3,000 3,500 4,000 4,500 5,000 5,500 6,000 6,500

WUA per 1000 linear feet

Discharge (cfs)

Hardhead Adult Hardhead Juvenile Sacramento Splittail Juvenile Splittail Adult Spawning
129

Evaluation of the effects of water temperature on usable habitat indicated that 

significant reductions in habitat suitability for Chinook salmon and steelhead occurred 

downstream from Crocker-Huffman diversion dam as a result of increasing water 

temperatures. Water temperature thresholds for all steelhead and Chinook salmon life 

stages (EPA, 2003) were exceeded in at least 1 month at Crocker-Huffman diversion 

dam. At the Shaffer Bridge evaluation point, more than 40 percent of months analyzed 

showed habitat reductions of 50 percent or greater. The spawning life stages, which are 

the most sensitive to elevated water temperatures, showed the most significant reduction 

in habitat suitability. Water temperature thresholds for Chinook salmon spawning were 

exceeded 100 percent of the time in September and October at all hydrologic nodes from 

Crocker-Huffman diversion dam downstream to Shaffer Bridge, resulting in no suitable 

spawning habitat during these months (Merced ID, 2013a). Suitable temperatures for 

Chinook salmon spawning were achieved only 10 to 14 percent of the time in November, 

equating to a loss of usable habitat of 86 to 90 percent during the peak month for 

spawning. Temperature thresholds for steelhead spawning in March and April were 

exceeded approximately half of the time, effectively reducing usable spawning habitat by 

about 50 percent during the peak steelhead spawning period (Merced ID, 2013a). 

Habitat for black bass, which often occupy off-channel and backwater habitat 

(e.g., abandoned dredger mining pits), became connected to the main channel 

downstream of Crocker-Huffman diversion dam at a range of flows. Of 79 potential offchannel bass habitat units identified, 12 were hydraulically connected to the main channel 

at the maximum discharge that occurs from Crocker-Huffman diversion dam during a 

normal water year (2,236 cfs)

24 (Merced ID, 2013a). Nine of the 12 off-channel units had 

connections occur at discharges of 700 cfs or higher and were connected up to 40 percent 

of the time for each month on record. Three of the 12 off-channel units had connections 

established at flows less than 369 cfs and a range of inundation frequency from 18 

percent in the summer to 77 percent in May (Merced ID, 2013a). Salmon fry, juveniles, 

and smolts may be more vulnerable to predation where and when the off-channel habitats 

that support high densities of predatory black bass become hydraulically connected to the 

main channel habitats used by rearing and out-migrating salmonids. Under these 

circumstances, predation rates are elevated because: (1) the bass from the off-channel 

habitats gain access to the main channel habitats used by salmonids, and (2) salmonids 

can enter and become trapped in the off-channel habitats where bass densities are high. 

Elevated water temperature is a primary factor that can limit in-river and hatchery 

Chinook salmon production in the Merced River. As discussed earlier in this section 

under Water Quality, the lower Merced River is on the CWA 303(d) list as impaired for 

temperature. Merced ID compared water temperature monitoring data collected from 

1991 through 2010 at seven locations between RM 52.0 and RM 13.0 with the U.S. 

 

24 Based on historical gage data from water year 1969 to 2006. 
130

Environmental Protection Agency’s (EPA) (2003) recommended 7-day average daily 

maximum water temperature criteria for salmonids to evaluate the frequency with which 

the criteria were exceeded for each fall-run Chinook salmon life stage. Merced ID’s 

conclusions regarding existing conditions were: 

 During the October through December upstream migration period, the 

18.0°C (64.4°F) criterion for adult salmon migration was exceeded 4 to 10 

percent of the time at locations between RM 52.0 and RM 33.0, and 23 

percent of the time at RM 13.0. 

 During the October through March spawning and incubation period, the 

13.0°C (55.4°F) criterion to protect salmon spawning, incubation, and fry 

emergence life stages was exceeded 39 to 54 percent of the time between 

RM 52.0 and RM 13.0.

 During the January through May juvenile rearing, emigration, and 

smolting period, the 16.0°C (60.8°F) juvenile rearing criterion was not 

exceeded at any location during January, and in February it was exceeded 

only at RM 41.9 (3 percent of the time) and RM 13.0 (8 percent of the 

time). From March through May, the 16.0°C (60.8°F) juvenile rearing 

criterion was exceeded at RM 46.3 and all locations downstream from 4 to 

90 percent of the time. The juvenile rearing criterion was never exceeded 

at RM 52.0 during the January through May evaluation period.

 During the January through May juvenile rearing, emigration, and 

smolting period, the 15.0°C (59.0°F) smoltification criterion was exceeded 

in January only at RM 41.9 (1 percent of the time). In February, the 

15.0°C (59.0°F) criterion was exceeded at RM 44.2 and downstream 

locations from 4 to 15 percent of the time. In March and April, the 15.0°C 

(59.0°F) criterion was exceeded at RM 46.3 and all downstream locations

from 20 to 81 percent of the time. In May, the 15.0°C (59.0°F) 

smoltification criterion was exceeded at all locations from 12 to 100 

percent of the time.

Low DO levels can also reduce habitat suitability for salmonids and other 

coldwater fish species. Merced ID monitored DO in summer and fall 2010 between 

Merced Falls dam and Crocker-Huffman diversion dam and in summer and fall 2011 

downstream of Crocker-Huffman diversion dam to evaluate compliance with Basin Plan 

objectives (Merced ID, 2012c). Results of DO monitoring, including the frequency of 

compliance with Basin Plan objectives for salmonids and other coldwater fishes, are 

discussed in the Water Quality subsection. 
131

Aquatic Invertebrates 

Merced River Project

No known studies or reports regarding aquatic invertebrates in Lake McClure or 

McSwain reservoir are available. The USGS monitors and reports accounts of invasive 

mollusk species as part of the nonindigenous aquatic species information program and 

provides real-time updates on its website (USGS, 2013). Invasive mollusk species 

identified by the nonindigenous aquatic species website include Asian clam (Corbicula 

fluminea), quagga mussel (Dreissena rostriformis bugensis), zebra mussel (Dreissena

polymorpha), and New Zealand mud snail (Potamopyrgus antipodarum). According to 

the nonindigenous aquatic species website, there are no reported accounts of these 

species within the Merced River Project boundaries.

Merced Falls

A benthic macroinvertebrate (BMI) study was previously conducted by Stillwater 

Sciences (2008) downstream of the project. This study sampled BMIs in fall 2006, 

spring/summer 2007, and fall 2007 approximately 1.5 miles downstream of the dam. 

Using multi-habitat composite samples, and using several metrics, including measures of 

Ephemeroptera, Plecoptera, and Trichoptera (EPT taxa) (the orders of insects—noted to 

be intolerant of impaired water quality and degraded habitat) and percent collectors and 

filterers among BMIs, the study found the sample site to be healthy, comparable to other 

sites at similar elevations. Noteworthy results from this study were that New Zealand 

mudsnails were absent from this reach, and the BMI index trends showed no obvious 

community impairment from water management.

Lower Merced River

BMI from the lower Merced River have been the subject of studies designed to 

evaluate the associations between invertebrate assemblages and environmental variables 

in a broad-scale ecoregion analysis by Brown and May (2000) and in an analysis focused 

on San Joaquin river tributaries (Markiewicz et al., 2003). Other studies were directly 

intended to monitor BMI in the lower Merced River to establish baseline conditions 

related to restoration projects (Stillwater Sciences 2008, 2006). These studies used BMI

from the orders Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera 

(caddisflies) (EPT) as a metric to indicate environmental conditions. EPT taxa are 

considered intolerant of water quality impairment and habitat degradation (Barbour et al., 

1999). 

Results from these studies show EPT taxa to be present at all sites sampled in the 

lower Merced River. Brown and May (2000) found a combined total of 20 BMI taxa at 

two lower Merced River sites, including seven EPT taxa. Markiewicz et al. (2003) 

reported that two upstream sampling sites in the lower Merced River (at the Highway 59 

bridge [RM 42.0] and the Oakdale Road bridge [RM 32.4]) recorded the highest overall 

percent EPT scores when compared with other San Joaquin River tributary sampling sites 
132

in the study. The study also showed that the Oakdale Road site, located downstream of 

an agricultural drainage (Ingalsbe Slough), had higher percent insect and percent

amiphipod scores than the upstream site, suggesting little or no degradation from the 

slough. The downstream-most site sampled, located at Hatfield Park (RM 1.4) showed a 

considerable portion of the BMI community was composed of EPT and other insects. 

These results suggest that the water quality impairment of the lower Merced River due to 

pesticides, unknown toxicity, and water temperature25 was not severe enough to exclude 

these taxa. 

Combined results of the baseline monitoring studies conducted between 2005 and 

2008 from RM 53.5 (1.5 miles downstream of the Merced Falls dam) downstream to 

RM 1.0 showed that total taxonomic richness ranged from 16 to 55 taxa, and the number 

of EPT taxa ranged from 4 to 22. Species composition showed low inter‐site variability 

and no upstream to downstream trends in richness, composition, or tolerance metrics. 

Tolerance metrics indicated moderately tolerant BMI assemblages. At least two EPT 

taxa were included in the top five numerically dominant taxa at each monitoring site. In 

addition to their use as bioindicators, BMI are an essential component of the food web in 

aquatic habitats. They cycle nutrients in their aquatic environment by feeding on algae 

and organic detritus and by preying on a wide range of small organisms and are an 

important food resource for fish, amphibians, reptiles, birds, and mammals. The 

Stillwater Sciences (2006) study showed that the majority of dominant taxa observed 

were likely available as a food source for juvenile Chinook salmon.

There are no known studies or surveys in the lower Merced River specifically 

targeting mollusks. However, mollusks have been identified in most of the BMI 

sampling dating back to 1994. Bivalves collected in the lower Merced River include the 

Asian clam, western pearlshell mussel, and fingernail clam (Pisidium sp.). Gastropods 

collected include the ancylid snail (Ferrissia sp.), ram’s horn snails (Hilisoma sp. and 

Planorbella sp.), sprite snail (Menetus sp.), gyro snail (Gyraulus sp.), and Physa sp.

(Brown and May, 2000; Stillwater Sciences, 2008, 2006). Of these, only the Asian clam 

is considered an invasive species (Sousa et al., 2008). 

Although the New Zealand mud snail was not documented in BMI studies in the 

lower Merced River, the nonindigenous aquatic species monitoring program lists four 

records of New Zealand mud snail occurring in the lower Merced River from 2010 

through 2013, all of which are located between Crocker-Huffman diversion dam (RM 

52.0) and the Highway 59 bridge (RM 42.0) (USGS, 2013).

 

25 The Merced River, including the project reservoirs and the river downstream of 

the project, is on the 2010 EPA 303(d) list of water quality limited segments due to 

pollution by pesticides, unknown toxicity, and water temperature (see Water Quality).
133

3.3.1.2 Environmental Effects

Merced River Project 

Coordination between Resource Agencies and Stakeholders 

Merced ID proposes to establish a Merced River Anadromous Fish Committee to 

include, by invitation, representatives from NMFS, FWS, California DFW, the Water 

Board, and a non-governmental organization member selected by Merced ID that would 

participate at its own expense. Merced ID would organize four committee meetings each 

year to review the results of draft annual reports pertaining to Chinook salmon and 

O. mykiss downstream of Crocker-Huffman diversion dam and to identify potential 

modifications to monitoring methods and protocols (excepting monitoring duration), as 

follows:

 March—Review draft adult monitoring study; review flow and temperature 

history and projections.

 May—Evaluate and complete adult monitoring report in preparation for 

the following fall monitoring; review temperature history and emigration 

monitoring results and late-spring temperature conditions.

 August—Review draft juvenile monitoring study; finalize fall monitoring; 

discuss finalization of juvenile monitoring plan, including plans for the 

following winter-spring monitoring.

 October—Finalize juvenile monitoring annual report and identify any 

modifications to the following winter-spring monitoring, including 

implementation approach.

BLM specifies in preliminary 4(e) condition 2 that Merced ID form a consultation 

group that meets four times a year to discuss resource plans, monitoring, and projectrelated issues within and outside BLM’s jurisdiction that are not addressed in the annual 

meeting, and the implementation of license conditions affecting BLM-managed land. 

BLM also specifies that the group should establish mutually agreeable guidelines for 

conducting effective and efficient meetings. The Water Board specifies in preliminary 

WQC condition 1 that Merced ID organize an anadromous fish committee. NMFS [10(j) 

recommendation 7] recommends Merced ID establish an anadromous fish committee 

similar to that proposed, but adds that a technical advisory plan should be established that 

defines membership, meeting responsibilities, ground rules for consensus-based decision 

making, and a process for implementing the decisions. FWS [10(j) recommendation 5] 

recommends that Merced ID establish a technical advisory committee that would provide 

study plan and fishery report oversight and approve entities conducting field work. 

California DFW [10(j) recommendation 1] recommends that Merced ID establish a 

Merced ecological resource committee to review and evaluate implementation of license 

measures and monitoring plans and results; the committee would meet quarterly for at 

least the first 5 years of a new license, and would not be restricted to anadromous fish. 
134

Similarly, the Conservation Groups recommend the establishment of an ecological 

resource group that meets at least annually to discuss monitoring reports and plans. 

Our Analysis

The topics proposed for discussion by Merced ID at each of the four annual 

meetings illustrate the complexity of balancing multiple variables to achieve satisfactory 

environmental protection and enhancement while meeting a primary purpose of the 

project, which is to supply water for irrigation. Proposed and recommended flow 

releases and measures to provide suitable temperatures for salmonids downstream of 

Crocker-Huffman diversion dam require balancing many factors, including the water year 

type (which could change during the course of a year); the volume of cold water in Lake 

McClure that can be used for downstream temperature moderation (which varies from 

year to year); and the total volume of water in Lake McClure that can be used by 

irrigators. Balancing also requires interpreting the results of monitoring studies of 

incoming adult and outmigrating juvenile salmonids to assess the effectiveness of 

ongoing measures. Establishing a committee to assess ongoing study results and project 

operations would provide an effective forum for making decisions regarding future 

project operations within the constraints of a new license. 

Providing a framework within which a committee operates would help to ensure 

that meetings are conducted in an orderly manner and make productive use of 

participants’ time. We agree that establishing a technical advisory plan or process 

guidelines, as NMFS recommends and BLM specifies, that defines membership 

attributes, including the selection of an appropriate non-governmental organization 

representative, ground rules for decision making, and a process for implementing 

decisions would provide a useful framework within which the committee could 

effectively operate. 

Merced ID proposes, NMFS recommends, and the Water Board specifies that the 

role of the technical committee be restricted to topics pertaining to anadromous fish. 

FWS expands the scope of the committee by recommending that the committee focus on 

fisheries topics, which could include anadromous and resident fish. California DFW and 

the Conservation Groups expand the scope further by including all ecological studies and

monitoring as topics to be addressed by the committee. BLM broadens the scope to 

include issues that could affect BLM-managed land but are not covered during its 

specified annual consultation (discussed in section 3.3.2.2, Terrestrial Resources). As 

previously discussed, many of the environmental measures associated with this project 

focus on enhancing habitat for anadromous fish downstream of Crocker-Huffman 

diversion dam. Consequently, we expect the primary topic at any technical committee 

meeting to be related to anadromous fish. However, actions related to flows and 

maintaining downstream water temperatures would also have a bearing on the 

management of the water levels in Lake McClure, which would influence the resident 

fish community and adjacent riparian and wetland habitat. We conclude that having the 

committee focus exclusively on anadromous fish could preclude appropriate discussions 
135

of inter-related resident fish and other ecological topics. Such additional discussions by a 

committee could also potentially include issues that could have a direct or indirect effect 

on BLM-managed land, such as recreational facilities. 

Coordinated Operation between the Merced River and Merced Falls Projects

Flows released from the Merced River Project for environmental and irrigation 

purposes must pass through the Merced Falls Project before reaching the irrigation 

diversion point at Crocker-Huffman diversion dam. Although the Merced Falls Project 

operates in a run-of-river mode, where inflow to the project equals outflow, there are 

circumstances that could occur, such as routine maintenance events, that could have a 

bearing on the multi-purpose releases from Crocker-Huffman diversion dam to the lower 

Merced River and irrigation flows into the Main Canal.

Merced ID proposes to develop and implement a coordinated operation plan for 

the Merced River and Merced Falls Projects to assure implementation of flow-related 

measures at the two projects. Merced ID would develop the plan in consultation with the 

licensee of the Merced Falls Project and would file it with the Commission within 1 year 

of license issuance. BLM [preliminary 4(e) condition 4] specifies that Merced ID 

develop the proposed plan, but adds BLM, FWS, California DFW, the Park Service, 

NMFS, and the Water Board to the list of consulted entities as interested parties to project 

flow-related measures. BLM also specifies that the plan be provided to the consulted 

agencies, and filed with the Commission within 90 days of license issuance. California 

DFW [10(j) recommendation 2] recommends that Merced ID develop the proposed plan 

and file it with the Commission, California DFW, the Water Board, FWS, and NMFS 

within 90 days of license issuance.

Our Analysis

As indicated in the previous section, releases from the Merced River Project at 

McSwain dam are intended to fulfill a balanced approach to meeting the complex needs 

of both irrigators and anadromous fish. Achieving the intended goals of releases from 

McSwain dam rely on passing those flows in a consistent run-of-river mode from the 

Merced Falls Project. A coordinated operation plan for the Merced River and Merced 

Falls Projects would document the process by which flows released at McSwain dam 

would be available for intended purposes at Crocker-Hoffman diversion dam. Although 

developing this plan is likely to entail technical discussions about the fine points of 

project operation, inviting interested parties to provide input on the draft plan could 

provide valuable insights that enhance its effectiveness.

Protecting Water Quality and Aquatic Habitat from Erosion during Project 

Construction, Operation, and Maintenance

Construction of new recreation facilities, modification of existing recreation 

facilities, or other ground-disturbing activities could increase soil erosion and fine 

sediment delivery to project waterways. Fine sediment can adversely affect water quality 
136

and associated aquatic habitat by increasing turbidity and total suspended solids. 

Accumulation of fine sediment in aquatic substrate can adversely affect fish spawning 

success and limit habitat suitability for many aquatic invertebrates.

Merced ID proposes to develop an erosion control and restoration plan in 

consultation with BLM for erosion and restoration actions carried out by Merced ID on or 

affecting BLM land that is in or adjacent to the project boundary. Merced ID would file 

the BLM-approved plan with the Commission at least 90 days in advance of initiating 

construction of recreation or other project facilities. Merced ID indicated that the plan 

was not included in the license application because Merced ID expected the plan to be 

specific for work approved by the Commission in any new license issued, which would 

not be known until the Commission issues a new license and would be specific regarding 

the construction approach proposed by Merced ID’s contractor. 

The Water Board includes the following measures pertaining to the protection of 

water quality and aquatic habitat from erosion and sedimentation in its preliminary WQC 

conditions:

 Preliminary WQC condition 23: Control measures for erosion, excessive 

sedimentation and turbidity should be implemented and in place at the 

commencement of and throughout any ground clearing activities, excavation, or 

any other project activities that could result in erosion or sediment discharges to 

surface waters. Erosion control blankets, liners with berms, and/or other erosion 

control measures should be used for any stockpile of excavated material to control 

runoff resulting from precipitation, and prevent material from contacting or 

entering surface waters.

 Preliminary WQC condition 24: Waters should be free of changes in turbidity 

(due to project activities) that cause nuisance or adversely affect beneficial uses. 

Increases in turbidity attributable to project controllable water quality factors 

should not exceed the limits in the Central Valley Basin Plan. 

BLM preliminary 4(e) condition 5 is identical to Merced ID’s proposed measure. 

No other entity filed measures pertaining to erosion and sedimentation control.

Our Analysis 

Merced ID proposes to rehabilitate and construct new recreation facilities at Lake 

McClure and McSwain reservoir (see table 3-24 under Implementation Schedule for 

Recreation Enhancements). Such construction is likely to require ground-disturbing 

activities that if left unchecked, could result in erosion and associated water quality and 

habitat degradation to the project reservoirs and, potentially, reaches downstream of New 

Exchequer and McSwain dams. Developing Merced ID’s proposed erosion control and 

restoration plan, in consultation with appropriate agencies, and providing it to the 

Commission for approval at least 90 days prior to initiating ground-disturbing activities 

could serve as an effective tool to minimize potential erosion and sedimentation. We 

recognize that each ground-disturbing activity that may be approved by the Commission 
137

in a new license would require site-specific erosion control measures that consider local 

topography and soils. Such details are typically incorporated into the final design for 

ground-disturbing activities. Review and approval of such final designs, including 

proposed erosion control measures, by agencies and the Commission would provide 

appropriate oversight of site-specific erosion control techniques. 

However, Merced ID provides no details regarding what would be included in its 

proposed plan for each ground-disturbing activity. Consequently, we have no basis to 

conclude whether or not this proposed measure would be effective in controlling erosion. 

An effective erosion control and restoration plan could include the following: (1) a 

description of BMPs for erosion control that would be applied in specific circumstances; 

(2) provisions for inspecting erosion control measures while they are in place; (3) 

emergency protocols for erosion and sedimentation control (e.g., steps that would be 

taken if control measures fail during a storm event); (4) techniques that would be used to 

stabilize sites once construction is completed; and (5) a description of when and what 

type of water quality monitoring of surface waters would occur during and after grounddisturbing activities. Identifying such measures and protocols in the proposed erosion 

control and restoration plan would assure that erosion does not unacceptably degrade 

water quality adjacent to construction and other ground-disturbance sites. We note that 

Merced ID’s proposed Vegetation Management Plan (discussed in section 3.3.2.2, 

Terrestrial Resources) includes provisions for identifying and protecting sensitive areas, 

including riparian zones and wetlands, and revegetation and monitoring of disturbed sites 

following completion of construction and other ground-disturbing activities. 

Any ground-disturbing activity, including non-routine maintenance, has the 

potential to result in erosion and sedimentation. By replacing its original measure with 

BLM preliminary 4(e) condition 5, Merced ID has appropriately expanded the scope to 

include all construction and non-routine maintenance activities that could result in ground 

disturbance to ensure water quality and aquatic habitat are protected from sedimentation 

caused from erosion. However, it still would restrict the plan to activities on BLMmanaged land. Any project-related ground-disturbing activities have the potential to 

cause erosion and sedimentation. Consequently, site-specific erosion control plans would 

be appropriate for activities anywhere within the project boundary, not just on BLMmanaged land. 

Merced ID proposes to develop its proposed erosion control and restoration plan in 

consultation with BLM. Erosion has the potential to influence both aquatic and terrestrial 

resources. Consultation with the Water Board, California DFW, and FWS, in addition to 

BLM, would provide a reasonable balance of input regarding appropriate erosion control 

measures. 
138

Protecting Water Quality from Contaminants during Project Construction, 

Operation, and Maintenance

Construction of new project facilities, modification of existing project facilities, 

and routine and non-routine maintenance could affect water quality if pollutants (e.g., 

fuels, lubricants, herbicides, pesticides, and other hazardous materials) are discharged 

into project waterways.

To minimize potential contamination of project waters, Merced ID proposes to 

develop a recreation facilities hazardous material spill prevention, control, and 

countermeasures plan (measure WR1) in consultation with appropriate agencies. Merced 

ID would file the plan with the Commission, including evidence of consultation, at least 

90 days in advance of initiating construction for recreation facilities. Merced ID 

indicated that the plan was originally not included in the license application because it 

expected the plan to be specific for work approved by the Commission in any new license 

issued, which would not be known until the Commission issues a new license, and would 

be specific regarding the construction approach proposed by Merced ID’s contractor.

The Water Board specifies the following measures pertaining to the protection of 

water quality and aquatic habitat in its preliminary WQC conditions:

 Preliminary WQC condition 25: (1) all imported riprap, rocks, and gravels 

used for construction within or adjacent to any watercourses should be prewashed; (2) wash water generated on-site should not contact or enter surface 

waters; and (3) wash water generated on-site should be contained and disposed 

of in compliance with state and local laws, ordinances, and regulations.

 Preliminary WQC condition 26: (1) construction material, debris, spoils, soil, 

silt, sand, bark, slash, sawdust, rubbish, steel, or other inorganic, organic, or 

earthen material, and any other substances from any project-related activity 

should be prevented from entering surface waters; (2) all construction debris 

and trash should be contained and regularly removed from the work area to the 

staging area during construction activities; and (3) upon project completion, all 

project-generated debris, building materials, excess material, waste, and trash 

should be removed from all the project sites for disposal at an authorized 

landfill or other disposal site in compliance with state and local laws, 

ordinances, and regulations.

 Preliminary WQC condition 27: (1) no unset cement, concrete, grout, 

damaged concrete, concrete spoils, or wash water used to clean concrete 

surfaces should contact or enter surface waters; (2) any area containing wet 

concrete should be completely bermed and isolated with a berm constructed of 

sandbags or soil and lined with plastic to prevent seepage; (3) no leachate from 

truck or grout mixer cleaning stations should percolate into project area soils; 

(4) concrete trucks or grout mixers should be cleaned so that wash water and 

associated debris is captured, contained, and disposed of in compliance with 
139

state and local laws, ordinances, and regulations; (5) washout areas should be 

of sufficient size to completely contain all liquid and waste concrete or grout 

generated during washout procedures; and (6) hardened concrete or grout 

should be disposed at an authorized landfill, in compliance with state and local 

laws, ordinances, and regulations.

 Preliminary WQC condition 28: (1) all equipment should be washed prior to 

transport to the project site and be free of sediment, debris, and foreign matter; 

(2) any equipment used in direct contact with surface water should be steam 

cleaned prior to use; (3) all equipment using gas, oil, hydraulic fluid, or other 

petroleum products should be inspected for leaks prior to use and monitored 

for leakage; (4) stationary equipment (e.g., motors, pumps, and generators) 

should be positioned over drip pans or other types of containment; and (5) spill 

and containment equipment (e.g., oil spill booms, sorbent pads) should be 

maintained onsite at all locations where such equipment is used or staged. 

 Preliminary WQC condition 29: onsite containment for storage of chemicals 

classified as hazardous should be away from watercourses and include 

secondary containment and appropriate management as specified in California 

Code of Regulations, title 27, section 20320. 

Our Analysis 

Merced ID proposes to rehabilitate and construct new recreation facilities at Lake 

McClure and McSwain reservoir (see table 3-24 under Implementation Schedule for 

Recreation Enhancements). Such construction is likely to require the use of on-site 

hazardous materials and contaminants associated with construction equipment that if left 

unchecked, could result in water quality and habitat degradation to the project reservoirs 

and, potentially to reaches downstream of New Exchequer and McSwain dams. 

Developing Merced ID’s proposed site-specific hazardous materials spill prevention, 

control, and countermeasure plan, in consultation with appropriate agencies, and filing it 

with the Commission for approval at least 90 days prior to initiating any activities that 

could lead to water contamination could serve as an effective method for minimizing 

potential contamination of project waters. We recognize that each construction activity 

that may be approved by the Commission in a new license would require site-specific 

contaminant control measures that consider local topography, soils, and the specific 

equipment that would be used by Merced ID’s contractors. Such details are typically 

incorporated into the final design for activities involving potential water contamination. 

Review and approval of such final designs, including proposed contaminant control 

measures, by agencies and the Commission would provide appropriate oversight of sitespecific contaminant control techniques. 

However, Merced ID provides no details regarding what would be included in its 

proposed plan for each activity that may involve use of contaminants. Consequently, we 

have no basis to conclude whether or not this proposed measure would be effective in 

controlling the release of contaminants. An effective hazardous materials spill 
140

prevention, control, and countermeasure plan could include the following: (1) a 

description of the BMPs for contaminant control that would be applied in specific 

circumstances; (2) emergency protocols for spill containment and remediation; (3) the 

location of emergency cleanup equipment in the event of contaminant release; 

(4) identification of entities to be contacted in the event of a spill; (5) designated 

equipment refueling and maintenance areas; (6) provisions requiring equipment to be 

cleaned and inspected prior to entering a construction site to ensure it is in proper 

functioning condition; (7) post-spill water quality monitoring protocols to ensure 

remediation measures are effective; and (8) a listing of applicable local, state, and federal 

regulations that pertain to prevention of spills and protection of water quality. Identifying 

such measures and protocols would assure that surface water and groundwater are 

protected from contaminants. 

Any activity, not just those associated with recreation facility construction, 

involving heavy equipment, including non-routine maintenance, has the potential to 

release contaminants into project waters. In addition, maintenance of all project facilities 

typically requires on-site storage and use of hazardous materials. Expanding the scope of 

site-specific hazardous materials spill prevention, control, and countermeasure plans to 

all land within the project boundary would assure measures are in place to protect project 

groundwater and surface water. 

Merced ID proposes that its hazardous material spill prevention, control, and 

countermeasures plan be developed in consultation with appropriate agencies. The 

agencies to be consulted are not specified. Release of hazardous materials has the 

potential to influence both aquatic and terrestrial resources. Consultation with the Water 

Board, California DFW, BLM, and FWS would provide a reasonable balance of input 

regarding appropriate contaminant control measures.

Determining Water Year Type

Precipitation and runoff patterns vary considerably in the San Joaquin River Basin, 

and aquatic communities have adapted to these variances. Water management in this 

region accounts for this variability by establishing water year types that guide water 

allocation decisions. The water year type determination at the Merced River Project 

would govern how instream flow releases are adjusted based on meteorological 

conditions. Several different approaches to establishing water year types have been 

developed.

Merced ID proposes to implement measure AQR1 (part 3) to determine water year 

type, following its existing methods to dictate instream flow releases. It would determine 

water year type beginning within 90 days of license issuance and continuing in 

subsequent years in February, March, April, and May. Merced ID would calculate a 

water supply index for the Merced River based on unregulated runoff below Merced Falls 

(i.e., inflow to Lake McClure) using the same methods currently used for the San Joaquin 

Valley Water Year Hydrologic Classification (San Joaquin Valley 60-20-20 Index), 
141

which was developed by the Water Board for the San Joaquin River Basin as part of its 

Bay-Delta regulatory activities (Water Board 2006b). Five water year types would be 

established within this index: wet, above normal, below normal, dry, and critically dry. 

The water year types would be calculated as 60 percent of the current year’s April 

through July inflow plus 20 percent of the current year’s October through March inflow 

plus 20 percent of the previous year’s index. Merced ID would begin using its proposed 

approach to determining water year type within 90 days of license issuance. For each 

year, water year type would initially be established in February and updated in March, 

April, and May. From May 15 to February 14 of the following year, Merced ID would 

base water year type on California Department of Water Resources’ (California DWR)

forecast published in May. Merced ID states that the water-supply indices for February 

and March would be calculated using the 90 percent exceedance forecast for unregulated 

runoff and the April and May indices would be calculated using the 75 percent 

exceedance forecast for unregulated runoff. Additional details on the “Merced 60-20-20 

Index” are presented above in section 3.3.1.1, Affected Environment, Water Quantity, 

Merced River Project, Water Storage and Hydrology. 

NMFS [10(j) recommendation 1.1A(7)] and California DFW [10(j) 

recommendation 3A] recommend that Merced ID incorporate the “Hughes method” to 

determine water year type for instream flow releases. NMFS and California DFW state 

that Merced ID’s approach to water year determination using a 90 percent exceedance 

forecast for February and March and 75 percent exceedance forecast for April and May 

creates overly conservative predictions of inflows. California DFW estimates that this 

would result in drier than actual water year operations being implemented for February 

and March 40 percent of the time and for April and May, 25 percent of the time. The 

Hughes method is based on the water year forecast of unimpaired runoff of the Merced 

River below Merced Falls published near the beginning of each month from February 

through May in California DWR’s Bulletin 120. Unlike the Merced 60-20-20 Index that 

factors current and past-year conditions, the Hughes method does not rely on carry over 

storage within Lake McClure. NMFS and California DFW note that the Merced 60-20-

20 Index provides a disincentive for water conservation by reducing environmental flows 

when carry-over storage is low. California DFW recommends that the water year types 

be defined as having the following numerical breakpoints (in thousands of acre-feet) 

based on unregulated inflow to Lake McClure reported for water years 1901 to 2012:

 Wet: ≥1,307 (75th percentile of record)

 Above normal: >919 (median) and <1,307

 Below normal: >546 (25th percentile) and ≤919

 Dry: >339 (5th percentile) and ≤546

 Critical: ≤339

California DFW also recommends that Merced ID perform an update to the water 

year type determination at the end of the water year using California DWR’s “October 
142

update,” which, if published, uses observed monthly unregulated runoff for the river 

rather than forecasted runoff.

FWS [amended 10(j) recommendation 3(A1)] recommends that water year type be 

determined using the Merced 60-20-20 Index, but provides no background for this 

recommendation. The Conservation Groups recommend that Merced ID determine water 

year types based on the Merced 60-20-20 Index as proposed in measure AQR1, with one 

change. They recommend that Merced ID determine water year type for February

through May based on 75 percent exceedance forecasts instead of the more conservative 

90 percent exceedance forecast for February and March proposed by Merced ID, for 

which they state is more appropriately reserved for short-term drought management. The 

Conservation Groups agree that including the previous year’s conditions and an index 

specific to the Merced River “...have strong arguments in their favor,” although they

consider the Merced 60-20-20 Index to be more conservative than the Hughes method.

Our Analysis

As defined by California DWR, the Merced River Watershed is part of the San 

Joaquin Valley hydrologic region. The water year classification within this region is 

based on the sum of unregulated (unimpaired) flow at: Stanislaus River below Goodwin 

reservoir (i.e., inflow to New Melones reservoir), Tuolumne River below La Grange (i.e., 

inflow to New Don Pedro reservoir), Merced River below Merced Falls (i.e., inflow to 

Lake McClure), and San Joaquin River inflow to Millerton Lake). The San Joaquin 

Valley water year classification by numerical breakpoints is presented in table 3-8.

Adopting the Merced 60-20-20 Index water-year type classification proposed by 

Merced ID under measure AQR1 (table 3-8) and recommended by FWS, rather than the 

classification values used for the regionally broader San Joaquin Valley 60-20-20 Index, 

accounts for the unique hydrology of the Merced River Watershed, which typically 

receives less precipitation than the Tuolumne and Stanislaus Watersheds to the north. 

The numerical breakpoints selected by Merced ID for its proposed classification are 

based on the more recent portion of the unregulated runoff record. In contrast, California 

DFW’s recommended breakpoints (table 3-8) are based on a time period more than 

double that considered by Merced ID (1901–2012). California DFW’s longer view of the 

hydrologic record encompasses many more representative wet and dry cycles, which 

results in higher value numerical breakpoints for the non-dry years compared with the 

values used for Merced ID’s breakpoints. California DFW and NMFS state that this

approach would result in about half of all water years being classified as above normal, 

with the other half being classified as being below normal. In its license application, 

Merced ID does not present the proportional distribution of above normal and below 

normal water years in the historic record using its proposed numerical breakpoint system.
143

Table 3-8. Comparison of alternative water-year type classifications. 

Water year type

San Joaquin Valley 

60-20-20 Index 

Classificationa

Merced ID’s 

Proposed Merced 

60-20-20 Index 

Classification

California DFW’s 

Recommended 

Classification 

(Hughes Method)

(in thousands acre-feet)

Wet >3,800 >650 >1,307

Above Normal >3,100 and <3,800 >530 and <650 >919 and <1,307

Below Normal >2,500 and <3,100 >420 and <530 >546 and <919

Dry >2,100 and <2,500 >360 and <420 >339 and <546

Critical <2,100 <360 <339

a Source: Water Board 2006b.

Merced ID’s proposal and NMFS and California DFW’s recommendation to base 

water year type on California DWR’s forecast of unregulated runoff of the Merced River 

would both follow an accepted approach implemented in similar watersheds contributing 

to the San Joaquin and Sacramento Valleys. The agencies and the Conservation Groups 

agree in their comments that the Merced 60-20-20 Index as proposed by Merced ID 

would result in more conservative water-year type estimates than would the Hughes 

method. Specifically, calculation of the February and March indices and the April and 

May indices using California DWR’s 90 and 75 percent exceedance forecasts, 

respectively, instead of the median (50 percent exceedance) forecast would produce 

lower runoff estimates that are biased towards ascribing below normal conditions. 

Additionally, incorporating updated, observed unregulated runoff volumes published by 

California DWR in October, when available, would improve water year type 

determination throughout the water year and into the subsequent one compared with the 

forecast-based determination proposed in AQR1. 

Based on our analysis, adoption of the water year type determination 

recommendations of NMFS and California DFW would accomplish the following: 

(1) continued adherence to the California DWR’s forecasts for annual unregulated runoff 

in the Merced River during February, March, April, and May, (2) incorporation of 

updated observed runoff (full natural flows), when available, rather than complete 

reliance on forecast-based water year type, and (3) use of type classifications (numerical 

breakpoints) based on a quartile-based distribution of the full hydrologic record for the 

watershed. This measure would be potentially subject to adjustment following any future 

update to the Bay-Delta Plan by the Water Board or to environmental flow programs 

informed by a technical advisory committee. 
144

Minimum Instream Flows

Merced ID proposes to implement measure AQR1 to (1) provide minimum and 

target streamflows downstream of the project to Shaffer Bridge (tables 3-9 and 3-10), 

(2) compute water-year types, and (3) monitor instream-flow compliance. Merced ID’s 

proposed minimum streamflows, which are defined as required streamflows depending 

on water-year type, would be maintained at all times. Merced ID’s proposed target 

streamflows, which are greater than the proposed minimum streamflows, would be 

maintained in good faith. Both the minimum and target streamflows would be monitored 

by Merced ID at Shaffer Bridge. Flow measurements and compliance determinations 

would be based on instantaneous (i.e., 15-minute recordings) and mean daily recordings 

for minimum and target streamflows, respectively. For compliance purposes, the 

instantaneous minimum flow in any day would be at least 90 percent of the designated 

minimum flow for that day. Failure to satisfy a target streamflow would not be 

reportable to the Commission, unless the deviation occurs on more than 20 percent of the 

days in any one calendar month. 

Both the minimum and target streamflow measures proposed by Merced ID would 

be subject to temporary modification if required by equipment malfunction, in 

emergencies, or during events outside of Merced ID’s control. Merced ID would make 

all reasonable efforts to promptly resume performance of the flow requirements within 48 

hours of the modification. Where facility modification is required to implement the 

efficient release of minimum and target streamflows, Merced ID would submit 

applications for permits within 1 year after license issuance and complete the facility 

modifications as soon as reasonably practicable, but no later than 2 years after receipt of 

all required permits and approvals. Prior to completion of such required facility 

modifications and within 90 days after license issuance, Merced ID would make a good 

faith effort to provide the specified minimum and target streamflows within the 

capabilities of the existing facilities.

The Water Board [preliminary WQC condition 2] reserves its right to condition 

the project with minimum instream flows in light of the whole record, but does not 

specify a minimum flow. The Water Board considers the whole record to include, but 

not be limited to, the Commission’s record (i.e., recommendations by the resource 

agencies), the final EIS document, and the final California Environmental Quality Act

document. 
145

Table 3-9. Proposed and recommended minimum and target flows (cfs) by water year type during the irrigation season 

(March through October) as measured at Shaffer Bridge (Source: staff).

Entity Wet Above Normal Below Normal Dry Critically Dry

Merced ID (minimum)

i. March-May 120 120 120 120 80

ii. June-Oct 15 160 120 60 60 40

iii. Oct 16-Oct 31 180 160 140 100 80

Merced ID (target)

iv. March-May 150 150 150 150 100

v. June-Oct 15 200 150 75 75 50

vi. Oct 16-Oct 31 225 200 175 125 100

NMFS (minimum without fish passage)

Mar 1-15 500 450 300 225 200

Mar 16-31 550 500 300 225 200

Apr 1-15 600 600 400 250 200

Apr 16-30 800 700 400 250 200

May 1-15 1,200 1,000 600 250 200

May 16-31 1,000 800 400 350 350

June 1-15 800 600 350 350 350

June 16-Sep 

15 500 450 350 350 350

Sep 16-Oct 15 250 250 200 200 200

Oct 16-Oct 31 200 200 200 150 150
146

Entity Wet Above Normal Below Normal Dry Critically Dry

FWS (target)a

vii. Mar 248-1,146 248-1,146 248-1,146 248-1,146 248-877

viii. Apr 1,176-2,044 150-1,176 125-1,176 125-646 125

ix. May 2,074-2,972 150-160 150-160 150-160 150-160

x. June 225-2,472 225 225 225 225

xi. July 340-350 340-350 340-350 340-350 340-350

xii. Aug 320-330 320-330 320-330 320-330 320-330

xiii. Sep 280-320 280-320 280-320 280-320 280-320

xiv. Oct 1-15 180 180 180 100 100

xv. Oct 16-19 1,200 1,200 1,200 1,200 1,200

xvi. Oct 20-25 1,200 1,200 1,200 100 100

xvii. Oct 26-31 175 175 125 100 100

California DFW (minimum)

Mar 1-15 270 270 270 240 200

Mar 16-31 410 410 370 370 310

Apr 1-15 590 590 620 510 560

Apr 16-30 790 790 780 570 570

May 1-15 1,140 1,140 1,190 870 1,040

May 16-31 1,580 1,580 2,060 1,420 200

June 1-15 2,330 2,330 200 200 200

June 16-30 200 200 200 200 200

Jul-Oct 15 200 200 200 200 200
147

Entity Wet Above Normal Below Normal Dry Critically Dry

Oct 16-Oct 31 275 250 225 150 140

Conservation Groups (minimum)

xviii. Mar-June

60% of 

unregulated 

(1,520-2,905 

cfs)b or 220 cfs, 

whichever is 

higher; irrigation 

deliveries 75% of 

demand

60% of unregulated (347–

980 cfs) or 220 cfs, 

whichever is higher; 

irrigation deliveries 75% 

of demand

Irrigation deliveries 50% 

of demand but 40% if 

preceded by a critically

dry year and 30% if 

storage in Lake McClure 

is less than 200,000 acrefeet on April 1

xix. Mar-May

60% of unregulated (980–

1,629 cfs) or 220 cfs, 

whichever is higher; 

irrigation deliveries 75% 

of demand

180

xx. Mar-Apr

60% of unregulated 

(672–1,130 cfs) or 180 

cfs, whichever is higher; 

irrigation deliveries 60% 

of demand

xxi. May-June 180

xxii. June 220

xxiii. July-Oct 200 200 175 150 150 

a FWS target flows reflect amended flow recommendations, filed with the Commission on October 22, 2014.

b To provide an approximation of the flows associated with 60 percent unregulated flows, we used the inflows to Lake McClure shown in table 

3-1 with the 20 percent exceedance representing wet water years, the 50 percent exceedance representing above and below normal water years, 

and the 80 percent exceedance representing dry and critically dry water years. Actual values would vary from these approximations.
148

Table 3-10. Proposed and recommended minimum and target flows (cfs) by water year type during non-irrigation season 

(November-February) as measured at Shaffer Bridge (Source: staff).

Agency Wet Above Normal Below Normal Dry Critically Dry

Merced ID (minimum)

Nov-Jan 180 160 140 100 80

Feb 120 120 120 120 80

Merced ID (target)

Nov-Jan 225 200 175 125 100 

Feb 150 150 150 150 100

NMFS (minimum without fish passage)

Nov-Jan 200 200 200 200 200

Feb 1-14 400 350 300 200 200

Feb 15-28 450 400 300 200 200

FWS (target)a

Nov-Feb 175 175 125 100 100

California DFW

(minimum)

Nov-Jan 15 275 250 225 150 140

Jan 16-Feb 400 400 400 400 400
149

Agency Wet Above Normal Below Normal Dry Critically Dry

Conservation Groups (minimum)

Nov-Jan 220 220 220 180 180 

Feb

60% of unregulated 

(1,235 cfs)aor 220 

cfs, whichever is 

higher; irrigation 

deliveries 75% of 

demand 

60% of unregulated 

(445 cfs) or 220 cfs, 

whichever is higher; 

irrigation deliveries 

75% of demand

220; irrigation 

deliveries 75% of 

demand

180; irrigation 

deliveries 60% of 

demand

180; irrigation 

deliveries 50% of 

demand but 40% if 

preceded by a 

critically dry year

a FWS target flows reflect amended flow recommendations, filed with the Commission on October 22, 2014.

b To provide an approximation of the flows associated with 60 percent unregulated flows, we used the inflows to Lake 

McClure shown in table 3-1 with the 20 percent exceedance representing wet water years, the 50 percent exceedance 

representing above and below normal water years, and the 80 percent exceedance representing dry and critically dry 

water years. Actual values would vary from these approximations.
150

NMFS [10(j) recommendation 1.1A(1)] recommends that Merced ID provide 

minimum instream flows, as measured at Shaffer Bridge, by dates and water year type 

following one of two flow schedules. The flow schedules both range between 150 and 

1,200 cfs depending on time period and water year type, but differ depending on whether 

Merced ID provides fish passage at Crocker-Huffman diversion dam—higher flows are 

recommended between late spring and late summer for the fish-passage scenario in all 

water year types (tables 3-9 and 3-10 for the no-fish passage recommended flows). 

NMFS [10(j) recommendation 1.1A(5)] and the Conservation Groups both recommend 

that required flow releases made by Merced ID at Crocker-Huffman diversion dam for 

Cowell Agreement diversions would be in addition to the minimum flow requirements 

(see section 2.1.1.5, Existing Environmental Measures). 

FWS [amended 10(j) recommendation 3(A1)] recommends that Merced ID 

provide instream flow targets, as measured at Shaffer Bridge, by day and water year type 

(tables 3-9 and 3-10).

26

 The recommended flows, which include pulse flows and other 

recommended flow changes, range from 100 to 2,972 cfs. A technical advisory 

committee would have the ability to modify the timing of the flow releases as necessary. 

California DFW [10(j) recommendation 3B(a)] recommends that Merced ID 

provide a minimum flow of 25 cfs below New Exchequer dam at all times. It also 

recommends that Merced ID provide an instantaneous minimum flow, as measured at 

Shaffer Bridge, between 140 and 2,600 cfs depending on date and water year type (tables 

3-9 and 3-10). Embedded in this minimum flow recommendation are extended late 

spring pulse flows intended to stimulate salmonid outmigration prior to high temperature 

summer conditions. During periods of drought, Merced ID would notify the resource 

agencies by March 10 of any potential concerns related to meeting the recommended 

flow releases, provide the Commission with any comments provided by the resource 

agencies, and implement revised operations upon receiving Commission and all other 

necessary regulatory approvals.

The Conservation Groups recommend that Merced ID provide minimum instream 

flows ranging from at least 150 to 220 cfs, as measured at Shaffer Bridge, according to 

time periods, water year type, and reservoir levels (tables 3-9 and 3-10). The 

recommendation also includes various irrigation delivery percentages that would depend 

on water year type ranging from 30 to 75 percent of demand. The instream flow 

requirement at Shaffer Bridge would drop to 100 cfs in all months until 130,000 acre-feet 

of storage at Lake McClure is re-established. Flows would be released as a percent of 

unregulated flow as applicable, with no 5 day running average being less than 50 percent 

of unregulated flow, and no 14-day running average being less than 60 percent of 

unregulated inflow to Lake McClure. As we indicate in tables 3-9 and 3-10, when the 60 

 

26 FWS does not define “flow targets,” or how they may differ from minimum 

flows.
151

percent of unregulated inflow criteria is applied from February through June, the 

minimum flows would range from about 347 to 2,905 cfs.

NMFS [10(j) recommendation 1.1B(1–4)] recommends that the minimum 

instream flow compliance point would be at a new river gage at Shaffer Bridge capable 

of measuring flows up to 6,000 cfs.27 Measurement methodology and compliance 

standards at all existing and new gages would follow guidelines specified in NMFS’ 

recommendation.

Our Analysis

Release of minimum or target instream flows to the lower river influences aquatic 

habitat availability and water temperatures. Merced ID developed a simulated flow 

scenario for water years 1970–2006 based on existing baseline conditions, the proposed 

measure (AQR1), and each of the flow recommendations using the project relicensing 

operations model. Simulated flow at Shaffer Bridge (RM 32.8) was used as a comparison 

point to evaluate flow conditions in the Merced River from downstream of CrockerHuffman diversion dam, which include both the irrigation season (March through 

October) and the non-irrigation season (November through February). 

Tables 3-9 and 3-10 clearly show that the proposed and recommended minimum 

and target flow regimes are all substantially different. Balancing the different resource 

values associated with each flow regime represents a complex series of tradeoffs (e.g., 

enhancing temperature conditions for specific fish species and lifestages with the limited 

amount of cold pool water in Lake McClure, enhancing physical habitat for specific life 

stages of anadromous fish, providing flows that encourage juvenile outmigration because 

the temperature regime is unlikely to be favorable, and conserving water for irrigation 

purposes) to derive a reasonable flow regime.

The proposed measure (AQR1) is generally consistent with baseline conditions 

throughout the period of record. In most instances, large flood control releases that occur 

with similar timing and magnitude under the baseline and proposed measure either do not 

occur, occur with lower magnitude, or occur at different times under the other flow 

recommendations.

Flow recommendations by NMFS result in consistently higher flows during 

summer months in each year compared to baseline conditions. The FWS and California 

DFW flow recommendations result in consistently higher flows during most months of 

most years compared to baseline conditions. Although the Water Board did not specify a 

flow regime in its preliminary WQC condition, the Water Board’s potential flow 

 

27 Although not explicitly stated in the recommendation, we assume NMFS 

intended Merced ID to be responsible for installing and maintaining this new gage at 

Shaffer Bridge.
152

requirements28 would be generally higher than baseline conditions during the spring and 

early summer and lower during fall and winter. Flow recommendations by the 

Conservation Groups result in generally higher flows in most years, with a variable 

pattern of spring flows associated with flow releases based on a percentage of 

unregulated flow. 

Merced ID evaluated habitat availability for anadromous salmonids, including 

Central Valley steelhead and fall-run Chinook salmon in the Merced River downstream 

of Crocker-Huffman diversion dam based on an Effective Habitat Analysis that included 

results from PHABSIM model output for various life stages in conjunction with output 

from the project relicensing operations and water temperature models. Results were 

developed to show the percent of habitat that becomes unavailable based on thermal 

requirements of various species and life stages as defined by EPA (2003) guidelines. 

This analysis was performed using existing minimum instream flow requirements as 

baseline conditions and included minimum instream flows proposed by Merced ID along 

with flows referred to in comments by the Water Board and flow recommendations by 

NMFS, FWS, California DFW, and the Conservation Groups. 

Table 3-11 presents the percentage of maximum habitat that is unavailable under 

existing baseline conditions and for the proposed and recommended flow regimes. The 

modeling results shown in table 3-11 show variable habitat availability by flow regime 

and modeled life stage for Central Valley steelhead and fall run Chinook salmon. The 

results indicate that conditions for Central Valley steelhead juvenile rearing using the 

EPA (2003) guideline of 16.0°C (60.8°F) are currently the most affected, especially 

during the summer, and that these conditions remain largely unchanged under all flows 

analyzed. 

Results of the Effective Habitat Analysis indicated that implementation of Merced 

ID’s proposed, FWS’ amended, or NMFS’ recommended flow regimes would not result 

in any tangible enhancements (i.e., effective habitat would increase by 4 percent or less) 

to anadromous salmonid habitat compared to baseline conditions. Merced ID’s and 

FWS’ amended flow regimes increase the amount of unavailable habitat for steelhead 

spawning and incubation by 5 percent compared to existing conditions. Increases in 

unavailable habitat of 8 percent and 5 percent for Chinook salmon spawning and 

incubation would result from implementation of the Water Board and FWS flow regimes, 

respectively. 

 

28 Based on a Water Board comment in its Draft Bay-Delta Draft Substitute 

Environmental Document, the Water Board’s potential flow requirements for the project 

would be 35 percent of unimpaired flow from February through June annually and 

baseline conditions for the remaining months.
153

Table 3-11. Effective habitat analysis results showing percent of maximum habitat that is unavailable over the life stage 

period due to thermal conditions associated with various flow measures (Source: Merced ID, 2014b,c,d, as 

modified by staff).

Species Life Stage

Life Stage 

Timing

Percent of Habitat that is Unavailable over the Life Stage Period (expressed as % of the 

maximum)

Environmental 

Baseline

Merced ID 

Proposed

Water 

Boarda

Conservation 

Groups

FWS 

(amended) NMFS

California 

DFW

Central 

Valley

Steelhead

Adult 

rearing Year-round 54% 53% 57% 53% 53% 50% 50%

Spawning 

and egg 

incubation

December 

through 

May

50% 55% 50% 50% 55% 49% 46%

Fry rearing

March 

through 

June

70% 70% 61% 58% 67% 68% 54%

Juvenile 

rearing

(16.0°C)b

Year-round 73% 73% 72% 72% 73% 73% 70%

Juvenile 

rearing

(18.0°C)c

Year-round 66% 64% 65% 65% 63% 65% 64%

Juvenile 

oversummer 

rearing

(16.0°C)b

June 

through 

September

95% 95% 94% 92% 95% 93% 93%
154

Species Life Stage

Life Stage 

Timing

Percent of Habitat that is Unavailable over the Life Stage Period (expressed as % of the 

maximum)

Environmental 

Baseline

Merced ID 

Proposed

Water 

Boarda

Conservation 

Groups

FWS 

(amended) NMFS

California 

DFW

Fall-run 

Chinook 

Salmon

Spawning 

and egg 

incubation

October 

through 

March

60% 64% 68% 62% 65% 64% 62%

Fry rearing

January 

through 

May

63% 62% 58% 56% 60% 62% 57%

Juvenile 

rearing

January 

through 

May

65% 64% 60% 59% 61% 61% 59%

a Water Board results are based on a flow scenario developed by Merced ID that incorporates 35 percent of unimpaired flow from February 

through June annually and baseline conditions for remaining months as provided by a Water Board comment reflecting potential flow 

requirements released in the Water Board’s Draft Bay-Delta Draft Substitute Environmental Document. 

b EPA (2003) guidelines designate a 16.0°C (60.8°F) threshold for “core” juvenile salmonid populations defined as moderate to high density.

c EPA (2003) guidelines designate an 18.0°C (64.4°F) threshold for “non-core” juvenile salmonid populations defined as moderate to low 

density. 
155

The greatest habitat enhancement when compared to existing conditions (and 

Merced ID’s proposed flow regime) is evident for steelhead fry rearing under California 

DFW’s flow regime, when unavailable habitat decreases from 70 percent to 54 percent 

during the spring. Lesser enhancements would also be achieved by the Conservation 

Groups’ (58 percent unavailable habitat for steelhead fry rearing) and Water Board’s (61 

percent unavailable habitat for steelhead fry rearing) recommended flow regimes. Other 

reductions of from 5 to 7 percent in unavailable habitat (an enhancement) for Chinook 

salmon fry and juvenile rearing would be achieved by the Water Board’s, Conservation 

Groups’, and California DFW’s suggested or recommended flow regimes. 

Not reported in table 3-11 are the effects of each flow regime on the availability of 

the remaining water for irrigation purposes. Based on Merced ID’s modeling, its

proposed flows would result in reduced canal deliveries compared to irrigation demand in 

6 of the 36 years modeled, which is the same as existing conditions. The FWS’ 

recommended and Water Board’s suggested flow regimes would result in reduced canal 

deliveries in 12 of 36 years; NMFS’ recommended flows would result in reduced canal 

deliveries in 19 of 36 years; California DFW’s recommended flows would result in 

reduced canal deliveries in 22 of 36 years, and the Conservation Groups’ recommended 

flow regime would result in reduced canal deliveries in all 36 years that were modeled.

We consider the approach to establishing an appropriate minimum flow regime 

presented in the California DFW rationale document for its 10(j) recommendations 

(California DFW, 2014a) to be a reasonable framework on which to build a minimum 

flow regime compared to approaches provided by FWS, NMFS, and the Conservation 

Groups. California DFW provides significant detail (12 pages) on its recommended 

flows for the entire year. FWS and NMFS’ rationale does not cover the entire year, and 

the Conservation Groups embed irrigation restrictions into most of its flow 

recommendations. The California DFW flow regime seeks to: (1) enhance physical 

Chinook salmon spawning and incubation habit during late fall and early winter when 

water temperatures are not overly constraining; (2) consider density-dependent variables 

as fry emerge from spawning gravel in late January through February; (3) enhance water 

temperatures for smoltification during the spring; and (4) provide reasonable physical 

habitat for O. mykiss juveniles and adults during the summer. 

The California DFW recommended flow regime from October 16 through January 

15 is intended to enhance Chinook salmon spawning and incubation habitat (California 

DFW, 2014a). California DFW’s recommended minimum flows during this time for wet, 

above normal, and below normal water years (225 to 275 cfs) would provide about 80 to 

100 percent of the maximum WUA, depending on the specific reach between CrockerHuffman diversion dam and Shaffer Bridge (Merced ID, 2013a). However, providing a 

minimum flow of 175 cfs during wet and above normal water years (which is the same as 

the FWS recommended target flow from October 16 through February 28 and 

comparable to Merced ID’s proposed 180 and 160 cfs during wet and above normal water 

years from October 16 through January 31) would provide about 73 to 96 percent of 

maximum WUA and conserve Lake McClure water for use later in the year compared to 
156

the higher minimum flows during comparable water years recommended by NMFS, 

California DFW, and the Conservation Groups. The California DFW recommended 

minimum flows of 150 and 140 cfs during dry and critically dry water years would 

provide about 67 to 85 percent and 65 to 80 percent of the maximum WUA, respectively, 

and we consider this to be a reasonable enhancement when water is scarce. Applying the 

150 cfs minimum flow to below normal water years, which we also consider to be 

representative of relatively scarce available water, would also represent a reasonable 

enhancement compared to existing conditions. Merced ID’s proposed minimum flow 

from October 16 through January of 100 and 80 cfs during dry and critically dry water 

years would only provide 48 to 55 percent and less than 37 percent of the maximum 

WUA, respectively. Although this would represent an enhancement compared to the 

existing 60 cfs minimum flow, it would be unlikely for such a minor increase in potential 

Chinook salmon spawning and incubation habitat to result in tangible biological benefits 

to the community in the Merced River.

California DFW presents data that indicates that upon emergence, Chinook salmon 

fry survival is density dependent, with lower survival rates associated with higher 

densities (California DFW, 2014a). Increasing flows reduce density and enhance 

survival. Survival of newly emerged fry between January 16 and the end of February 

would be between 60 and 100 percent for initial fry densities of 1,000,000 to 100,000, 

respectively, with flows of 400 cfs. This is the basis for the California DFW 

recommended minimum flow of 400 cfs during this period, regardless of water year type. 

Considering that minimum flows that would support spawning and incubation would be 

scaled back by most proposed and recommended flow regimes during less than wet water 

year types, we consider it appropriate to scale back the initial recommended flow of 400 

cfs accordingly to conserve Lake McClure water for later use. Flows of 350 and 300 cfs 

during above normal and below normal water years, respectively, would still provide 

from about 98 to 100 percent fry survival assuming a starting density of 100,000 fry 

(which we consider a reasonable assumption because of the low escapement of Chinook 

salmon of natural origin during recent years; see figure 3-22). These minimum flows are 

consistent with the recommended NMFS minimum flows for the first half of February in 

above normal and wet water years and exceed the Merced ID proposed and FWS 

recommended minimum flows for January and February. Continuing the California 

DFW recommended late fall-early winter minimum flow of 150 and 140 cfs during dry 

and critically dry water years from mid-January to the end of February would provide 

about 92 and 91 percent fry survival, respectively, assuming a starting density of 100,000 

fry. We consider this to represent a reasonable enhancement that would conserve water 

for later use when water is scarce.

During March and April, the California DFW minimum flow regime focuses on 

attempting to achieve the EPA temperature guideline of 16°C (60.8°F) for Chinook 

salmon and steelhead rearing and emigration (California DFW, 2014a). During wet and 

above normal water years, the recommended minimum flows achieve this objective from 

the Crocker-Huffman diversion dam to Shaffer Bridge, but in below normal water years, 
157

the California DFW minimum flow modeling results show the goal would be achieved 

down to RM 38, in dry water years to RM 45, and critically dry water years to RM 46.5 

(about 3.5 miles downstream of the diversion dam). The reach from Crocker-Huffman 

diversion dam to RM 45.0 currently includes some of the best salmonid spawning and 

rearing habitat in the lower Merced River. However, we find two flows recommended by 

California DFW to be unnecessary. During the April 1 through April 15 time frame, a 

higher minimum flow of 620 cfs would not be necessary during below normal water 

years to achieve the EPA guideline of 16°C (60.8°F) at RM 38.0 considering that a 

minimum flow of 590 cfs would achieve the guideline downstream to Shaffer Bridge 

(RM 32.5). For other 2-week periods during March and April, California DFW modeling 

shows that decreasing minimum flows as water years become drier would achieve the 

temperature goal at the designated river locations. Similarly, during April 1 through 

April 15, the California DFW recommended flow of 560 cfs during critically dry water 

years is not necessary to achieve the temperature goal at RM 46.5 considering that a 

minimum flow of 510 cfs would achieve the goal down to RM 45.0. We find that 

minimum flows of 560, 560, and 510 cfs during below normal, dry, and critically dry 

water years, respectively, from April 1 through April 15, would likely achieve 

appropriate water temperature enhancements comparable to the California DFW 

analogous flows of 620, 510, and 560 cfs, while conserving water during below normal 

and critically dry water years. Monitoring water temperature would confirm our findings. 

We further discuss water temperature in the following section, Managing and Monitoring 

Water Temperatures. NMFS and the Conservation Groups’ minimum flow regimes 

during March and April are generally higher than those recommended by California 

DFW, and although higher flows could further enhance the lower Merced River 

temperature regime, it would come at the cost of reduced water storage in Lake McClure, 

which means that there would be less water available during the irrigation season and 

reduced cold pool water for late spring temperature enhancement. 

During May, most stakeholders recommend a pulse flow or high minimum flows 

that would inundate riparian floodplains and serve to stimulate young salmonid 

outmigration. The FWS target flow recommendation would inundate floodplains for 69 

days from late March through early June in wet water years, 27 days in late March 

through mid-April in above normal water years, 12 days in late March through early 

April in below normal water years, and 5 days in late March during dry water years. 

These high spring flows are discussed under Pulse Flows; however, during any such 

pulse or high flow releases, there would likely be water temperature enhancements in the 

lower Merced River unless the cold pool storage in Lake McClure had been expended 

during previous flow releases. Extending the California DFW recommended minimum 

flows for the April 16 through April 30 time frame into May until the beginning of a 

spring pulse flow would maintain any enhanced temperature condition if there is 

sufficient cold pool storage available.

With the relatively high spring minimum flows described previously, we expect 

there to be little if any Lake McClure cold pool water available to provide temperature 
158

enhancements to the lower Merced River during the summer. Assuming most Chinook 

salmon juveniles and smolt emigrate from the lower Merced River with a spring pulse 

flow, we focus on flows that provide suitable physical habitat for O. mykiss juveniles and 

adults, some of which are likely to remain in the lower Merced River throughout the 

summer. A minimum flow of 200 cfs that begins at the conclusion of a spring pulse flow 

(which we assume would be on June 1) and continues until October 15 or the start of a 

fall adult Chinook salmon attraction pulse flow would provide 90 to 98 percent of the 

maximum WUA for juvenile and adult O. mykiss (Merced ID, 2013a). This summer 

minimum flow is recommended by California DFW and comparable to the minimum 

flows recommended by the Conservation Groups. However it is lower than most of the 

minimum or target flows recommended by NMFS and FWS. It is unclear what 

additional habitat value higher summer minimum or target flows would provide, and 

higher flows would further deplete water storage in Lake McClure.

As stated previously in this section, establishing an appropriate minimum flow 

regime in the lower Merced River entails attempting to balance habitat values with the 

water demands of irrigators. This is especially difficult when the supply of available 

water is limited during dry or critically dry water years. In recognition of this, we 

conclude that a reasonable guiding principal in establishing an appropriate minimum flow 

during dry or critically dry water years would be to have no minimum flow exceed the 

average monthly unregulated flow (table 3-12). These represent the flows that would 

occur without the Merced River or Merced Falls Projects.

The minimum flow compliance point in the current license is an existing gage at 

Shaffer Bridge. The reach upstream of Shaffer Bridge to Crocker-Huffman diversion 

dam currently includes the best spawning and rearing habitat for fall run Chinook salmon, 

as well as numerous water diversion points. Therefore, we consider Shaffer Bridge to be 

an appropriate compliance point for a minimum flow regime because protective flows 

would be in the channel regardless of diversions that may occur upstream of Shaffer 

Bridge, including those associated with the Cowell Agreement. NMFS does not 

elaborate on why a new compliance gage capable of measuring up to 6,000 cfs would be 

necessary to measure project-related flows. No entity has offered a flow-related measure 

with a maximum flow provision.

California DFW [10(j) recommendation 3B(a)] recommends that Merced ID 

provide a minimum flow of 25 cfs below New Exchequer dam at all times. This is 

identical to what is required by article 40 of the current license. Merced ID contends that 

McSwain reservoir backs up to New Exchequer dam and there is no need for an instream 

flow requirement. However, although McSwain reservoir may back up to the base of 

New Exchequer dam when McSwain reservoir is at full pool, this is likely not the case 

when McSwain reservoir is drawn down, which figures 3-3, 3-5, and 3-7 show occurs 

during typical wet, normal, and dry water years. During drawdowns, a short riverine 

section exists and releasing a minimum flow of 25 cfs would ensure that this channel is 

not dewatered. 
159

Table 3-12. Average monthly unregulated flow by year type (cfs) (Source: Merced ID, 

2014a).

Wet

Above 

Normal

Below 

Normal Dry

Critically

Dry

October 180 240 130 100 120

November 430 540 370 220 130

December 900 900 640 340 190

January 2,700 1,200 1,300 390 220

February 2,900 2,100 850 560 470

March 3,200 1,700 1,200 1,000 1,000

April 3,500 2,300 1,700 2,200 1,600

May 5,900 5,100 3,600 3,000 1,800

June 5,400 2,500 2,700 1,000 900

July 2,300 600 570 220 230

August 560 230 150 70 60

September 320 130 90 60 60

Managing and Monitoring Water Temperatures

The water quality objective for temperature in the Basin Plan specifies, “at no time 

or place shall the temperature of any COLD water be increased by more than 5°F above 

natural receiving water temperature.” Water temperatures at Crocker-Huffman diversion 

dam generally range from approximately 8.0 to 17.0°C (46.4 to 62.6°F) annually during 

both wet and dry water year types (see figures 3-21 and 3-22). The lower Merced River

is listed under CWA section 303(d) as impaired for temperature. Under current 

conditions, warm water temperatures reduce habitat suitability for Chinook salmon and 

steelhead downstream of Crocker-Huffman diversion dam, particularly for spawning. 

Temperatures in this reach exceeded thresholds for Chinook salmon spawning 100 

percent of the time in September and October, resulting in no suitable spawning habitat. 

During November, the peak month for fall-run Chinook salmon spawning, suitable 

temperatures occurred only 10 to 14 percent of the time, with 86 to 90 percent of 

spawning habitat unsuitable because of high water temperatures. Temperature thresholds 

for steelhead spawning during March and April were exceeded about 50 percent of the 

time. NMFS considers O. mykiss in the Merced River downstream of Crocker-Huffman 

diversion dam to belong to the California Central Valley steelhead DPS, which is 

federally listed as threatened. Critical habitat includes the Merced River downstream 

from Crocker-Huffman diversion dam. 
160

Based on Merced ID’s modeling studies, the Merced River Project affects water 

temperatures in the main channel of the lower Merced River from Crocker-Huffman 

diversion dam (RM 52.0) downstream to Shaffer Bridge during the off-irrigation season 

(November through February). During the irrigation season, the project and other 

disturbances to the channel (e.g., diversions and agricultural return) contribute to 

cumulative increases in water temperature. Merced ID proposes to implement water 

temperature monitoring (T&E1) at four locations (determined by a technical advisory 

committee) from Crocker-Huffman diversion dam to Shaffer Bridge.

The Water Board [preliminary WQC condition 19] specifies that Merced ID 

develop a water temperature monitoring plan in consultation with a technical advisory 

committee that includes provisions for the installation of four to eight water temperature 

monitoring devices. The plan would include: (1) a statement of goals and objectives; 

(2) a description of monitoring protocols; (3) a description of factors that may affect 

water temperature and identification of the ones that are project-related; (4) monitoring 

and reporting schedules; and (5) a plan for corrective actions if data indicate that project 

operations are increasing water temperature. The Water Board [preliminary WQC 

condition 8] also specifies that Merced ID develop a fish passage or habitat restoration 

plan in consultation with a technical advisory committee. We address fish passage in a 

separate subsection. The habitat restoration plan would be developed within 1 year of 

license issuance and designed to decrease water temperatures in and downstream of the 

project.

NMFS [10(j) recommendation 8] recommends that water temperature and flows 

be measured at 10 locations ranging from RM 62.0 to a location between Shaffer Bridge 

and the confluence with the San Joaquin River. NMFS states that measuring flow at 

temperature monitoring stations is important because temperature is related to flow and 

having both would better enable interpretation of the monitoring results given the many 

diversions that occur in the lower Merced River. 

FWS [10(j) recommendation 5(j)] recommends that Merced ID continuously 

monitor water temperature at about 5-mile intervals between New Exchequer dam (RM 

62.0) and Shaffer Bridge (RM 32.8), which would include six locations. FWS [10(j) 

recommendations 3(A3) and 5 (G and H)] also recommends that Merced ID conduct a 

riparian microclimate study and collect data for calibrating a HEC-5Q water temperature 

model analysis to determine the optimum length and width of riparian forest in the 10 

miles from Merced Falls dam to a point 1.2 miles downstream of the Snelling Road 

Bridge needed to achieve temperature objectives downstream of Crocker-Huffman 

diversion dam.

California DFW [10(j) recommendation 9(7)] recommends that Merced ID include 

in an overall monitoring plan (other parameters would also be included in this plan) 

provisions for continuously monitoring water temperature a RMs 62.0, 56.0, 52.0 (below 

Crocker-Huffman diversion dam), 46.5, 45.0, 42.0, 38.0, and 32.8 (Shaffer Bridge). 
161

NMFS, California DFW, and FWS recommend increasing flow releases to 

maintain the following 7-day average of daily maximums (7DADM) water temperature 

criteria downstream of Crocker-Huffman diversion dam: 

 NMFS [10(j) recommendation 1.1A(3a)] recommends maintaining a 7DADM 

water temperature of <18.0°C (64.4°F) at the Highway 59 bridge (RM 42.0). 

 California DFW [10(j) recommendation 3C] recommends maintaining a

7DADM from January to February 14 of 13.0°C (55.4°F) at Shaffer Bridge 

(RM 32.8) during wet and above normal water years, RM 38.0 in below 

normal water years, RM 45.0 in dry water years, and 46.5 (Snelling) in 

critically dry water years. From February 15 through June 15, California DFW 

recommends maintaining a 7DADM of 16.0°C (60.8°F) at Shaffer Bridge in 

wet and above normal water years; from February 15 through May 31 at 

16.0°C (60.8°F) at RM 38.0 in below normal water years and RM 45.0 in dry 

water years; and from February 15 through May 15 at 16.0°C (60.8°F) at RM 

46.5 (Snelling) in critically dry water years. California DFW’s recommended 

flow regime is designed to meet these temperature criteria, but it states that 

during unusual meteorological conditions, it may be necessary to release 

additional flows to meet the recommended criteria.

 FWS [amended 10(j) recommendation 3(A1a)] recommends maintaining a 

7DADM of <18.0°C (64.4°F) at Snelling Bridge (RM 46.5) from April 1 to 

October 31 to the extent possible.

NMFS [10(j) recommendation 1.1A(3c)] recommends developing a long-term 

water temperature improvement plan that includes a feasibility study of potential options 

for decreasing water temperature downstream of Crocker-Huffman diversion dam, 

including: (1) installing an underground pipe for New Exchequer dam that bypasses 

McSwain reservoir and/or Merced Falls reservoir; (2) modifying the McClure outlet 

structure to allow water withdrawal from varying depths; and (3) developing engineering 

alternatives that do not require large volumes of water. 

California DFW [10(j) recommendation 4] also recommends that Merced ID 

prepare a long-term water temperature management plan. The plan would include: 

(1) developing a long term strategy for meeting seasonal temperature objectives for 

Chinook salmon and O. mykiss ranging from 13.0°C (55.4°F) to 18.0°C (64.4°F) during 

the time frames included in the recommendation; (2) a feasibility study on submerged 

pipes capable of delivering at least 200 cfs to a location downstream of Crocker-Huffman 

diversion dam; (3) measures to prolong and stabilize the irrigation delivery season; 

(4) measures to restore the natural channel morphology, floodplain habitats, and riparian 

forest in the approximately 10-mile reach downstream of Crocker-Huffman diversion 

dam; (5) provisions to provide coldwater refugia when water temperatures exceed 

objectives for more than 14 days; and (6) evaluating the effects on instream flow releases 
162

of implementing alternatives, and the estimated funding and schedule needed for the 

alternatives.

Our Analysis

In general, although the project directly affects flows and temperatures in the 

lower Merced River downstream of Crocker-Huffman diversion dam, the ability of the 

project to reduce water temperatures during the irrigation season (March through 

October) is limited by non-hydroelectric project withdrawals, which account for up to 52 

percent of the average annual unregulated discharge from the watershed and limit 

availability of water for instream flows (Stillwater Sciences, 2002). Past disturbance to 

the channel, floodplain, and riparian habitat and other factors also limit the project’s 

ability to reduce water temperatures during the irrigation season. During the nonirrigation season (November through February), little to no water is diverted at CrockerHuffman diversion dam, and the magnitude and duration of releases from New 

Exchequer dam directly affect flows and water temperature in the lower Merced River 

and the amount of water stored for the remainder of the year. Increasing flows to reduce 

water temperatures in the spring and early summer generally reduces storage for 

coldwater releases in the summer and fall from Lake McClure. This relationship is a 

major factor when attempting to balance flow releases to meet temperature criteria for 

protecting coldwater species such as steelhead and Chinook salmon. 

Increasing flow releases to maintain lower 7DADM water temperatures at various 

locations downstream of Crocker-Huffman diversion dam, as recommended by NMFS, 

California DFW, and FWS, depends on the volume of cold water stored in Lake 

McClure, and in many cases, would require large volumes of water for relatively minor 

increases in the number of days that temperature criteria would be met downstream in dry 

and critically dry water years. Merced ID’s temperature modeling illustrates that meeting 

temperature criteria would generally require flows exceeding those recommended by the 

agencies and that increasing flow releases earlier in the season reduces coldwater storage 

for lowering temperatures in the summer and fall.

Table 3-13 compares the EPA 7DADM water temperature guideline exceedances 

under existing conditions and the proposed and recommended flow regimes for all life 

stages of Central Valley steelhead and fall-run Chinook salmon from below CrockerHuffman diversion dam to Shaffer Bridge. The table shows that generally, flows under 

the environmental baseline and the proposed project would provide similar temperature 

regimes in the lower Merced River. A minor exception occurs for Chinook salmon 

upstream migration, where the proposed flow regime has the lowest exceedance 

percentage of nearly all flows analyzed (although the Conservation Groups’ flow regime 

results are comparable to Merced ID’s flow regime results). The reason for this is that 

the other flow regimes call for higher flow releases throughout the year and by 

September, the start of the adult Chinook salmon upstream migration period, most of the 

cold water in Lake McClure is gone. In contrast, the exceedances for Chinook salmon 

upstream migration for the NMFS and California DFW flow regimes are greater than 
163

what currently occurs under existing conditions. This is because both agencies focus on 

spring flows that would increase growth of steelhead and Chinook salmon and stimulate 

outmigration before summer. Consequently, the exceedances for steelhead smoltification 

and juvenile Chinook salmon rearing and emigration are by far the lowest for the 

California DFW flow regime, and, to a lesser extent, the NMFS flow regime. 

Overall, table 3-13 shows the pros and cons of each flow regime that result from 

differing approaches to balancing competing demands for available water. It also shows 

the challenges of attempting to meet the EPA temperature guidelines for salmonids. 

NMFS recommends maintaining a 7DADM water temperature of <18.0°C 

(64.4°F) at the Highway 59 bridge (RM 42.0); however, based on Merced ID’s modeling 

results, NMFS’ minimum flow recommendations would not be adequate to meet its 

recommended water temperature criteria 18 percent of the time. Therefore, flows greater 

than the NMFS recommended minimum flows would be necessary to meet NMFS’ 

recommended water temperature criteria. 

California DFW acknowledges that achieving EPA water temperature objectives 

in the lower Merced River throughout the entire year does not appear feasible given 

current facilities and constraints. Consequently, in an effort to narrow the temporal scope 

of the EPA objectives to the most critical time periods, it developed temporal water 

temperature objectives for different Chinook salmon and Central Valley steelhead life 

stages. In summary, the performance standard for Chinook salmon and steelhead 

spawning and incubation would be 13.0°C (55.4°F), which would apply from January 1 

through February 14, and for Chinook salmon juvenile core rearing 16.0°C (60.8°F), 

which would apply from February 15 through May 15 or to June 15, depending on water 

year type. We agree that adjusting temperature objectives to reflect the limitations and 

constraints of achieving ideal conditions in the lower Merced River, as California DFW 

has done, would set more realistic goals for all parties responsible for restoration of this 

important salmonid habitat. We expect the California DFW recommended minimum 

flows to achieve these objectives during the spring to the extent possible. However, 

during the irrigation season, water temperature in the lower Merced River is influenced 

by non-project factors such as flow diversions. It is unclear how often unusual 

meteorological events would occur that would result in the need to release flows in 

excess of the recommended minimum flows to meet salmonid temperature criteria. We 

therefore have no basis to determine the effects on irrigators or project generation 

associated with any such excess flow releases. Consequently, although monitoring water 

temperature in the lower Merced River is important, requiring Merced ID to release flows 

that would achieve specific temperature objectives may not be directly related to a project 

effect and, in some instances, may not be possible.
164

Table 3-13. Comparison of 7DADM simulated water temperature guideline exceedance between the environmental 

baseline conditions and proposed and recommended flow regimes for all life stages of Central Valley 

steelhead and fall-run Chinook salmon between Crocker-Huffman diversion dam (RM 52.0), Snelling Bridge 

(RM 46.4), Highway 59 Bridge (RM 42.0), and Shaffer Bridge (RM 32.8) (Source: Merced ID, 2014b,c,d).

Species Life Stage Life Stage 

Timing

EPA (2003) 

Guideline 

(7DADM 

°C)

Location

Percent of Time EPA (2003) Guideline Exceeded

Environmental 

Baseline

Merced 

ID 

Proposed

Water 

Boarda

Conservation 

Groups FWS NMFS California DFW

Central 

Valley 

Steelhead

Adult 

upstream 

migration

October 

through 

April

18°C

Below 

CHDb 1% 1% 1% 30% 2% 8% 1%

Snelling 

Bridge 1% 1% 2% 1% 2% 8% 2%

Highway 

59 Bridge 3% 3% 3% 1% 4% 8% 3%

Shaffer 

Bridge 11% 10% 5% 84% 10% 10% 5%

Adult 

rearing

Yearround 18°C

Below 

CHD 5% 4% 10% 15% 6% 14% 13%

Snelling 

Bridge 24% 16% 24% 21% 11% 16% 22%

Highway 

59 Bridge 35% 31% 29% 31% 29% 18% 30%

Shaffer 

Bridge 44% 43% 35% 438% 44% 40% 35%

Spawning 

and egg 

incubation

December 

through 

May

13°C

Below 

CHD 34% 35% 29% 29% 32% 29% 27%

Snelling 

Bridge 36% 37% 32% 32% 34% 32% 31%

Highway 

59 Bridge 38% 38% 36% 35% 35% 36% 35%
165

Species Life Stage Life Stage 

Timing

EPA (2003) 

Guideline 

(7DADM 

°C)

Location

Percent of Time EPA (2003) Guideline Exceeded

Environmental 

Baseline

Merced 

ID 

Proposed

Water 

Boarda

Conservation 

Groups FWS NMFS California DFW

Shaffer 

Bridge 44% 45% 43% 44% 45% 44% 44%

Juvenile 

rearing and 

emigration

Yearround 16°C (core)

Below 

CHD 29% 27% 32% 436% 27% 27% 33%

Snelling 

Bridge 42% 41% 37% 40% 43% 36% 37%

Highway 

59 Bridge 48% 48% 42% 44% 50% 46% 39%

Shaffer 

Bridge 54% 55% 51% 50% 54% 54% 47%

Juvenile 

rearing and 

emigration

Yearround18°C (noncore)

Below 

CHD 5% 4% 10% 13% 6% 14% 13%

Snelling 

Bridge 24% 16% 24% 26% 11% 16% 22%

Highway 

59 Bridge 35% 31% 29% 34% 29% 18% 30%

Shaffer 

Bridge 44% 43% 35% 40% 44% 40% 35%

Juvenile 

oversummer 

rearing

June 

through 

September

16°C

Below 

CHD 64% 59% 69% 81% 51% 46% 73%

Snelling 

Bridge 85% 83% 78% 86% 84% 66% 82%

Highway 

59 Bridge 90% 90% 86% 88% 91% 88% 87%

Shaffer 

Bridge 95% 95% 93% 91% 95% 95% 91%
166

Species Life Stage Life Stage 

Timing

EPA (2003) 

Guideline 

(7DADM 

°C)

Location

Percent of Time EPA (2003) Guideline Exceeded

Environmental 

Baseline

Merced 

ID 

Proposed

Water 

Boarda

Conservation 

Groups FWS NMFS California DFW

Smoltificatio

n

October 

through 

May

14°C

Below 

CHD 40% 41% 33% 36% 39% 36% 32%

Snelling 

Bridge 43% 44% 38% 38% 41% 39% 35%

Highway

59 Bridge 45% 46% 42% 40% 43% 42% 39%

Shaffer 

Bridge 49% 50% 48% 47% 48% 48% 47%

Fall-run 

Chinook 

Salmon

Adult 

upstream 

migration

September 

through 

December

18°C

Below 

CHD 9% 8% 17% 27% 12% 31% 16%

Snelling 

Bridge 27% 18% 32% 23% 19% 31% 27%

Highway 

59 Bridge 33% 30% 36% 32% 31% 32% 35%

Shaffer 

Bridge 38% 37% 41% 439% 42% 48% 42%

Spawning 

and egg 

incubation

October 

through 

March

13°C

Below 

CHD 43% 45% 43% 44% 44% 45% 43%

Snelling 

Bridge 44% 45% 44% 45% 46% 46% 44%

Highway 

59 Bridge 45% 46% 45% 45% 47% 47% 45%

Shaffer 

Bridge 48% 49% 48% 548% 51% 50% 49%

Juvenile 

rearing and 

January 

through 16°C Below CHD 5% 4% 0% 34% 4% 1% 0%
167

Species Life Stage Life Stage 

Timing

EPA (2003) 

Guideline 

(7DADM 

°C)

Location

Percent of Time EPA (2003) Guideline Exceeded

Environmental 

Baseline

Merced 

ID 

Proposed

Water 

Boarda

Conservation 

Groups FWS NMFS California DFW

emigration May

Snelling 

Bridge 16% 16% 1% 8% 13% 5% 0%

Highway 

59 Bridge 25% 25% 6% 14% 21% 11% 1%

Shaffer 

Bridge 31% 33% 21% 21% 25% 22% 14%

a Water Board results are based on a flow scenario developed by Merced ID that incorporates 35 percent of unimpaired flow from February 

through June annually and baseline conditions for remaining months as provided by a Water Board comment reflecting potential flow 

requirements released in its Draft Substitute Environmental Document.

b CHD = Crocker-Huffman diversion dam
168

The long-term water temperature improvement plans recommended by NMFS and 

by California DFW contain some elements pertaining to engineering options to deliver 

colder water from Lake McClure to downstream of Crocker-Huffman diversion dam that 

have already been studied by Merced ID and presented in its reservoir water temperature 

management and feasibility study. In Technical Memorandum 2-5 (Merced ID, 2014e) 

Merced ID concludes that:

 Providing abbreviated compliance with modified temperature objectives 

similar to those recommended by California DFW between February and 

September would require about 800,000 to 1,000,000 acre-feet of water, which 

is nearly 100 percent of the average annual inflow to Lake McClure.

 Installing a temperature control device that allows releases to be made from 

three different depths in Lake McClure may provide a minor increase in the 

ability to meet temperature objectives in wet years, minimal ability to increase 

the frequency of meeting temperature objectives in normal years, and no ability 

to significantly decrease downstream water temperatures in dry and critically 

dry years. 

 Construction of a pipe to deliver water released from Lake McClure to 

Crocker-Huffman diversion dam would require from 7.5 to 10-miles of 

construction. Reducing the amount of cold water released into McSwain 

reservoir would increase the temperature of water released from McSwain 

dam, which could cancel out the beneficial temperature effects to the lower 

Merced River. 

 Construction of a cold water channel through McSwain reservoir to reduce the 

warming of water as it passes through the reservoir may enhance the average 

daily water temperature of releases from McSwain dam, but would reduce the 

degree of mixing within the reservoir and increase the temperature of the 

remaining water. If mixing is limited during certain times of the day, such as 

when peaking flows are released from New Exchequer powerhouse, it could 

result in highly variable daily water temperatures of water released at McSwain 

dam.

 Reconfiguring releases from Lake McClure so that higher volumes of water are 

released at certain times of year to reduce heating of water as it moves 

downstream would require tradeoffs in temperature management. For 

example, higher releases in the spring could benefit the lower Merced River 

temperature regime, but at the cost of reduced ability to meet temperature 

objectives in late summer and fall. 

Merced ID concludes that none of the alternatives analyzed were feasible and 

defined feasible as “being accomplished in a successful manner within a reasonable 

period of time, taking into account economic, environmental, social, and technological 

factors.”
169

FWS recommends conducting a riparian microclimate study and collecting data 

for calibrating a HEC-5Q water temperature model analysis to determine the optimum 

length and width of riparian forest needed to achieve temperature objectives downstream 

of Crocker-Huffman diversion dam (we discuss aspects of the FWS’ recommendation 

regarding establishing a riparian forest canopy in the Habitat Restoration and 

Management section). We agree that establishing a riparian forest canopy adjacent to the 

Merced River from Crocker-Huffman diversion dam to Shaffer Bridge could help to 

decrease water temperatures compared to existing conditions. In its April 1, 2011, study 

determination letter, the Commission concludes that the primary reason for the absence 

of a riparian forest is in-channel and floodplain dredger and aggregate mining, not 

operation of the hydroelectric project. Consequently, having Merced ID be responsible 

for conducting modeling to determine the optimal configuration for a restored floodplain 

forest would be more like a research study not directly related to hydropower operation. 

A properly timed spring pulse flow, discussed under Pulse Flows, would create optimal 

conditions for germination of riparian cottonwood trees, which eventually would provide 

shading and some water temperature relief. Enhanced floodplain configuration could 

also result from implementation of gravel augmentation, discussed in Spawning Habitat 

Enhancement, which could also serve to foster establishment of riparian vegetation. Both 

of these measures would address project-related cumulative effects, whereas establishing 

the ideal riparian forest width may or may not lead to meaningful water temperature 

enhancements. 

With regard to California DFW’s recommendation that Merced ID evaluate the 

feasibility of prolonging and stabilizing the irrigation delivery season to provide the 

benefit of shorter residence times, Merced ID did evaluate reducing the residence time 

downstream of Lake McClure by releasing larger volumes of water from New Exchequer 

dam (Merced ID, 2014e). California DFW does not provide sufficient detail for us to 

analyze how prolonging and stabilizing of irrigation deliveries by using irrigation storage

capacity downstream of the project would enhance the temperature regime of the lower 

Merced River. Therefore, we have no basis to recommend that Merced ID evaluate the 

feasibility of this measure.

Merced ID modeling indicates that the divergent stakeholder flow 

recommendations to reduce temperature would have relatively small effects compared to 

environmental baseline and proposed project flows, and the recommended flows would 

still be inadequate to meet applicable temperature criteria. Most of the recommended 

alternatives would increase the frequency of water supply shortages and increase 

temperatures in summer and fall of some water years due to the high flows necessary for 

release in the spring to lower temperatures. Achieving temperature and physical

anadromous fish habitat enhancements depends on water available for flow releases 

during different times of the year and the amount of storage in Lake McClure.

Regardless of the outcome of recommendations regarding flow regimes, minimum 

pool levels, and temperature management, water temperature monitoring of some kind as 

proposed, specified, and recommended by the stakeholders would be appropriate to 
170

document conditions in the project-affected reach downstream of Crocker-Huffman 

diversion dam to Shaffer Bridge and its relationship to anadromous fish habitat. 

Although monitoring water temperature upstream of Crocker-Huffman diversion dam 

would have some value for interpreting downstream results, releases from New 

Exchequer dam have a relatively short residence time in McSwain reservoir, Merced 

Falls reservoir, and the Crocker-Huffman impoundment. 

Any temperature management measures included in a new license would most 

likely pertain to the Crocker-Huffman to Shaffer Bridge reach. As such, monitoring 

water temperature immediately downstream of Crocker-Huffman diversion dam at or 

near the existing gage near Snelling would document conditions at the upstream limit of 

anadromous fish habitat. Monitoring water temperature at the existing gage at Shaffer 

Bridge would document conditions at the downstream end of the project-affected reach. 

The diversions that occur within this reach are not project-related, but monitoring water 

temperature at intermediate locations would help to interpret whether temperature 

measurements at Shaffer Bridge are related to non-project factors such as irrigation 

returns. Overall, monitoring water temperature at several locations would provide data 

on whether project-related flow releases from Lake McClure are achieving expected 

water temperature enhancements within the limitations of the available cold water pool 

and enable such effects to be separated from non-project effects. Ultimately, when 

combined with flow and anadromous fish monitoring, this monitoring would provide a 

basis for evaluating the need for future adjustments to the project flow regime. 

Developing the water temperature monitoring plan specified in preliminary WQC 

condition 19 would allow four to eight temperature monitoring gages to be placed at 

locations agreed upon by a technical advisory committee. Placement of gages at the 

upstream and downstream end of the project-affected reach would enable temperature to 

be correlated with associated flows because there are currently flow gages located at 

these two locations. Provisions in the plan specified in preliminary WQC condition 19 

would also enable identification of factors that may affect water temperature and which 

factors are project related. In addition, if monitoring shows that project operation is

increasing water temperatures, provisions for developing a plan for corrective actions are 

included. The Water Board preliminary WQC condition 8 would have Merced ID 

develop a plan for decreasing water temperatures in the lower Merced River without 

necessarily establishing a relationship to project operation. The Water Board’s approach 

specified in preliminary WQC condition 19 bases corrective actions on monitoring results 

and a linkage to project operation. We find this approach to basing corrective actions on 

monitoring results and a linkage to project operation to be reasonable. Monitoring flows 

at interim locations or downstream of Shaffer Bridge, as recommended by NMFS, would 

not have a relationship to hydroelectric project operation. 
171

Pulse Flows

Pulse flows are defined as discrete water releases into the lower Merced River to 

benefit the upstream migration of adult salmonids during the fall, and downstream 

migration of juvenile/smolt salmonids during the spring. Additionally, pulse flow 

releases that inundate the floodplain are designed to promote recruitment of riparian tree 

species. Merced ID currently releases an October pulse flow of 12,500 acre-feet in 

addition to the required minimum flows (which range from 15 to 75 cfs in October) under 

a Memorandum of Understanding with California DFW, but this measure is not included 

in the current license for the project. Merced ID does not propose fall or spring pulse 

flow releases. 

NMFS [10(j) recommendation 1.1A(2)] recommends a spring pulse flow with a 

variable flow volume based on water year type, ranging from 10,000 acre-feet in dry and 

critically dry years to 60,000 acre-feet in wet years. The dry and critically dry year 

spring pulse flows are designed to provide outmigration pulses for juvenile and smolt 

salmonids. The pulse flows during wetter water years are designed to have a gradual 

ascending and descending hydrograph beginning in May, up to 9 days of floodplain 

inundation to provide salmonid rearing and foraging habitat and promote riparian forest 

recruitment, and 2 to 3 days of peak discharge. The peak discharges would be intended 

to provide channel maintenance flows, mobilize sediments, reduce or stop the rate of 

vegetation encroachment into the channel, and promote LWD recruitment from local 

channel banks. NMFS also recommends a fall pulse flow volume of 12,500 acre-feet in 

all water year types. NMFS recommends that the pulse flow timing and duration be 

determined annually by a technical advisory committee. NMFs recommends that any 

spring and fall pulse flows be in addition to minimum flows that may be included in a 

new license. 

FWS [amended 10(j) recommendation 3(A1)] recommends a fall pulse flow of 

1,200 cfs with a total volume of 19,830 acre-feet in below normal to wet years and a total 

volume of 7,932 acre-feet in dry and critically years. FWS does not recommend a 

discrete spring pulse flow during wet, above normal, below normal, and dry water years 

but rather includes a gradually increased minimum flow that begins in March, peaks in 

late March, April, or May, depending on water year type, then gradually decreases to a 

base minimum flow in spring or early summer (table 3-14). FWS further recommends 

that a technical advisory committee establish spring pulse flows for outmigrating juvenile 

salmonids during dry and critically years. In addition, FWS recommends that when 

possible during above normal and wet water years, flows should inundate floodplain 

surfaces for at least 5 days beginning in late May or early June.

California DFW [10(j) recommendation 3D] recommends a spring floodplain 

inundation flow in cfs over a 2-day period between March 14 and March 28 in below 

normal, above normal, and wet water year types, with no requirement in dry and critically 

dry years. The spring floodplain inundation flow volume (as converted from cfs) varies 

by water year type and includes: 15,840 acre-feet (4,000 cfs per day) in wet years, 
172

11,880 acre-feet (3,000 cfs per day) in above normal years, and 7,920 acre-feet (2,000 cfs 

per day) in below normal years. In addition, California DFW’s minimum flow 

recommendation, discussed in the previous section, includes an extended pulse flow of 

from 2 to 6 weeks. The 2 week pulse flows that would occur in May of dry and critically 

dry years are intended to stimulate salmonid outmigration prior to the summer months 

when water temperature becomes stressful under all flow scenarios. The 3 to 6 week 

pulse flows during wet, above normal, and below normal water years would serve the 

outmigration function but also open up floodplain habitat for salmonid rearing and 

foraging. California DFW [10(j) recommendation 3E] recommends adult Chinook 

attraction flows of 1,000 cfs over varying periods during October and November in all 

water year types. The attraction flow volumes vary by water year type and include; 

23,760 acre-feet (12 days) in wet and above normal years, 17,820 acre-feet (9 days) in 

below normal years, and 11,880 acre-feet (6 days) in dry and critically dry years. 

The Conservation Groups recommend a spring pulse flow volume of 20,000 acrefeet in critically dry years unless storage in Lake McClure is less than 200,000 acre-feet, 

in which case the pulse flow would be 5,000 acre-feet, and an annual fall pulse flow 

volume of 12,500 acre-feet in all water year types. The Conservation Groups do not state 

that spring or fall pulse flow releases should be in addition to the minimum flow that may 

be included in a new license. Although the Conservation Groups do not recommend a 

discrete spring pulse flow during wet, above normal, below normal, or dry water years, 

by tying their minimum flow during the spring to a percentage of inflow to Lake 

McClure, the flows would gradually increase until April or May and then gradually 

decrease after that, similar to the inflow to Lake McClure pattern shown in table 3-1. 

Our Analysis

Pulse flows recommended by FWS, NMFS, California DFW, and the 

Conservation Groups are variable in terms of both volume and how they are defined. We 

converted all recommended pulse flows to acre-feet to enable an equal comparison of the 

recommendations (table 3-14). In general, the recommendations are more similar for fall 

pulse flows where they range from 7,932 to 13,881 acre-feet in dry years and from 

12,500 to 19,830 acre-feet in wet years. The recommendations of NMFS and the 

Conservation Groups would represent a continuation of existing conditions under the 

Memorandum of Understanding with California DFW, with a constant fall attraction flow 

release regardless of water year type. California DFW and FWS recommend providing 

1,000 or 1,200 cfs, respectively, for varying numbers of days depending on water year 

types, which equates to 11,880 to 23,760 acre-feet, for California DFW’s 

recommendation and 7,932 to 19,830 acre-feet for FWS’ recommendation. The primary 

purpose of fall pulse flows is to attract anadromous fish to upstream spawning areas of 

the Merced River. California DFW notes its reason for its recommended maximum pulse 

flow of 1,000 cfs is to (1) avoid floodplain inundation, which would not be desirable 

during the spawning season, and (2) keep spawning Chinook salmon in the channel 

proper. Fall floodplain inundation is atypical during the Chinook salmon spawning 

period and if redds should be constructed in the inundated floodplain during a short-term 
173

attraction flow release, they would be dewatered when the flows recede. The reduction in 

the fall pulse flow duration during dry and critically dry water years embedded in the 

California DFW and FWS recommendations, respectively, would allow the preservation 

of water and associated cold pool storage in Lake McClure while at the same time would 

provide the benefits of fall pulse flows to attract adult Chinook salmon to the mouth of 

the Merced River.

We agree with the rationale of the agencies and Conservation Groups that a fall 

pulse flow release would continue to attract adult Chinook salmon to the Merced River 

for spawning. We also concur that pulse flows should not be such that over bank flows 

occur to ensure that spawning occurs in the channel proper and therefore should be 

restricted to no more than 1,000 cfs. Releases of 1,000 cfs would need to occur for 

between 6 and 7 days to reach the current, NMFS, and Conservation Groups’ 

recommended fall block pulse flow of 12,500 acre-feet. If block flows do not include the 

volume associated with minimum flows, as NMFS recommends, it may be possible to 

extend the number of days of releases of up to 1,000 cfs for salmon attraction, but it 

would deplete the available storage in Lake McClure for later use. Similarly, increasing 

the number of days that fall pulse flows are released to 10 or 12 days, as FWS and 

California DFW recommend during wet, above normal, and below normal water years, 

could result in enhanced salmon attraction. However, it would also result in an additional 

depletion in the volume of water in Lake McClure. We consider the value of carrying 

over as much water as possible for use for habitat enhancement in the lower Merced 

River and irrigation during a following year to outweigh the potential increased attraction 

of Chinook salmon that could be achieved with an additional 3 to 6 days of fall releases. 

However, monitoring salmonid upstream migration in the lower Merced River, discussed 

in detail later, would provide data to assess the effectiveness of any fall pulse flow 

releases that may be included in a new license and provide a basis for adjustments, if 

necessary.

Recommended discrete spring pulse flow volumes range from 7,920 to 10,000 

acre-feet in dry years and from 15,840 to 60,000 acre-feet in wet years (table 3-14). In 

general, NMFS and California DFW recommend higher pulse flows during wetter water 

years with the objective of providing at least some floodplain inundation that would 

enhance riparian floodplain vegetation development and increase food availability for 

rearing native salmonids. In contrast, FWS and the Conservation Groups only 

recommend discrete spring pulse flows during the driest water years, although an 

extended spring pulse flow is embedded in the FWS and California DFW minimum flow 

recommendations. The basis for this approach given by the Conservation Groups and 

California DFW is that a late spring pulse flow would facilitate successful outmigration 

of those salmonids that are able to survive through the spring, prior to encountering low 

flow and high temperature conditions during the summer. Similarly, FWS states that by 

providing relatively cold water (i.e., cooler than 15oC) to the lower Merced River during 

the spring, smoltification of juvenile salmon and steelhead would be expedited, and 

outmigration would occur prior to low flow, high temperature conditions that promote 
174

disease and predation by warmwater predators. We consider the stated reasons for these 

approaches to be valid and selecting the most appropriate spring pulse flow approach 

necessitates balancing environmental benefits against the effects on available storage in 

Lake McClure for use during the primary irrigation season.

Table 3-14. Stakeholder recommendations for discrete spring and fall pulse flow 

volumes (acre-feet)

Agency Season Wet Above 

Normal

Below 

Normal Dry CriticallyDry

NMFS

Spring 60,000 50,000 30,000 10,000 10,000

Fall 12,500 12,500 12,500 12,500 12,500

FWS

Spring N/A N/A N/A N/A N/A

Fall 19,830 19,830 19,830 7,932 7,932

California 

DFW

Springa 15,840 11,880 7,920 45,064 30,942

Fall 23,760 23,760 17,820 11,880 11,880

Conservation 

Groups

Spring N/A N/A N/A N/A 20,000

Fall 12,500 12,500 12,500 12,500 12,500

a California DFW includes a discrete 2-day pulse flow in wet (4,000 cfs/day), above 

normal (3,000 cfs/day), and below normal water years (2,000 cfs/day), and a 2 week 

pulse flow of 1,420 cfs in dry water years and 1,040 cfs in critically dry water years 

within its minimum flow recommendation shown in table 3-9; we converted this to 

acre-feet in this table for comparison purposes.

N/A = not applicable; however, FWS and the Conservation Groups embed extended 

spring pulse flows in their minimum flow recommendations shown in table 3-9.

We agree that during all but dry and critically dry water years, a spring pulse flow 

that achieves some floodplain inundation would enhance development of floodplain 

vegetation, including cottonwoods and other riparian trees and shrubs that could provide 

shade to the channel during warmer months when water temperature limits the suitability 

of lower Merced River salmonid habitat. It would also provide rearing and foraging 

overbank habitat for juvenile salmonids that would be confined to the channel proper 

without such pulse flows. Although California DFW’s recommended 2-day pulse flow in 

March would provide young salmonids with access to floodplain cover and food sources, 

a short term pulse flow could also expose fish that occupy the floodplain to stranding as 

flows recede into the channel proper. 

If a spring pulse flow is to be implemented, we consider the overall approach 

taken in the NMFS pulse flow recommendation to be reasonable. This would entail a 

gradual increase of flows to a 2 or 3 day maximum followed by a gradual decrease in 
175

flows to stimulate germination of cottonwood and other riparian vegetation with the goal 

of up to 9 days of floodplain inundation. We recognize that there is natural variability in 

the magnitude of spring pulse flows during different water years and mimicking this 

variability would be ideal. However, the lower Merced River is regulated and if the 

floodplain inundation and channel maintenance objectives can be achieved with a release 

of 30,000 acre-feet (the below normal water year NMFS recommendation), we are not 

convinced that the additional 20,000 to 30,000 acre-feet recommended for above normal 

and wet water years, respectively, would warrant the additional loss of Lake McClure 

water storage. We also note that, as mentioned for the NMFS recommended fall pulse 

flow, requiring that any spring pulse flow volume be in addition to the minimum flows 

that may be included in a new license would deplete the supply of water stored in Lake 

McClure.

Both the spring pulse flows embedded in the FWS and California DFW minimum 

flow recommendations would result in substantial periods of floodplain inundation. 

Assuming floodplain inundation occurs at flows above 1,000 cfs, the FWS 

recommendation would result in more than 2 months of floodplain inundation in a wet 

water year, nearly a month in an above average water year, nearly 2 weeks in a below 

normal water year, and 5 days in a dry water year. The California DFW recommendation 

would result in about 6 weeks of floodplain inundation in wet and above normal water 

years and 4 weeks of floodplain inundation in a below normal water year. We do not 

dispute the environmental benefits that such extended periods of floodplain inundation 

would achieve, but we are not convinced that the volume of water necessary to achieve 

these benefits warrant the additional loss of Lake McClure water storage.

If a spring pulse flow is released in wet, above normal, or below normal water 

years, such releases could also serve the dual purpose of stimulating salmonid 

outmigration prior to stressful summer flow and temperature conditions, if timed 

appropriately. A technical advisory committee could serve a valuable function in 

providing input on the timing of any spring pulse flow. 

We also agree with the stakeholders that during dry or critically dry water years, 

when spring floodplain inundation flows are not released, a short-term pulse flow would 

likely stimulate salmonid emigration from the lower Merced River prior to stressful 

summer conditions. The range of critically dry water year flows to achieve this objective 

offered by stakeholders is broad: 10,000 acre-feet by NMFS, 20,000 acre-feet by the 

Conservation Groups, and 30,942 by California DFW. We expect that if a critically dry 

water year pulse flow is effective in stimulating salmonid outmigration, a similar release 

during dry water years would achieve the same outcome. We have no data to support 

which of these flows would result in a meaningful stimulation of salmonid outmigration. 

It is possible that a release of 10,000 acre-feet in dry or critically dry water years could be 

configured to effectively stimulate outmigration of salmonids prior to the summer. 

Again, input from a technical advisory committee regarding the duration and magnitude 

of the release would increase the likelihood of success and conserve Lake McClure water 

compared to spring pulse releases of 20,000 or 39,942 acre-feet recommended by the 
176

Conservation Groups and California DFW, respectively. Monitoring outmigration, as 

proposed by Merced ID and stakeholders, during dry or critically dry pulse flow releases, 

would provide a measure of effectiveness and a basis for adjusting future dry and 

critically dry water year pulse releases. 

Ramping Rates

Rapid changes in river flow associated with hydroelectric project operations may 

adversely affect aquatic resources. If water recedes in a project-affected stream reach 

faster than it naturally would, adverse effects can include fish stranding in shallow, lowgradient areas and off-channel habitat (causing immediate or delayed mortality); 

temporary loss of habitat or loss of habitat access; and dewatering of fish redds, 

amphibians, aquatic insects, and plant life (Hunter, 1992). Rapid changes in stream flow 

(both increases and decreases) also can affect fish behavior that could reduce survival or 

growth. Limits governing the rate and timing of project-induced river stage changes 

(ramping rates) are often established to protect aquatic organisms from these projectrelated effects. A ramping rate is the rate of change in stage resulting from regulated 

discharges. For the Merced River Project, pulse flow releases and flood control releases 

are most likely to result in rapid changes in river flows that may warrant establishment of 

ramping rates.

Under normal project operation, flood control or irrigation releases have the 

potential to result in rapid increases or decreases in flows. In these events, for all 

controllable flow rate changes above a base flow of 200 cfs, Merced ID proposes to 

restrict the rate of change of release from McSwain dam during any 1-hour period to not 

more than double (upramping) or less than one-half (downramping) the amount of the 

controlled release from the reservoir at the start of the change, with noted exceptions for 

emergency situations.

NMFS [10(j) recommendation 1.1B(7)] recommends that minimum instream flow 

upramping and downramping rates occur evenly over a 24-hour period, with a maximum 

of 500 cfs per 24-hour period in all water years, with the exception of spring pulse flows 

in above normal and wet water years, when downramping rates are recommended to 

occur evenly over a 24-hour period at a maximum of 100 cfs per day (about 1 inch per 

day) to promote riparian seedling survival. The compliance point is not specified. FWS 

[amended 10(j) recommendation 3A1] also recommends this gradual downramp of 100 

cfs per day as measured at Shaffer Bridge in late May or early June during above normal 

and wet water years.

California DFW [10(j) recommendation 3G] recommends a ramping rate for 

increasing flows that restricts the rate of change to not more than double the amount of 

the release during any 1-hour period. For decreasing flows, California DFW 

recommends the rate of change be no more than 2 inches per hour as measured at the 

existing gage near Snelling Bridge, downstream of Crocker-Huffman diversion dam, and 
177

at flows above 200 cfs, the rate of change in any one 24-hour period, the flow rate should

not drop by more than 500 cfs.

Our Analysis

Flow releases for hydroelectric project operation occur at New Exchequer and 

McSwain dams. These releases flow directly into impoundments, which minimize 

adverse effects typically associated with upramping and downramping in riverine habitat. 

The rate of change in flows downstream of Crocker-Huffman diversion dam is influenced 

by both hydroelectric project flow releases from McSwain dam and diversions for 

irrigation into the Main Canal, a non-jurisdictional facility. Therefore, California DFW 

and FWS’ recommended downramping compliance point downstream of the diversion 

dam, and any other ramping rate compliance point downstream of Crocker-Huffman 

diversion dam would measure both the rate of change of releases from McSwain dam, 

which would be subject to the Commission’s jurisdiction, and gate operation at the Main 

Canal in response to changing flows, which would not be subject to the Commission’s 

jurisdiction.

Merced ID’s proposed upramping and downramping rate compliance point would 

be at the outflow from the McSwain powerhouse and there would be no ambiguity 

regarding the Commission’s ability to document and enforce any ramping rates that may 

be included in a new license. California DFW’s recommended upramping rate (not more 

than double the flows during any 1 hour) and compliance point is the same as Merced

ID’s. Merced ID’s proposed and California DFW’s recommended upramping rate would 

serve to control the increases in flow associated with the onset of the irrigation season 

and any pulse flows that may be included in a new license. The benefits of the 

upramping rate recommended by NMFS (a maximum increase of 500 cfs evenly spread 

over a 24-hour period) are difficult to evaluate because as worded, it would only pertain 

to changes in minimum instream flows and the compliance point is not specified. Few 

increases in the minimum flows proposed or recommended by any entity change by more 

than 500 cfs between any designated release periods.

Merced ID’s proposed downramping rate would restrict the rate of change within a 

1-hour period to not less than one-half the amount of the controlled release at the start of 

the change. Similar to the proposed upramping rate, the point of outflow from McSwain 

powerhouse would be the compliance point. This is similar to article 42 of the current 

license, which requires Merced ID to restrict the rate of change of release during any 

1-hour period to not less than one-half the amount of release at the start of the change at 

Crocker-Huffman diversion dam. The Merced Falls Project operates in a run-of-river 

mode, so flow changes at McSwain powerhouse essentially reflect the flow changes that 

reach Crocker-Huffman diversion dam.

California DFW recommends a downramping rate of no more than 2-inches per 

hour as measured downstream of Crocker-Huffman diversion dam. To support its 

recommended ramping rate, California DFW relies on the work of Hunter (1992), which 

concludes that in unregulated river systems, aquatic biota are rarely exposed to drops in 
178

stage of more than 2-inches per hour and therefore are not adopted to more excessive 

stage changes. In addition, California DFW notes that a controlled downramping rate in 

late spring that approximates a natural recession rate promotes recruitment of willows 

and cottonwoods to riparian floodplains. Both California DFW and NMFS’ 

recommended spring downramping rates would achieve this goal. California DFW states 

that under Merced ID’s proposed downramping rate, using the maximum release of 6,000 

cfs allowed by the current Corps’ flood control rules, flows could be dropped by 3,000 

cfs in 1 hour and by 1,500 cfs during the next hour with no ecological rationale.

Controlling downramping rates can reduce the potential for aquatic biota stranding 

and, in the spring, stimulate the growth of riparian trees and shrubs. However, the 

downramping rates that occur in Merced River downstream of Crocker-Huffman 

diversion dam are a function of releases from McSwain powerhouse and operation of the 

gates for irrigation purposes at the Main Canal. Only releases from the McSwain 

powerhouse are within the Commission’s ability to regulate. Our review of typical 

releases from McSwain powerhouse during a normal and dry water year indicates that the 

maximum range of decreases in flow during a relatively short period of time is from 650 

to 1,000 cfs (see figures 3-5 and 3-7). Therefore the scenario that California DFW 

presents is unlikely to occur except in emergency situations. Implementing Merced ID’s 

proposed downramping rate would provide control over flows that reach CrockerHuffman diversion dam. The ramping rates further downstream would be influenced by 

the rate of additional flow diversions and returns associated with non-project facilities 

and natural attenuation of flows, making it more difficult to establish a direct relationship 

with the downramping protocol when compared to using the existing gage near Snelling. 

However, we have no data to assess how this current operating mode translates into 

downramping rates downstream of the diversion dam. Monitoring flows and the 

downramping rate at the existing gage near Snelling immediately downstream of 

Crocker-Huffman diversion dam, as California DFW recommends, would provide the 

Commission with data regarding the downramping protocol and whether adjustments to 

that protocol may be needed in the future to reduce stranding risk and stimulate 

floodplain revegetation. 

Project Reservoir Management

The volume of water required in Lake McClure affects Merced ID’s ability to

address water supply, carryover storage, and power generation needs associated with 

managing the project reservoirs. The volume of water in Lake McClure also affects 

Merced ID’s ability to achieve minimum instream flows, pulse flows, and water 

temperature objectives. Establishing a minimum pool elevation sets the minimum 

volume of water available for downstream water uses. Maintaining relatively high 

reservoir water levels enhances recreation use of the project reservoirs. McSwain 

reservoir operates as a re-regulating afterbay for flows released from Lake McClure 

resulting in relatively stable releases at McSwain dam.
179

Merced ID proposes to make a good faith effort to maintain Lake McClure’s water 

surface elevation as high as possible from April through October, consistent with the 

primary purposes of the reservoir, and to maintain a minimum pool of not less than 

115,000 acre-feet (which equates to an elevation of about 640 feet), except for drawdown 

necessary to maintain minimum and target streamflows. This is nearly identical to 

operation under article 44 of the current license. At McSwain reservoir, Merced ID 

proposes to make a good faith effort to operate the reservoir for recreational purposes in 

such a manner that at no time would the reservoir be drawn down below elevation 388 

feet except for drawdowns necessary to maintain minimum streamflows and as necessary 

for repairs.

The Water Board [preliminary WQC condition 15] reserves the right to condition 

the project with a minimum pool requirement for Lake McClure in light of the whole 

record, but does not yet specify a minimum pool. The Water Board [preliminary WQC 

condition 9] also specifies that Merced ID submit a drought plan within 1 year of license 

issuance. The plan would provide overarching guidance for operation during an 

emergency drought and/or multiple critically dry years and would be created in 

consultation with a committee. The plan would include Commission license or water 

quality certification variances that Merced ID may request. No further details were 

provided as to the content of the plan.

NMFS [10(j) recommendation 1.1A(8)] recommends a contingency for multiple 

consecutive dry and/or critically dry water years that would modify project operation. 

Merced ID would notify the resource agencies of drought concerns by March 10 of the 

second or subsequent dry/critically dry water year. By May 1 of these same years, 

Merced ID would consult with the resource agencies to discuss operational plans to 

manage the drought conditions. Following this consultation, Merced ID would file a 

drought plan with the Commission. Merced ID states in its response letter of September 

5, 2014, that it accepts NMFS’ recommendation, and on September 22, 2014, filed its 

revised, proposed measure with the Commission that includes a provision for 

contingency planning during a multi-year drought that is nearly identical to the NMFS 

recommendation.

FWS [amended 10(j) recommendation 3(A1)] recommends Merced ID maintain a 

minimum pool of 130,000 acre-feet (an elevation of about 650 feet) in Lake McClure. 

Once the minimum pool storage drops below 130,000 acre-feet, all irrigation diversions 

would cease and the only flow releases from Lake McClure would be to maintain 

designated minimum instream flows. The Conservation Groups make a similar 

recommendation.

California DFW [10(j) recommendation 3F] recommends Merced ID maintain 

Lake McClure as high as possible from April through October, with a target minimum 

pool of no less than 200,000 acre-feet (an elevation of about 680 feet) on September 30 

of each year, by maintaining a minimum pool of no less than 265,000 acre-feet (an 

elevation of about 710 feet) at all times by ceasing all irrigation diversions, except for 
180

drawdowns as necessary to maintain minimum instream flows. Additionally, California 

DFW recommends that Merced ID submit an annual draft plan to the Commission 

describing planned operation to maintain Lake McClure levels, including the estimated 

delivery pattern needed to achieve a 200,000 acre-feet minimum pool target by the end of 

September, with a final operation plan submitted annually to the Commission by May 15. 

California DFW further recommends that when a dry or critically dry water year is 

immediately preceded by a dry or critically dry water year, Merced ID should notify the 

agencies by June 1 of any potential concerns related to meeting the required Lake 

McClure minimum pool, and implement revised operation upon Commission approval. 

No stakeholders made any recommendations relating to the minimum pool at 

McSwain reservoir.

Our Analysis

Merced ID provided model results that compare water supply, carryover storage, 

and power generation for its proposed measure and the stakeholder recommended flow 

regimes and minimum pool elevations to existing baseline conditions. The Merced ID 

model runs were developed without considering any additional flow measures that could 

be necessary to meet either NMFS, FWS, or California DFW water temperature 

objectives. California DFW also provided model output of reservoir operations based on 

its recommendation and compared results to existing baseline conditions, although 

detailed model documentation was not included. The Merced ID model runs provide 

results summarized over a 36-year period of record (1970–2006). The California DFW 

model results were presented using 2004 as a reference year.

Table 3-15 shows predictions of water supply shortage and carryover storage in 

Lake McClure for the Merced ID proposed measure along other stakeholder 

recommendations and compares them to baseline conditions. Water supply shortages 

increase when Lake McClure is operated under California DFW’s recommended 

minimum pool volume of 200,000–265,000 acre-feet compared with operation under the 

baseline volume of 115,000 acre-feet (which is also Merced ID’s proposed minimum 

pool). The Conservation Groups’ flow regime builds into the measure irrigation delivery 

restrictions based on water year type and results in the greatest total water delivery 

shortage of any alternative proposed or recommended. Carryover storage in Lake 

McClure is substantially reduced under all recommended minimum pool requirements 

and flow regimes compared with the Merced ID proposed measure and the baseline 

conditions. 
181

Table 3-15. Predicted water supply shortage and carryover storage compared to baseline 

conditions (Source: Merced ID, 2014b,c,d).

Water Year Type Water Supply Shortage

(acre-feet)

Lake McClure Carryover 

Storage (acre-feet)

Merced ID proposed measure compared to baseline

Wet 0 -11,000

Above normal 0 -16,000

Below normal 0 -17,000

Dry 0 -29,000

Critically dry <2,000 -12,000

Totala 0 -15,000

FWS amended recommendation compared to baseline

Wet 4,000 -86,000

Above normal 0 -73,000

Below normal 7,000 -184,000

Dry 0 -202,000

Critically dry 69,000 -108,000

Totala 24,000 -115,000

California DFW recommendation compared to baseline

Wet 7,000 -70,000

Above normal 32,000 -360,000

Below normal 100,000 -244,000

Dry 276,000 -230,000

Critically dry 278,000 -8,000

Totala 138,000 -135,000

NMFS recommendation compared to baseline

Wet 16,000 -154,000

Above normal 9,000 -289,000

Below normal 119,000 -293,000

Dry 167,000 -358,000

Critically dry 198,000 -212,000
182

Water Year Type Water Supply Shortage

(acre-feet)

Lake McClure Carryover 

Storage (acre-feet)

Totala 101,000 -234,000

Water Board suggested regime compared to baselineb

Wet 1,000 -59,000

Above normal 0 -128,000

Below normal 28,000 -246,000

Dry 0 -246,000

Critically dry 93,000 -87,000

Totala 34,000 -121,000

Conservation Groups’ recommendation compared to baseline

Wet 126,000 -91,000

Above normal 133,000 -204,000

Below normal 138,000 -65,000

Dry 186,000 -86,000

Critically dry 155,000 9,000

Totala 144,000 -73,000

a

In Merced ID’s table, the term “total” refers to the total of all modeled water year 

types based on actual flows from 1970 through 2005. These values represent a 

weighted average of all water year types combined.

b Water Board results are based on a flow scenario developed by Merced ID that 

incorporates 35 percent of unimpaired flow from February through June annually and 

baseline conditions for remaining months as provided by a Water Board comment 

reflecting potential flow requirements released in its Draft Substitute Environmental 

Document.

Under baseline conditions and the Merced ID proposed measure, Lake McClure 

reaches maximum storage (reservoir is filled) ten times over the 36-year period of record. 

Based on Merced ID’s modeling results, this total is predicted to be reduced to six under 

FWS’ flow and minimum pool recommendation, five under the NMFS flow 

recommendation, four under the Water Board’s suggested flow and California DFW’s 

flow and minimum pool recommendation, and Lake McClure would not fill in any of the 

36 years under the Conservation Groups’ flow and minimum pool recommendation. 

Average annual power generation under existing conditions is about 387 GWh. 

With Merced ID’s proposed flow and minimum pool levels, annual generation is 

predicted to increase to about 389 GWh. The flow and minimum pool recommendations 
183

of stakeholders would decrease predicted average generation to the following amounts: 

FWS—377 GWh; Water Board—375 GWh; Conservation Groups—358 GWh; 

California DFW—352 GWh; and NMFS—346 GWh). 

Merced ID’s modeling results show that maintaining a higher minimum pool than 

115,000 acre-feet in Lake McClure would negatively affect water supply, carryover 

storage, and power generation in all water year types. Additional flow requirements that 

may be necessary to reach target temperatures downstream of Crocker-Huffman 

diversion dam would only increase these effects. We discuss water temperature effects in 

a separate section, Managing and Monitoring Water Temperature.

Merced ID’s proposed measure (AQR2) would maintain a minimum pool 

requirement of 115,000 acre-feet in Lake McClure and provide conditions similar to 

baseline conditions. Increasing the minimum pool as recommended by the agencies 

would serve to retain more coldwater pool in Lake McClure that would enable somewhat 

cooler temperatures to be maintained downstream of Crocker-Huffman diversion dam 

compared to existing conditions or Merced ID’s proposed measure. Figure 3-37 shows 

the effect of preserving the cold pool volume by stopping irrigation diversions when 

storage drops below 265,000 acre-feet during a critically dry water year (2004), as 

California DFW recommends. Water temperature immediately downstream of the 

diversion dam and at the Snelling Bridge are 3 to 5oF cooler from mid-July to midOctober compared to Merced ID’s proposed measure. However, water temperatures 

during this time frame would still be well above the 18.0oC (64.4oF) 7DADM EPA 

guideline for adult steelhead rearing and juvenile rearing and emigration and the 16.0oC 

(60.8oF) guideline for juvenile over-summer rearing shown in table 3-13. 
184

Note: TAF Min Pool = thousands of acre-feet minimum pool.

Figure 3-37. Comparison of lower Merced River water temperatures in 2004 (a critically

dry water year) under 115,000 acre-feet (Merced ID’s proposed measure) 

and 265,000 acre-feet (California DFW) recommended measure) minimum 

pool alternatives at Crocker Huffman diversion dam (RM 52) and Snelling 

Bridge (RM 46.5). (Source: California DFW, 2014a)

Maintaining the recommended higher Lake McClure storage level would have an 

effect on the water available for delivery to irrigators. To illustrate this effect, we 

reviewed Lake McClure storage volumes for summer 2014, a critically dry water year 

within a severe drought (letter from H. EITal, Deputy General Manager, Water 

Supply/Rights, Merced ID, to T.J. LoVullo, FERC, Chief, Aquatic Resources Branch, 

Division of Hydropower Administration and Compliance, filed on October 10, 2014). 

Our analysis only provides a general concept of the effect on irrigation diversions 

because in 2014, Merced ID released the minimum flow of 15 cfs required by the current 

license. Releases of higher minimum flows as recommended by the agencies would 

result in the storage meeting the trigger for cessation of irrigation flows sooner. The 

Conservation Groups’ recommended minimum flow would have irrigation diversions 

equal to 30 to 40 percent of demand in 2014. This would serve to preserve some storage 
185

in Lake McClure, but would occur at the expense of irrigators. Under California DFW’s 

recommendation, irrigation diversions would have stopped after July 4, 2014, and under 

the FWS and Conservation Groups’ recommendations, after September 23, 2014. 

Deliveries of irrigation water would have continued through September with Merced ID’s 

proposed minimum pool trigger for curtailing irrigation diversions. 

Dry, warm summers create stressful conditions for salmonids in the lower Merced 

River and for irrigators that depend on the water supply that had been provided by 

Merced ID long before the project was operated for hydroelectric power generation. We 

acknowledge that preserving the cold pool in Lake McClure could be used to create 

slightly less stressful water temperature conditions for salmonids in the lower Merced 

River, as shown in figure 3-37. Irrigation diversions have the most value to irrigators 

during the driest years. Curtailing all irrigation diversions at the beginning of the 

summer would have a substantial effect on irrigated cropland and the associated 

agricultural community. Whether this adverse economic effect would be worth a 

marginally enhanced water temperature regime in the lower Merced River is 

questionable. Completely shutting down irrigation diversions when a target storage level 

is reached transfers all of the costs of any environmental benefits that such an approach 

would achieve to the irrigators. The recommended approach of the Conservation Groups 

would entail a reduction in irrigation deliveries that escalates during dry years but is 

never reduced to less than 30 percent of demand. Consequently, the irrigators would not 

bear the entire cost of enhanced lower Merced River habitat enhancements that relate to 

available water storage in Lake McClure. 

California DFW recommends that Merced ID annually submit a draft operation 

plan to the Commission by March 1 and a final operation plan by May 15 that includes 

the estimated delivery pattern needed to achieve the 200,000 acre-feet end of September 

minimum pool target. If a minimum pool level should be specified in a new license, we 

would expect Merced ID to comply with any such condition. How Merced ID operates 

its project to comply with a minimum pool requirement would be up to them. However, 

if Merced ID is not able to meet a minimum pool requirement, the Commission would 

expect a report to be filed documenting the reasons for not meeting a specified minimum 

pool. Consequently, we find that there would be no need to file an annual operation plan 

with the Commission as California DFW recommends. 

Adoption of the Water Board’s preliminary WQC condition 9 to develop a drought 

plan in consultation with a technical advisory committee would provide overarching 

guidance for operation during an emergency drought and/or multiple critically dry years. 

We prefer this proactive approach rather than waiting until a drought is imminent or in 

progress to develop all of the details regarding how each drought would be managed. In 

addition, NMFS’ [10(j) recommendation 1.1A(8)] recommendation, now also proposed 

by Merced ID, for a contingency for multiple, consecutive dry and/or critically dry water 

years that may entail modifications to project operation would ensure prompt notification 

of drought concerns to the resource agencies, and effective consultation and development 

of appropriate emergency operational plans. California DFW’s recommendation 
186

regarding operation during a multi-year drought would be accommodated by the NMFS 

recommendation.

Merced ID’s proposed measure to make a good faith effort to maintain the water 

level in Lake McClure as high as possible from April through October and the minimum 

pool at McSwain reservoir pertain primarily to recreation and is therefore discussed in 

section 3.3.4.2, Recreation Resources.

Flood Protection

In accordance with article 39 of its existing license, Merced ID operates the 

project in compliance with the Corps’ document entitled New Exchequer Dam and 

Reservoir, Merced River, California; Water Control Manual; Appendix VII to Master 

Water Control Manual, San Joaquin River Basin, California dated October 1981. This 

manual sets year-round flood control limits in Lake McClure for rain flood space, and 

March through July flood control limits for snowmelt flood space or conditional space 

(table 3-2).

Merced ID proposes (WR3) to continue operating the project for flood control in 

accordance with the rules and regulations specified by the Corps. No other entity offered 

environmental measures pertaining to flood control.

Our Analysis

The proposed measure by Merced ID (WR3) would provide continued reservoir 

operation and flood protection in accordance with the Corps’ flood protection standards 

and guidelines. Merced ID currently releases water from Lake McClure to provide as 

much storage space as possible in Lake McClure when it anticipates that a storm or 

snowmelt runoff event may lead to potential downstream flooding if uncontrolled 

releases occur at the New Exchequer spillway. The current operating procedures are 

effective in minimizing uncontrolled releases from the spillway; there have been no 

spillway flows since the project began operating under the criteria specified in the Corps’

1981 manual. 

Water Supply to the Merced National Wildlife Refuge

Article 45 of its existing license requires Merced ID annually to provide up to 

15,000 acre-feet of project water to the Merced NWR. This water is intended to mitigate 

for the inundation of wildlife habitat associated with the construction of the project, 

primarily at New Exchequer dam.

Merced ID proposes to provide 15,000 acre-feet of water annually to the Merced 

NWR, unless otherwise agreed to in advance by FWS, to continue to mitigate for wildlife 

habitat inundated by Lake McClure. Water would continue to be delivered within the 

Merced ID irrigation season (March 1 through October 30). The current delivery flow 

rate of not to exceed 45 cfs and the current measurement point (at the weir in Deadman 

Creek) would remain unchanged. Merced ID would notify FWS at the onset of the 
187

irrigation season after which FWS would provide Merced ID with a preliminary water 

delivery schedule. Consistent with the current agreement, Merced ID includes a 

provision for FWS to request changes to the preliminary flow schedule within the 

irrigation season, with 48-hours notice.

FWS and California DFW make identical recommendations [10(j) 

recommendations 1 and 12, respectively] that Merced ID provide 15,000 acre-feet of 

water annually to the Merced NWR and include a delivery schedule that includes 

monthly deliveries ranging from 600 to 2,700 acre-feet throughout the year at the same 

delivery point, with a delivery flow rate not to exceed 55 cfs. Both agencies include a 

provision that Merced ID may reduce scheduled deliveries to 75 percent of requested 

amounts during designated critically dry water years and pay Merced NWR for the deep 

well pumping costs to compensate for the 25 percent delivery reduction. In addition, 

both agencies recommend that Merced ID install a device for delivering water to the 

Snobird Unit of Merced NWR along Bear Creek. Merced ID would deliver water to the 

Snobird Unit after Merced NWR is at capacity in areas serviced by the Merced NWR lift 

pumps at Deadman Creek, as determined by refuge staff. The Conservation Groups 

recommend Merced ID provide full deliveries of 15,000 acre-feet annually to the Merced 

NWR. 

Our Analysis

Both FWS and California DFW recommend specific monthly deliveries to the 

Merced NWR with maximum deliveries occurring from September through December to 

facilitate winter refuge flooding. Merced ID, in its letter filed on September 5, 2014, 

states that water is available for delivery to the Merced NWR only during the irrigation 

season (March 1 through October 31), and that providing water to the NWR from 

November through February is not possible because of the need for flood control (water 

levels in Yellowstone Lake, upstream of Lake McClure are kept low in the winter to 

capture spring high flows), dewatering the canals for maintenance, and health and safety 

considerations.

On May 22, 1992, the Commission ordered Merced ID to implement a plan for 

installing a water delivery system to provide 15,000 acre-feet to the entire refuge as 

required by article 45 of the current license.29 Included in the order was a provision to 

construct a 0.5-mile-long canal from Deadman Creek to the northeast corner of the 

Merced NWR. According to FWS, this canal was only used for one season and was 

ineffective in providing water to the refuge. FWS installed lift pumps on Deadman Creek 

to address the shortfall of water to this portion of the refuge; however, during years when 

capital to operate the pumps is unavailable, the northeast portion of the refuge does not 

receive water. FWS reports that from 2006 through 2013, actual deliveries to the Merced 

 

29 59 FERC 62,195
188

NWR never reached the 15,000 acre-feet specified in the current license and ranged from 

9,130 to 12,271 acre-feet (average of 10,501 acre-feet). In addition, FWS reports that 

Merced ID sold an average of 4,929 acre-feet of water per year to the U.S. Bureau of 

Reclamation and FWS for delivery to the San Luis NWR during September through 

February. FWS states that at least some of this water originated from Yellowstone Lake 

and that some of it passed to the San Luis NWR through the Snobird Unit of the Merced 

NWR. FWS points to this as evidence that it is possible for Merced ID to provide water 

for Merced NWR’s purposes during periods outside the irrigation season. We note that if 

the water delivery data provided by FWS is accurate, the amount of water sold to the San 

Luis NWR would have enabled full delivery to be achieved if it had been delivered to the 

Merced NWR.

The agencies and Merced ID also differ in how deliveries should be adjusted in 

drier water years. The agencies include a provision for a reduction in water provided to 

Merced NWR in critically dry water years but with Merced ID reimbursing FWS for the 

cost of pumping groundwater to make up for the shortfall. Merced ID makes no such 

provision in its proposed measure, but in its response to the agencies 10(j) 

recommendations, states that if Merced ID reduces water deliveries to irrigators during 

dry and critically dry water years, deliveries to the Merced NWR should also be reduced 

in an equal proportion.

The groundwater resources in the Central Valley are under increasing demand 

because of the limited availability of surface water (California DWR, 2014). We 

consider it uncertain that groundwater would be available to compensate for reduced 

deliveries by Merced ID during dry or critically dry water years, or that groundwater use 

for compensation would be recommended in future years. If irrigation water available for 

delivery by Merced ID to farmers is decreased because of increased flows to the Merced 

River downstream of Crocker-Huffman diversion dam, it would likely result in increased 

demand for groundwater by farmers to make up for this shortfall. 

There is no disagreement between the agencies and Merced ID that Merced ID 

should continue to provide 15,000 acre-feet of water to the Merced NWR as required 

under the current license. However, there remains disagreement regarding whether it is 

possible or feasible to deliver a portion of this total outside of the irrigation season. We 

agree with the agencies rationale that providing water to the refuge throughout the year 

would have environmental benefits. One of the factors that influences whether or not 

water can be delivered to the refuge outside of the irrigation season involves assessing a 

complex system of irrigation conduits that currently are not related to hydropower 

operation. It is also unclear based on the available information whether the agency 

recommendation to provide “a device for delivering water to the Snobird Unit of Merced 

NWR along Bear Creek” would be necessary to achieve the goal of delivering 15,000 

acre-feet of water to the refuge. We conclude that the most effective means to resolve 

this disagreement is for the entities most familiar with the system, Merced ID, FWS, and 

California DFW, to further consult regarding the feasibility of providing water to the 

Merced NWR outside the irrigation season. It is also evident that for license compliance 
189

purposes, there is a need to enhance documentation of how much water is delivered each 

year to the Merced NWR and the basis for the delivery estimates. 

Developing a Merced NWR water delivery plan, in consultation with FWS and 

California DFW, to ensure the delivery of 15,000 acre-feet to the refuge during times of 

the year when this water would provide the most benefit to wildlife would, after 

Commission approval, provide the Commission with a basis to maintain appropriate 

oversight of this environmental measure. Plan elements could include the following:

 Provisions to conduct a feasibility study for providing the recommended 

monthly volumes of water to the Merced NWR on a year-round basis, 

including an assessment of adverse and beneficial effects, estimated costs for 

any needed infrastructure changes, and a report with a recommendation 

regarding proposed actions. 

 An assessment of whether an enhancement of water delivery to the Snobird 

Unit of the Merced NWR is needed to achieve the overall annual or monthly 

water delivery objectives.

 A clear statement regarding where water delivery to the Merced NWR would 

be measured and the means for measuring and reporting monthly deliveries to 

the agencies and the Commission.

 An evaluation of the environmental effects on the refuge if monthly deliveries 

are curtailed during dry or critically dry water years and make-up water is 

obtained via groundwater, and the ramifications if there are future restrictions 

on the use of groundwater in the Central Valley.

Fish Passage

Crocker-Huffman diversion dam (RM 52.0) represents the upstream barrier to 

resident and anadromous fish in lower Merced River. Merced ID owns and operates the

diversion dam and the Main Canal as part of its water supply system and both facilities 

are not related to hydropower operation. Crocker-Huffman diversion dam is equipped 

with a fish ladder that has been non-operational since 1971 and would require 

replacement or retrofit to meet current standards for fish passage. Merced ID does not 

propose any measures relating to fish passage above Crocker-Huffman diversion dam. 

The Water Board [preliminary WQC condition 8] specifies that Merced ID either 

develop a fish passage plan to allow for passage upstream of Crocker-Huffman, 

McSwain, and New Exchequer dams, or, develop a habitat restoration plan to decrease 

water temperatures in and downstream of the project. 

FWS [10(j) recommendation 2] recommends Merced ID, in coordination with 

PG&E, develop a salmonid conservation, rescue, and passage plan to include: 

(1) planning, permitting, design, scheduling, costs, construction implementation, and 

monitoring of anadromous and resident salmonid passage at Crocker-Huffman diversion 

dam; (2) screening at the Merced ID Main Canal; (3) water filtration for the existing 
190

hatchery; (4) refrigeration facilities at the existing hatchery for protecting salmonids from 

sub-lethal and lethal water temperatures resulting from project operation; and 

(5) cooperating with California DFW in trapping and hauling local wild fish when 

temperatures in the lower Merced River are expected to be stressful. 

NMFS [10(j) recommendation 1.1A(3c] recommends that until a long-term water 

temperature improvement plan is developed, Merced ID should provide fish with access 

to the cold water habitat upstream of Crocker-Huffman diversion dam. California DFW 

[10(j) recommendation 6] makes a similar recommendation but adds the option of using 

self-contained water temperature controlled holding units.

The Conservation Groups recommend that Merced ID: (1) open the CrockerHuffman fish ladder on a temporary basis for seasonal use by O. mykiss when fall-run 

Chinook salmon are not present and develop monitoring and reporting protocols to 

quantify fish passage at this dam; (2) develop a plan for infrastructure needed for longterm upstream and downstream O. mykiss passage at Crocker-Huffman diversion dam 

including transporting adult anadromous fish upstream of Lake McClure and young 

anadromous fish from upstream of Lake McClure to downstream of the diversion dam; 

(3) evaluate the suitability of habitat in the upper Merced River Watershed for 

reintroducing spring-run Chinook salmon and steelhead, including a literature review, 

field studies to fill data gaps, and a habitat feasibility evaluation report; (4) conduct an 

engineering study to define capture and transport options for moving adult and juvenile 

anadromous fish to and from habitat upstream of Lake McClure; and (5) develop a plan 

for reintroduction of anadromous fish to the upper Merced River Watershed, including 

project description, conceptual drawing of facilities, costs, known and potential funding 

sources, and a time line for implementation.

Our Analysis

As discussed in the Commission’s April 1, 2011, study plan determination letter, 

anadromous fish do not pass upstream of the Merced Falls dam, which is downstream of 

the first project dam, McSwain dam, and therefore are not present in Lake McClure or the 

upper Merced River. The Crocker-Huffman diversion dam and any associated features, 

including the Main Canal, are not related to hydropower operation and are not included in 

the existing license. 

The Conservation Groups made similar requests in 2009 and 2011 to study habitat 

in the upper Merced River for anadromous fish reintroduction suitability. In its April 1, 

2011, study plan determination letter, Commission staff determined that there is no 

relationship of Merced River Hydroelectric Project operation on fish habitat upstream of 

Lake McClure. Commission staff further noted that the suitability of upstream habitat for 

anadromous salmonids, as it relates to recovery planning under NMFS guidelines, 

pertains to management decisions and actions that most appropriately fall under NMFS’ 

jurisdiction. We agree with the previous staff findings.
191

Recommendations pertaining to the hatchery and water temperature downstream 

of Crocker-Huffman diversion dam are addressed in separate subsections. 

Entrainment

Some fish entrainment is likely to occur at powerhouse intakes in both Lake 

McClure and McSwain reservoir. Neither Merced ID nor the stakeholders propose any 

measures related to entrainment at the project powerhouse intakes. However, FWS [10(j) 

recommendation 2] and the Conservation Groups recommend that Merced ID install a 

screen at the Main Canal to prevent fish from being entrained into the canal. 

Our Analysis

In Lake McClure, the powerhouse intake structure is located at the base of New 

Exchequer dam at a depth of 382 feet below the NMWSE of the reservoir. In rare events 

when the reservoir’s water surface elevation drops substantially, the intake depth can be 

as shallow as 100 to 150 feet below the surface. Based on a 10 percent discharge 

exceedance through the powerhouse of 2,912 cfs using data from 1970 to 2006, 

calculated approach velocities at the intake can be as great as approximately 2.1 feet per 

second. Entrainment probability is a function of proximity to the intake and a fish’s 

ability to avoid entrainment by swimming faster than the intake approach velocity. 

Gillnetting near the dam at depths up to 100 feet showed relatively low fish abundance; 

only kokanee (n=12), largemouth bass (n=3), rainbow trout (n=1), and spotted bass (n=5) 

were collected in deepwater habitat near New Exchequer dam. Merced ID’s calculation 

of estimated swim speeds for kokanee, largemouth bass, and rainbow trout suggests that 

these species have sustained swimming speeds that exceed the maximum reported 

approach velocity of 2.1 feet per second and thus could avoid entrainment. The burst 

speed of all species significantly exceeded calculated approach velocities. If a fish were 

to become entrained and pass through the turbines, Merced ID’s review of literature 

describing Francis turbines similar to those used at New Exchequer powerhouse suggests 

that the potential for survival would be 81.0 to 99.6 percent. 

In McSwain reservoir, the powerhouse intake structure is located about 70 feet 

upstream of McSwain dam at a depth of 30 to 40 feet, depending on water levels. Based 

on a 10 percent discharge exceedance through the powerhouse of 2,900 cfs using data 

from 1970 to 2006, calculated approach velocities at the powerhouse intake can be as 

high as approximately 2.7 feet per second. Gillnet sampling in McSwain reservoir in 

2010 found primarily Sacramento sucker in deep water near the reservoir bottom. 

Kokanee are present in the reservoir and may occur in deep water, but they were only 

found in mid-water (50 percent of maximum depth) sampling. Although the maximum 

calculated approach velocity of 2.7 feet per second exceeds the estimated sustained 

swimming speed of 2.4 feet per second for adult Sacramento suckers, it is significantly 

less than the sucker’s estimated burst speed of 12.3 to 13.5 feet per second (Stamp and 

Golden, 2005). Other species for which swimming speed was estimated (largemouth 

bass, rainbow trout, kokanee) have sustained swimming speeds that exceed the maximum 
192

approach velocity at the McSwain powerhouse intake. Merced ID’s review of literature 

describing Kaplan reaction turbines similar to those used at McSwain powerhouse 

suggests that if a fish were to become entrained and pass through the turbines, the 

potential for survival would be 88.0 to 96.1 percent.

Based on results from the Merced ID fish entrainment study that show low 

potential for entrainment at project powerhouse intakes and relatively high survival rates 

for any fish that may be entrained, we find no basis for Merced ID to implement any 

protective measures at the project powerhouse intakes. As discussed in the previous 

section, the Main Canal is not a feature of the Merced River hydropower project, nor 

does is there any information that suggests that Merced ID’s proposed project operation 

or maintenance activities would increase existing entrainment rates at the Main Canal; 

therefore, we find no basis for Merced ID to screen the Main Canal.

Spawning Habitat Enhancement

Availability and composition of river gravels influences suitability of spawning 

habitat for anadromous and resident fish. For example, salmonids deposit their eggs in 

redds created within gravel. Coarse gravel also provides substrate for growth of algae 

and invertebrates, both of which are important components of the aquatic food web.

Merced ID proposes no specific measures to address enhancing spawning habitat 

through gravel augmentation. The Water Board [preliminary WQC condition 4] specifies 

that Merced ID develop a gravel augmentation plan in consultation with a technical 

committee and submit the plan to the Water Board’s Deputy Director within 1 year of 

license issuance. The Water Board also specifies that the amount of gravel augmented 

should be consistent with the amount of gravel annually trapped behind New Exchequer 

and McSwain dams. No further details were provided as to the content of the plan. 

FWS [10(j) recommendation 4] recommends that Merced ID add approximately 

2,600 cubic yards30 of spawning-sized gravel annually between Crocker-Huffman 

diversion dam and Shaffer Bridge (RMs 52.0 to 32.8). Gravel augmentation sites would 

be selected each year based on monitoring and recommendations of a technical 

committee.

NMFS [10(j) recommendation 2] recommends that Merced ID add 20,000 tons of 

cleaned coarse sediment annually between Crocker-Huffman diversion dam and Shaffer 

Bridge to support the FWS’ Anadromous Fish Restoration Program’s Central Valley 

salmonid habitat doubling goal. Source aggregate would be harvested to create new 

 

30 The recommended volume of 2,600 cubic yards is derived from the Merced 

River Corridor Restoration Plan (Stillwater Sciences 2002), within which it was 

estimated that the equivalent weight would be 2,200 ton, based on the riverine sediments 

having an estimated dry bulk density of approximately 0.9 ton per cubic yard.
193

floodplain areas, and augmented in-channel sediments would be placed to increase local 

floodplain inundation by raising the channel bed. Harvested fine sediments would be 

used to support riparian recruitment on created floodplain habitats. Following the initial 

large-scale gravel augmentations, an annual maintenance augmentation would be added 

to the river reaches. Details of gravel-augmentation particle-size ranges, locations, and 

configurations in the river reaches would be developed in consultation with a technical 

committee and coordinated with LWD enhancement actions.

California DFW [10(j) recommendation 6] recommends that Merced ID develop a 

spawning gravel and floodplain habitat restoration plan that includes provisions for 

initially adding 50,000 cubic yards of cleaned spawning gravel downstream of CrockerHuffman diversion dam, followed by annual replenishment of 2,600 cubic yards. The 

spawning gravels and cobbles would be harvested from the nearby dredger tailings and 

placed in the river to create riffles and influence geomorphic processes. Sediment 

harvesting would be conducted to create new floodplain areas and increase local 

floodplain inundation.

The Conservation Groups recommend that Merced ID develop and implement a 

gravel augmentation and rehabilitation plan in consultation with a technical committee, 

and that the plan describe potential locations of gravel collection for the river reaches 

between Merced Falls dam and Shaffer Bridge, and potential geographic and physical 

options for initially placing 20,000 cubic yards and thereafter annually placing between 

2,600 and 10,400 cubic yards. The plan would address legal constraints on gravel 

placement and the permits that would be needed. The draft plan would be reviewed by 

the committee prior to submission to the Commission.

FWS [10(j) recommendation 5(K)], California DFW [10(j) recommendation 9(8)], 

and the Conservation Groups all recommend that Merced ID develop an aquatic 

monitoring program that includes provisions for monitoring sediment sizes between 

Crocker-Huffman diversion dam and Shaffer Bridge to determine if the prescribed 

gravel-augmentation rates are sufficient and to indicate where gravels would be needed to 

maintain spawning habitat quality. Additionally, spawner use of gravel-augmented and 

nearby control sites would be monitored for at least 5 years. The Conservation Groups 

also recommend that Merced ID annually monitor the locations, quantity, quality, and 

durations of placed gravel, as well as subsequent geomorphic distributions (e.g., 

movement, representative gravel quality, and bedload morphological change) and 

additions of suitable anadromous salmonid spawning and rearing habitat by individual 

reach. Monitoring results would be annually documented in a draft report to be provided 

to the technical committee for review and subject to revision prior to submission to the 

Commission.

Our Analysis

Pre-application studies indicated that New Exchequer and McSwain dams have 

cut-off access to historical spawning grounds in the upper reaches of the Merced River 

and have captured sediment that would otherwise move downstream to the lower reaches 
194

where limited spawning habitat remains. Within these reaches, habitat quality is affected 

by the legacy hydrologic and geomorphic changes associated with historic dredging for 

gold and aggregate resources, and dam and reservoir construction and operation. 

Although dredging activities have ceased and peak-flow reduction is unavoidable, coarsesediment entrapment behind the dams inhibits replenishment of riverine gravels 

considered vital for maintaining geomorphic features (i.e., gravel bars and riffles) and, 

therefore, suitable spawning opportunities in the lower reaches.

The two project dams have collectively intercepted a large amount of sediment 

that has contributed in part to bed coarsening, channel narrowing and simplification, and 

spawning-habitat loss in downstream reaches. Merced ID estimated the annual sediment 

capture behind New Exchequer dam to be 727,000 tons per year, with an estimated 

bedload31 fraction accounting for 36,000 to 73,000 tons per year. Merced ID estimated 

sediment deposited behind McSwain dam to be 29,000 tons per year, with an estimated 

bedload fraction amounting to 1,500 to 2,900 tons per year. Taken together, the sediment 

supply delivered annually to the downstream reaches has been substantially reduced. 

Other sediment sources are limited in these reaches; there are no streambank sources of 

sediment in the impounded reach between New Exchequer and McSwain dams, and only 

minimal sources occur between Merced Falls dam and Crocker-Huffman diversion dam. 

Merced ID has acknowledged that the project has continued to provide flows adequate to 

move sediment and mobilize (i.e., re-work) the river bed despite the extensive legacy 

effects of mining in the river channel.

Merced ID does not currently have a policy regarding placement of gravel 

downstream of New Exchequer and McSwain dams. Sediment augmentation projects 

implemented in recent years by California DFW and California DWR have included 

floodplain integration, pool filling and gravel augmentation, and riffle construction. For 

example, the Merced River Gravel Augmentation Project implemented immediately 

downstream of Crocker-Huffman diversion dam added approximately 8,000 tons of 

gravel between 1990 and 2003 (California DWR, 2004).

Our analysis indicates that development and implementation of a spawning-gravel 

augmentation plan is warranted in the project area. Implementation of the Water Board’s 

preliminary WQC condition 4, with modifications, that specifies that a plan be developed 

in consultation with a technical committee and include provisions to strategically place 

gravel substrates downstream of Crocker-Huffman diversion dam would enhance 

spawning and riparian habitat. 

 

31 Bedload is assumed to account for 5 to 10 percent of the total sediment load 

(Stillwater Sciences 2001), and is roughly equivalent to the fraction of sediment 

accounted for by gravel-sized materials.
195

However, there are differences in the various quantities and composition of gravel 

offered to augment the lower reaches. From the Water Board’s specified condition, the 

amount of gravel to be added should be consistent with the amount trapped behind the 

dams, which equates to between approximately 37,500 and 75,900 tons per year. NMFS 

recommends adding 20,000 tons annually throughout the four reaches downstream of 

Crocker-Huffman diversion dam over an approximate 30-year period, followed by 3,000 

tons per year as an annual maintenance supply intended to balance out the transport 

capacity of the regulated flow regime. California DFW recommends initially adding 

50,000 cubic yards (~42,000 tons) and then placing 2,600 cubic yards (~2,200 tons) per 

year thereafter for annual replenishment. FWS’ recommendation includes annual 

augmentation of 2,600 cubic yards (~2,200 tons) but not a larger initial amount. The 

Conservation Groups’ recommendation includes an initial placement of 20,000 cubic 

yards (~17,000 tons) followed by annual augmentation so that there is no net loss of 

spawning habitat thereafter (estimated to be from 2,600 to 10,400 cubic yards or ~2,200 

to 8,800 tons). There are pros and cons associated with each of the proposed 

augmentation amounts and directly addressing them during plan development would 

allow each to be considered while simultaneously balancing potentially conflicting 

resource values. Our analysis indicates that gravel augmentation amounts equal to at 

least the transport capacity of the supply-limited lower reaches, estimated to be 2,600 

cubic yards (~2,200 tons) per year, would offset the ongoing coarse-sediment entrapment 

behind the project dams that has a direct effect on spawning-habitat quantity. A larger 

initial placement of coarse sediments in the lower reaches would potentially benefit 

spawning habitat; however, doing so would address legacy effects not necessarily 

attributed wholly to past project effects and certainly not influenced by future projectrelated operation, construction, and maintenance activities. 

Obtaining the gravel to be placed in the lower reaches from the existing dredgertailings piles along the river, as recommended by California DFW and the Conservation 

Groups, would potentially make implementation relatively efficient, as opposed to 

importing gravels from outside of the project area, which could result in off-site 

environmental effects at the harvest site. Harvesting gravels here would also serve to 

create a more natural floodplain.

The plan, with input from a technical committee, would therefore consider the 

appropriate sources, quantities, composition, and augmentation sites of gravels to place in 

the lower reaches to ultimately benefit spawning habitat. Monitoring and mapping 

existing and augmented spawning gravels, as recommended by FWS, California DFW, 

and the Conservation Groups, would provide an indication of the performance of the 

augmentations and inform the need for future augmentation projects. 

Managing Large Woody Material 

LWM provides habitat structure in streams and can influence sediment storage and 

channel morphology through its effects on flow, water velocity, and sediment transport. 

LWM provides cover and holding habitat for fish, serves as substrate for the growth of 
196

algae and invertebrates (which are important components of the aquatic food web), and 

affects patterns of sediment deposition and scouring. Loss of LWM can result in reduced 

complexity of aquatic habitat and reduced carrying capacity for aquatic biota. 

Merced ID proposes to develop a LWM management plan (measure G&S2) to 

provide LWM to the Merced River downstream of Crocker-Huffman diversion dam 

within 1 year of license issuance and in consultation with California DFW. The plan 

would:

 describe existing locations of LWM collection in Lake McClure and McSwain 

reservoir; 

 describe potential options for moving LWM collected in Lake McClure and 

McSwain reservoir into the Merced River downstream of Crocker-Huffman 

diversion dam; 

 identify suitable locations in the Merced River downstream of CrockerHuffman diversion dam where LWM can be placed within the active channel 

and be passively mobilized by 2- to 5-year high-flow events; and

 prevent use of BLM-administered land, and particularly the Piney Creek redlegged frog core area, to stockpile or otherwise dispose of LWM material that 

Merced ID removes from the surface of Lake McClure or McSwain reservoir. 

Merced ID further proposes that the plan would not include requirements to 

anchor or otherwise stabilize LWM in the channel, and the scope of work under the plan 

would be such that Merced ID would not be required to obtain any approvals other than 

from the Commission for plan implementation. Merced ID would consult with the Corps 

and if the Corps expresses a concern regarding the effects of LWM on safety or 

maintenance of downstream bridges or railroad trestles, Merced ID would modify the 

plan to avoid any such issues. Merced ID would file the plan, including evidence of 

consultation with California DFW and the Corps, with the Commission for approval. 

NMFS [10(j) recommendation 3] recommends that Merced ID implement LWD32

enhancements in the four river reaches between Crocker-Huffman diversion dam and 

Shaffer Bridge (RMs 52.0–32.8). Merced ID would routinely count and acquire LWD

from project reservoirs and roads, and from nearby dredge tailings where sediment 

harvesting would occur. Boat surveys of the upper reaches of Lake McClure would be 

conducted within weeks of any large peak flow (i.e., greater than 1.5-year return 

interval). Collection and storage of LWD would avoid reducing the size or structural 

complexity of individual pieces, and stockpiles would be secured to minimize illegal 

 

32 NMFS defines LWD as structurally sound logs, with or without root wads, that 

are equal to or greater than 3-feet long and equal to or greater than 8-inches in diameter at 

5 feet from the large end.
197

firewood cutting, theft, or other non-designated consumptive uses. The technical 

committee would be consulted regarding placement of LWD in the reaches downstream 

of Crocker-Huffman diversion dam following guidelines specified in NMFS’ condition. 

A spatial inventory of existing LWD in these reaches would be created and housed within 

a GIS database. The inventory would be updated annually to account for manually 

placed LWD pieces, and comprehensively throughout the reaches during water years with 

a high-flow event of at least 4,000 cfs. Annual reports on status of LWD management 

and monitoring would be provided to the Commission and used for adaptive 

management. 

The Conservation Groups recommend that Merced ID develop a LWD 

management plan that includes the three elements proposed by Merced ID but also state 

that the plan should include consultation with state and federal agencies regarding effects 

of LWD on safety or maintenance of bridges and an evaluation of the efficacy, costs, and 

permitting requirements of providing permanent anchorage to the placed LWD. Much of 

the remainder of the recommended measure is similar to that recommended by NMFS. 

Additionally, the Conservation Groups recommend that Merced ID secure state or local 

approvals for implementation (e.g., Section 1600 Streambed Alteration Agreement from 

California DFW), develop the plan under the guidance of a technical committee, and file 

the plan, including evidence of consultation with the technical committee, with the 

Commission within 6 months of license issuance. 

BLM preliminary 4(e) condition 6 includes the same elements proposed by 

Merced ID. BLM also specifies its preference that Merced ID transport LWM past the 

dams over any other approach. Finally, BLM specifies that Merced ID acquire approval 

from California DFW, BLM, FWS, the Water Board, and NMFS on its LWM 

management plan before submitting the plan for Commission approval, and that the plan 

be implemented within 90 days of its approval by the Commission. The Water Board 

[preliminary WQC condition 14] specifies that Merced ID develop a LWM plan in 

consultation with a committee and submit it to the Water Board’s Deputy Director within 

1 year of license issuance. No further details were provided as to the content of the plan.

Our Analysis

Pre-application studies indicate that LWM is uncommon at the New Exchequer 

dam and reservoirs downstream, most likely because LWM transported into Lake 

McClure (most often during storm flows) sink or wash up on the reservoir shoreline 

before reaching the dam. Loss of LWM due to storage in Lake McClure is unavoidable. 

LWM input from the adjacent oak woodlands downstream of Lake McClure is also 

limited, and hardwood recruited to stream channels tends to be relatively small and shortlived in the channel. The resulting lack of LWM in waters downstream of New 

Exchequer and McSwain dams does not substantially affect the channel morphology of 

these reaches because they are impounded. The Merced River downstream of CrockerHuffman diversion dam is riverine, and LWM is scarce in the lower Merced River.
198

Merced ID does not currently have a policy regarding collection of LWM from 

Lake McClure. It reports that LWM does not accumulate at New Exchequer dam. At 

McSwain dam, only about two logs per year originating from sources local to Lake 

McSwain are removed at the trash rack and burned. 

Because LWM is scarce in the lower Merced River, placement of any LWM in 

these reaches would provide some benefits to riparian and aquatic plants and animals. 

Providing new substrate for algae and invertebrate colonization would increase habitat 

diversity and the structural diversity of the channel could possibly increase through 

creation of sediment storage sites or through local scour that may create pools. Rearing 

salmonids may benefit from the effects of increased cover even if storage of LWM in the 

channel is relatively short lived. The degree of habitat improvement would depend on 

the amount of LWM collected in the reservoirs and placed in the lower Merced River 

under Merced ID’s proposed plan or the alternative plans offered by the agencies and 

Conservation Groups. Habitat improvement would also depend on the characteristics of 

the material collected, which would influence its longevity in the channel.

Our analysis indicates that changes in LWM management are warranted in the 

project area. Implementation of Merced ID’s measure G&S2, with modifications, would 

lead to development of LWM and LWD management plan designed to identify sources of 

LWM collection in the project reservoirs, develop viable options for storing and 

transporting collected LWM, and identify suitable locations for LWM placement 

downstream of Crocker-Huffman diversion dam to benefit aquatic and riparian habitats. 

Monitoring and mapping the location of LWD and LWM placed between CrockerHuffman diversion dam and Shaffer Bridge, as recommended by NMFS and the 

Conservation Groups, would provide an indication of the stability of these enhancements 

and inform the need for future LWD and LWM placement projects. 

However, the various approaches offered for managing LWD and LWM differ. 

For example, NMFS and Conservation Groups recommend searching for wood rafts 

following high flow events and, if found, towing logs to a location where they can be 

securely stockpiled until decisions on placement projects in the lower Merced River can 

be made by the technical committee. BLM expresses concern with this approach and 

states that LWD or LWM could not be stockpiled on BLM-managed land because of 

concerns about associated habitat degradation at the storage sites. We expect these same 

concerns to be valid with stockpiling large quantities of LWD and LWM near much of 

the entire shoreline of both project reservoirs. In addition, stockpiles of wood may have 

an aesthetic effect that could detract from the experience of visitors to project recreation 

sites. There are pros and cons associated with both approaches and directly addressing 

them during plan development would consider and balance potentially conflicting 

resource values. 

Merced ID states that it should not be required to anchor LWM at deposition sites 

along the lower Merced River to simulate natural conditions. NMFS and the 

Conservation Groups recommend that the feasibility of anchoring LWD at deposition 
199

sites be considered. A decision regarding anchoring or not anchoring LWD should 

include consideration of potential adverse effects on downstream bridges and other 

structures, and the potential for increased flooding during high flow events if LWD 

should accumulate at bridges because they are not anchored securely. Consultation with 

appropriate state and federal agencies, including the California Department of 

Transportation and the Corps would inform such decisions. Including the results of that 

consultation in a plan would document the basis for the decisions. 

Development of a LWM and LWD management plan in consultation with a 

technical advisory committee would ensure that management and monitoring of 

collected and placed LWM satisfies biological needs and regulatory requirements. In 

response to Merced ID’s request that it implement its plan with only Commission 

approval, the federal and state resource agencies, not the Commission, would determine 

if additional permits or approvals would be needed for implementation of a Commissionapproved plan. 

Habitat Restoration and Management

Habitat restoration and enhancement projects have the potential to benefit aquatic 

biota as well as terrestrial vegetation and improve geomorphic processes in the lower 

Merced River. Merced ID does not propose any measures specifically relating to habitat 

restoration and enhancement projects along the lower Merced River. 

FWS [amended 10(j) recommendations 3(A2) and 3(A3)] recommends habitat 

restoration and enhancement measures for the lower Merced River. For the 10-mile 

reach between Merced Falls dam and RM 45.2 (1.2 miles downstream of Snelling Road), 

FWS recommends that Merced ID restore a dense, riparian tree canopy in at least a 30-

meter-wide zone on each side of the river to reduce water temperature by planting root 

stock, cuttings, or nursery stock using native tree species from the riparian corridor; 

protecting the plantings from beaver depredation; and, for restoration on lands not 

federally or state-owned, obtaining conservation easements and conveying them to an 

FWS-approved entity. For the reach from Shaffer Bridge to the confluence with the San 

Joaquin River, FWS recommends that Merced ID enhance at least 10 miles of habitat 

based on recommendations of a technical advisory committee and where conservation 

easements can be acquired to protect the restored habitat. FWS gives examples of 

potential habitat restoration projects, including addition of LWM, floodplain and riparian 

restoration, removal of riprap, and restoration of gravel mine pits. In 10(j) 

recommendations 5(I) and 9(9), FWS and California DFW recommend that Merced ID 

conduct long-term monitoring of riparian vegetation at floodplain restoration sites. The 

Conservation Groups make an identical recommendation. In addition to the 

recommendations described here, additional stakeholder habitat restoration 

recommendations are discussed in subsections Managing and Monitoring Water 

Temperature, Managing Large Woody Material, and Spawning Habitat Enhancement

(i.e., gravel augmentation). 
200

NMFS [10(j) recommendation 6] recommends that Merced ID implement NMFS’ 

Ecosystem Adaptive Management Process and actions related to habitat enhancements 

from Crocker-Huffman diversion dam to Shaffer Bridge. This process would entail 

collating the annual reports specified in applicable license conditions, and in consultation 

with a technical advisory committee, holistically assessing the information to determine 

if respective goals and objectives have been achieved; and, if goals and objectives are not 

achieved, determining adjustments needed to achieve habitat anadromous fish habitat 

restoration goals. In addition, in 10(j) recommendation 7.1(C), NMFS recommends 

that Merced ID establish a restoration implementation fund and use an independent 

financial advisor to manage, track, and report on the fund’s progress. Interest from the 

fund would be used to support habitat restoration projects recommended by a technical 

advisory committee.

Our Analysis

We do not dispute the environmental benefit to aquatic and riparian habitat of 

restoring a dense riparian tree canopy along the Merced River. However, in its April 1, 

2011, study plan determination, Commission staff concluded existing information 

indicates that non-project-related dredger and aggregate mining has elevated the 

floodplain downstream of Crocker-Huffman diversion dam from its original position, 

indicating that non-project variables affect the establishment of over-floodplain flows, 

which serve an important function in maintaining floodplain vegetation. In addition, 

Commission staff noted that the extensive aggregate mining both in the floodplain and 

the channel have created in-channel or captured mining pits. We agree with the staff’s 

previous findings.

In its April 1, 2011, study plan determination, Commission staff found that the 

effects of hydroelectric project operation are outweighed by other non-project factors 

downstream of Shaffer Bridge. We agree with staff’s previous findings and find no basis 

to recommend that Merced ID be responsible for any habitat enhancement measures 

downstream of Shaffer Bridge. Although FWS gives examples of the types of projects 

that could be considered in this downstream reach, it does not specify which types of 

activities would actually take place. Therefore, we have no basis to evaluate the 

environmental benefits of this aspect of FWS’ recommendation. 

The NMFS recommendation that Merced ID be responsible for implementing the 

Ecosystem Adaptive Management Process seems to reiterate the purposes of a technical 

advisory committee, previously discussed. Major functions of such a committee include 

review of information pertaining to environmental measures that may be included in a 

new license, including those that pertain to enhancement of anadromous fish habitat, and 

developing recommendations for future actions to be considered by other stakeholders. 

The Commission would ultimately determine if any conditions of a new license need to 

be adjusted based on recommendations from Merced ID and other stakeholders to more 

effectively achieve the stated goals of environmental measures.
201

NMFS recommends that Merced ID establish a restoration implementation fund 

and use the interest from the fund for activities recommended by a technical advisory 

committee. Given that NMFS has not specified how funds would be used, we are unable 

to analyze the environmental consequences of the recommended fund. Furthermore 

precisely how Merced ID plans to fund any environmental measures that may be included 

in a new license is not within the Commission’s purview. 

Fish Population Monitoring

Recent surveys of resident fish species found in both project reservoirs and in the 

Merced River, summarized in the affected environment section, provide baseline 

conditions of species diversity and relative abundance. Resident fish species found in 

project-affected waters are largely maintained by various stocking programs (in 

reservoirs) or natural reproduction in both reservoirs and riverine habitats. Merced ID 

does not propose, and no other entity offers, any measures relating to the monitoring of 

resident fish populations in project-affected waters.

Existing monitoring of fish populations in project-affected waters is currently 

focused on anadromous salmonids occurring in the lower Merced River downstream of 

Crocker-Huffman diversion dam (RM 52.0). Historical monitoring to estimate fall-run 

Chinook salmon escapement is still being conducted by California DFW and includes 

carcass surveys, spawning distribution, scale and otolith collection and analysis, length, 

sex, coded-wire-tag, and fecundity data and analysis. Since 1999, RSTs have been 

deployed to monitor Chinook salmon juvenile outmigration. RST configuration, 

sampling locations, and survey dates have varied slightly throughout the years. The 

current trap configuration uses a pair of RSTs at Hopeton (RM 37.5) and a pair at 

Stevinson (RM 4.8) from January 1 through June 15. In fall 2012, Merced ID operated a 

fish counting weir in the lower Merced River at RM 4.6. The counting weir included a 

VAKI RiverwaterTM system to monitor the timing, abundance, and composition of fish 

passing through the weir and was designed to estimate the escapement of adult Chinook 

salmon migrating upstream into the Merced River. Both the RSTs and counting weir also 

provided information on other anadromous species, including Central Valley steelhead, 

and other resident fish species, including rainbow trout and state-listed species of concern 

such as native hardhead and Sacramento splittail. There are no provisions for monitoring 

anadromous fish populations in the current license.

Merced ID proposes to monitor anadromous salmonids downstream of CrockerHuffman diversion dam (measure T&E2). The Merced ID monitoring program would 

use one RST and one counting weir to be located based on recommendations from a 

Merced River technical committee and contingent on land owner approval. The counting 

weir would operate annually from October 1 through December 31 to monitor adult 

Chinook salmon and O. mykiss migrating upstream into the Merced River and would 

acquire data on time, direction of migration, size, sex, and marks such as adipose fin 

clips. For all other fish species passing through the weir, Merced ID would collect data 

on time, direction of movement, number, species, and size. The RST would be operated 
202

annually from January 1 through May 31 to monitor juvenile Chinook salmon and O. 

mykiss migrating downstream from the spawning reaches in the lower Merced River and 

would acquire data on individual size, weight, and life stage from a representative sample 

of the catch.

The Water Board [preliminary WQC condition 20] specifies that Merced ID 

develop an anadromous fish monitoring plan that includes: (1) a statement of the goals 

and objectives; (2) a description of the proposed monitoring protocols; (3) a description 

of factors that could adversely affect California and federally listed species and whether 

the factors are related to project operation; (4) a monitoring and reporting schedule; (5) a 

plan for corrective actions if monitoring shows the project is adversely affecting 

anadromous fish or their habitat; and (6) protective measures.

NMFS, FWS, and California DFW [10(j) recommendations 4, 5(A-F), and 9(1-6), 

respectively] and the Conservation Groups recommend similar measures pertaining to 

anadromous fish monitoring. Compared with Merced ID’s proposed measure, these 

measures would include an expanded set of monitoring activities. The primary 

differences include (1) continuing existing California DFW carcass surveys, including 

data collection and analysis of scales, otoliths, length, sex, wire tags, and fecundity for 

fall-run Chinook salmon; (2) conducting RST sampling at both currently monitored 

upstream and downstream sites (although the Conservation Groups only recommend RST 

sampling at one location); and (3) conducting annual snorkel surveys of the O. mykiss

population. Additionally, California DFW [10(j) recommendation 3F] includes a 

provision that Merced ID prepare, implement, and fund a fisheries protection 

management plan that includes salmonid habitat and fish population monitoring to be 

approved by California DFW, FWS, NMFS, and the Water Board. California DFW notes 

that the plan should include a fish rescue component comparable to the drought 

emergency response planning and implementation that it conducted in the spring and 

summer of 2014. 

Our Analysis

We find that the Merced ID measure provides reasonable monitoring for adult and 

juvenile anadromous salmonids; however, Merced ID does not specify the locations of 

the upstream or downstream monitoring stations. Developing an anadromous fish 

monitoring plan to include elements specified by the Water Board, in consultation with a 

technical committee, would provide documentation of specific monitoring, consultation, 

and reporting procedures that would be implemented. We recognize the additional value 

that conducting carcass surveys, scale and otolith analysis, and fecundity determinations 

of adult anadromous fish would provide for resource management purposes, but we do 

not see how this information relates to the hydroelectric project operation or how it could 

be used to inform any project modifications. The Commission reached a similar 

conclusion regarding carcass surveys and fecundity determinations in its April 1, 2011, 

study plan determination when it noted that correlating the results of such studies to 

hydroelectric project variables would be difficult. 
203

Similarly, conducting additional snorkel surveys to monitor the O. mykiss

population would supplement the monitoring proposed by Merced ID. However, during 

six seasonal fish sampling efforts conducted between summer 2006 to spring 2008 using 

snorkel surveys, seining, and backpack and boat-mounted electrofishing units, a total of 

110 O. mykiss were observed. This included 73 O. mykiss resident rainbow trout 

observed in the Crocker-Huffman diversion dam impoundment that were most likely 

resident because there is no upstream passage facilities at the diversion dam and 37 

O. mykiss observed downstream of the diversion dam that could have been either 

anadromous or resident (Stillwater Sciences, 2008). Of the 37 O. mykiss observed by all 

collection methods in the reach downstream of the diversion dam, 30 were observed 

during snorkel surveys (an average of 5 per survey). The anadromy of any observed 

O. mykiss during snorkel surveys could not be determined and we expect very few O. 

mykiss to be observed based on the results of previous studies. Therefore, it is unclear 

how snorkel surveys could further inform decisions regarding the status of lower Merced 

River steelhead beyond what would be achieved by Merced ID’s proposed RST and 

counting weir monitoring, which would detect upstream and downstream migrating fish. 

Although monitoring is an important component for protecting these species, it 

does not in and of itself provide for adequate protection. However, monitoring 

anadromous fish, combined with water temperature monitoring, discussed in Managing 

and Monitoring Water Temperature, in the project-affected reach could form the basis for 

establishing immediate and long-term protection strategies for anadromous fish as 

developed by a Merced River technical committee with approval by the Commission and 

implemented by Merced ID. Protection strategies could include a provision for fish 

salvage when water temperatures in the reach between Crocker-Huffman diversion dam 

and Shaffer Bridge become overly stressful. If such a provision is included in a 

monitoring plan, the entities responsible for each element of the fish salvage program 

should be identified. We expect the need for adjustments to hydroelectric project 

operation or facilities would be identified within the first 10 years of a new license, 

unless substantial changes to project operation occur within that period.

Merced River Fish Hatchery Management

The Merced River Fish Hatchery has been operational since 1970 and is managed 

by California DFW. The initial construction of the hatchery was funded by California 

DFW, California DWR, and Merced ID, and its ongoing operation is cooperatively 

funded by California DFW in collaboration with state water contractors. The current 

population of Chinook salmon in the Merced River is supported by fish produced at the 

hatchery. Salmon produced at the hatchery are also routinely used for studies conducted 

within the San Joaquin River Watershed. The hatchery reports recent average annual 

hatchery production of Chinook salmon (2004 to 2009) to be 972,344 fish. The Merced 

River hatchery is located on the left bank of the river near Crocker-Huffman diversion 

dam and operates as a flow through facility that draws an average of 3 cfs from February 

through March and 7 cfs from April through January from the impoundment above the 
204

dam and releases water into the Merced River downstream of the dam. Merced ID does 

not propose any measures relating to the management of the Merced River Fish Hatchery.

California DFW [10(j) recommendation 5] recommends that Merced ID prepare a 

hatchery master plan in consultation with California DFW, FWS, and NMFS. The plan 

would include provisions for an initial design study to determine site capabilities and 

costs associated with operating the hatchery. The recommended plan would also address 

11 potential hatchery upgrades to be provided at the existing hatchery and provisions to 

assess the possible relocation of facilities to a site immediately below New Exchequer 

dam to meet the guidelines of the California Hatchery Scientific Review Group. 

California DFW states that Merced ID should be responsible for the annual hatchery 

release of 5 million fall-run Chinook salmon smolts with a single year maximum of 7.5 

million juveniles, and the annual release of 250,000 steelhead juveniles with a single year 

maximum of 425,000 juveniles. 

The Conservation Groups recommend that Merced ID develop and implement a 

Merced River fish management plan to design, construct, and operate a fish propagation 

facility for the production of native salmonids. The initial capacity would be a 5-year 

running average of 60,000 eyed eggs, fry, or fingerling Chinook salmon per year and 

multiple age class broodstock (capacity of 1,000 to 2,000 pounds). Initial capacity would 

also include up to a 5-year running total of 667,200 rainbow trout annual production, 

commensurate with the need to outplant fish in tributaries of the Merced River. The 

Conservation Groups identify a 22-acre site on Merced ID land immediately below New 

Exchequer dam as a potential location for this new facility.

Our Analysis

The current annual production goal of the Merced River Fish Hatchery is to take 2 

million fall Chinook salmon eggs and release 1 million Chinook salmon smolts 

(California HSRG, 2012). California DFW states that the current goal is based on facility 

constraints. The continued operation of the Merced River Fish Hatchery would support 

the Chinook salmon population in the lower Merced River until such time as natural 

reproduction in the river channel is sufficient to sustain or enhance the existing 

population. However, no aspect of the hatchery is included in the current license and the 

Commission has previously determined that the hatchery is not related to the ancillary 

use of project water for hydropower generation. The Crocker-Huffman diversion dam, 

which blocks upstream anadromous fish passage, was constructed in 1910, well before 

the Merced River Project received its hydroelectric license from the Commission. We do 

not dispute the assertion that upgrading and expanding the existing hatchery and 

assessing the potential relocation of the hatchery to a more favorable site could benefit 

efforts to artificially sustain Chinook salmon populations in the lower Merced River by 

stocking Chinook salmon smolts. We also recognize that the project plays a part in 

cumulative effects in the lower Merced River. However, other factors, such as instream 

mining and irrigation diversions, have had a much greater proportional effect than those 

associated with hydropower operation. We prefer to focus our analysis of potential 
205

measures that could benefit Central Valley fall-run Chinook salmon populations on 

factors that would enhance natural in-river production, such as an improved flow regime, 

reduced water temperatures to the extent controllable by the project, and spawning 

habitat enhancements. 

Benthic Macroinvertebrate Monitoring

BMI assemblages are an important part of the aquatic ecosystem and provide a 

fundamental food source for many resident fish. The description and characterization of 

BMI can also be used to provide an indication of the general health and condition of a 

stream.

Previous study results showed at least two EPT taxa (intolerant of water quality 

impairment) included in the top five numerically dominant taxa at each monitoring site in 

the lower Merced River, with the majority of dominant taxa likely available as a food 

source for juvenile Chinook salmon (Stillwater Sciences 2008, 2006). Tolerance metrics 

indicated moderately tolerant BMI assemblages under existing conditions. Merced ID 

does not propose any measures relating to the development of a BMI monitoring plan. 

FWS [10(j) recommendation 8] recommends that Merced ID develop a BMI 

monitoring plan describing sampling to be conducted in the project-affected bypass 

reaches to assess the effects on BMI under new flow regimes and other changes that may 

be included in a new license.

Our Analysis

The recent BMI studies on the lower Merced River provide an adequate baseline 

for evaluating effects under any potential change to the flow regime. The instream flow 

measures offered by various stakeholders would result in no decrease to the current flow 

schedule over all water year types and would, at a minimum, maintain existing conditions 

in the lower Merced River. Results of recent BMI studies indicate a moderately tolerant 

BMI assemblage that can be expected to be used as food by fish in the lower river. 

Additionally, if instream channel enhancements downstream of Crocker-Huffman 

diversion dam should be included in a new license, it should improve conditions for the 

BMI community. Although continued sampling of BMI in the lower Merced River 

would enable trends to be evaluated over time, we cannot envision a scenario where 

project hydroelectric operation with protection and enhancement measures included in a 

new license would result in a declining trend in BMI density and EPT taxa. 

Consequently, the benefits of this recommended monitoring are unclear.

Aquatic Invasive Species Management

New Zealand mud snails, quagga mussels, and zebra mussels are invasive aquatic 

mollusk species that have the potential to affect aquatic communities (e.g., New Zealand 

mud snails feed on the algae that is normally consumed by aquatic insects that make up a 

large portion of the diet of fish, and quagga mussels filter and remove plankton, which 

may also modify food webs). These species are not currently known to inhabit project 
206

reservoirs although the New Zealand mud snail has been documented in the lower 

Merced River between Crocker-Huffman diversion dam (RM 52.0) and the Highway 59 

bridge (RM 42.0). Non-native invasive plants including Eurasian milfoil, hydrilla, and 

didymo (Didymosphenia geminata) also have the potential to occur or to be introduced to 

project waters. Once introduced, populations of these species can rapidly expand, crowd 

out native aquatic plants, and become so dense that project operation and water-based 

recreational activities are adversely affected. 

Merced ID proposes to implement the Amended Aquatic Invasive Species 

Management Plan (AQR4) as filed with the Commission on April 23, 2014, and 

supplemented on September 5, 2014. The plan is intended to address quagga and zebra 

mussels, New Zealand mud snails, Eurasian milfoil, and Asian clams, and includes 

provisions for public education regarding prevention actions; consultation with agencies 

regarding appropriate signage and access restrictions if aquatic invasive species are 

detected within any project reservoir located in whole or in part on federal land; and 

development of BMPs for specific activities that have the potential to introduce aquatic 

invasive species into a project reservoir. Merced ID would discuss aquatic invasive 

species activities on land administered by BLM within the project boundary at the 

proposed annual meeting with BLM and incorporate any new information into the plan. 

Merced ID states in the plan that it currently follows all regulations set forth by 

California Assembly Bill 2065 that pertain to prevention of infestation by invasive 

mussels, including an assessment of project reservoir vulnerability, and would follow any 

future legislation at all project reservoirs. Any updates to the plan would be developed in 

consultation with BLM prior to being filed with the Commission. 

California DFW [10(j) recommendation 11] recommends that Merced ID 

implement its proposed Aquatic Invasive Species Management Plan. BLM [preliminary 

4(e) condition 8] specifies that Merced ID develop an aquatic invasive species 

management and monitoring plan that meets applicable state and federal laws and 

regulations. The BLM specified plan is similar to the plan proposed by Merced ID, but 

also includes zebra and quagga mussel surface surveys, veliger sampling, and artificial 

substrate monitoring in Lake McClure. It would also include provisions for documenting 

incidental observations during other aquatic monitoring in project reservoirs and projectaffected stream reaches of quagga and zebra mussels, New Zealand mudsnails, Eurasian 

milfoil, hydrilla; didymo, Asian clams, and American bullfrogs. BLM states that other 

aquatic invasive species may be identified through monitoring and incidental 

observations. Mapping and monitoring results would be provided to BLM, California 

DFW, and the Water Board. The Water Board comments that Merced ID’s plan should 

also include managing for the invasive aquatic plan, Brazilian elodea (Egeria densa). 

Additionally, the Water Board [preliminary WQC condition 17] specifies that Merced ID 

develop an aquatic invasive species management plan that includes some of the elements 

in the existing plan, but also includes a description of proposed monitoring protocols and 

a detailed monitoring and reporting schedule.
207

Merced ID filed an alternative to the BLM 4(e) condition stating that its Aquatic 

Invasive Species Management Plan provides adequate protection; therefore, its 

alternative condition is to implement its existing amended plan. Merced ID objects to the 

BLM monitoring provision because it provides “considerably more than adequate 

protection,” among other issues. Merced ID states that BLM 4(e) condition would 

require a level of compliance that exceeds that of any reservoir in the state and would 

require monitoring for two species where survey protocols do not currently exist. Merced 

ID also contends that BLM 4(e) conditions would apply only to BLM-administered land, 

which covers 37 percent of Lake McClure’s total shoreline and includes one recreation 

area located at Horseshoe Bend. Merced ID also notes that the Project Mussel 

Vulnerability Assessment, included as an attachment to the amended plan, shows that the 

likelihood of infestation of project waters by these two species is remote, and 

concentrated monitoring for them is unwarranted.

Our Analysis

Although invasive species have not been documented in project reservoirs, taking 

a proactive approach by establishing an Aquatic Invasive Species Management Plan as 

proposed by Merced ID would ensure that reasonable measures are in place to prevent 

colonization in project reservoirs, and if colonization should occur, procedures are in 

place to control the spread of invasive species. Merced ID included a vulnerability 

assessment in its amended plan, as required by California regulations. The assessment 

found that the vulnerability of project reservoirs to the introduction of quagga and zebra 

mussels is low. Merced ID’s conclusions are based on water quality measurements from 

its Water Quality Study (Merced ID 2012c) that compared the concentrations provided in 

Claudi and Prescott (2011) to project waters. This comparison showed that multiple 

factors, primarily calcium concentration and pH, but also temperature, alkalinity, total 

hardness, and phosphorus concentration, were all outside the range necessary for 

successful mussel infestation. Based on the available information in Merced ID’s 

vulnerability assessment, we find no basis to include a rigorous monitoring program for 

quagga and zebra mussels in the plan, as specified by BLM. 

Merced ID’s plan does not include any monitoring for aquatic invasive species 

other than to state that “any necessary monitoring for potential aquatic invasive species” 

would be included in activity-specific BMPs. Documenting incidental observations of 

aquatic invasive species (as well as the absence of target species), as BLM specifies, 

would provide a mechanism to detect if introductions have occurred in project waters and 

enable potential control strategies to be discussed with appropriate state and federal 

agencies. Merced ID’s proposed annual employee training, discussed further in section 

3.3.2.2, Terrestrial Resources, would provide a convenient forum to train project 

operation and maintenance staff to identify invasive species. We conclude that requiring 

the staff conducting field monitoring and studies at project reservoirs to be able to 

recognize and identify aquatic invasive species and document the presence or absence of 

such species would not be particularly onerous. However, because there are no project 

facilities (recreation or otherwise) downstream of the McSwain impoundment, we do not 
208

see how project operation or maintenance could influence the potential introduction of 

aquatic invasive species downstream of the McSwain impoundment. 

BLM specifies that hydrilla and the American bullfrog be added to the list of 

aquatic species addressed in an aquatic invasive species management plan and the Water 

Board suggests adding Brazilian elodea to the list. Both hydrilla and Brazilian elodea 

have been documented in the San Joaquin River Watershed, and the popularity of 

Brazilian elodea as a tropical fish aquarium decoration makes it a candidate for 

introduction anywhere unwanted aquarium contents are released into lakes and rivers 

(California DFA, 2014). Introduced American bullfrogs are known to be pervasive 

throughout California and threaten many native aquatic species. Adding these three 

species to the species targeted in the plan would enable control strategies to be 

implemented, as appropriate, if these species should be detected in project reservoirs. 

Merced ID’s plan includes provisions for plan revisions that include consultation 

with BLM. Other agencies in addition to BLM, such as California DFW and the Water 

Board, have an interest in ensuring aquatic invasive species are not introduced to project 

waters and if introduced, deciding effective means to control the spread of such species. 

Developing plan revisions in consultation with all three agencies would provide a means 

to ensure current applicable state and federal policies and regulations are considered 

during plan revisions. 

Merced Falls Project

Coordinated Operation between the Merced River and Merced Falls Projects

As previously discussed, flows released from the Merced River Project for 

environmental and irrigation purposes must pass through the Merced Falls Project 

before reaching the irrigation diversion point at Crocker-Huffman diversion dam. 

Although the Merced Falls Project operates in a run-of-river mode, where inflow to the 

project equals outflow, there are circumstances that could occur, such as routine 

maintenance events, that could have a bearing on the multi-purpose releases from the 

Crocker-Huffman diversion dam to the lower Merced River and irrigation flows into the 

Main Canal. Furthermore, due to the synergistic nature of the environmental effects of 

the two projects, the application of potential environmental measures could require the 

two applicants to communicate about the timing, access, or specific conduct of those 

measures. 

PG&E proposes to continue operating the project run-of-river and proposes no 

specific mechanism for coordinating project activities, such as operation, maintenance, or 

the implementation of any potential protection, mitigation, and enhancement (PM&E) 

measures with the upstream Merced River Project.

California DFW [10(j) recommendation 2] recommends that PG&E develop a 

coordinated operation plan in consultation with Merced ID and file it with the 
209

Commission, California DFW, the Water Board, FWS, and NMFS within 90 days of 

license issuance.

Our Analysis

By virtue of Merced Falls’ close proximity downstream to the Merced River 

Project and its operational dependence on that project, the environmental effects of the 

PG&E project within the project area and downstream are often intertwined with that of 

the Merced River Project. Although PG&E must maintain some level of communication 

with Merced ID to maintain and operate the Merced Falls Project, no formal plan exists 

to coordinate operating conditions or potential PM&E measures. As indicated in the 

previous section, a coordinated operation plan for the Merced River and Merced Falls 

Projects would document the process by which flows released at McSwain dam would be 

available for intended purposes at Crocker-Hoffman diversion dam. Furthermore, given 

the intrinsic link between the two projects and their environmental effects, a plan to 

enable coordination between the licensees would be valuable to ensure the timeliness, 

efficacy, and consistency in the application of any operational and environmental 

measures in the Merced Falls Project area and downstream Although developing this 

plan is likely to entail technical discussions about the fine points of project operation, 

inviting interested parties to provide input on the draft plan could provide valuable 

insights that enhance its effectiveness.

Coordination between Resource Agencies and Stakeholders 

California DFW [10j recommendation 1] recommends that PG&E establish an 

ecological resource committee for the purpose of consulting annually with resource 

agencies and other interested stakeholders on the implementation of license measures, 

implementation of monitoring plans, review and evaluation of monitoring data, and 

review and evaluation of required facility modifications. NMFS [10(j) recommendation 

6] recommends that Merced ID implement NMFS’ Ecosystem Adaptive Management 

Process and actions related to habitat enhancements from Merced Falls dam to the 

Crocker-Huffman diversion dam. This process would entail collating the annual reports 

specified in applicable license conditions, and in consultation with a technical advisory 

committee, holistically assessing the information to determine if respective goals and 

objectives have been achieved; and, if goals and objectives are not achieved, determining 

adjustments needed to achieve habitat anadromous fish habitat restoration goals. NMFS 

[10j recommendation 7] recommends Merced ID establish an anadromous fish committee 

that includes a technical advisory plan that defines membership, meeting responsibilities, 

ground rules for consensus-based decision making, and a process for implementing the 

decisions. The Water Board specifies [preliminary WQC condition 8] that PG&E hold a 

pentennial meeting with the resource agencies to provide an update of all monitoring and 

data required by the new license and WQC and a map that depicts locations that 

pesticides were applied, California ESA and ESA listed species, and topography. PG&E 

indicates that participation in regular consultation is unnecessary, given the minimal 

environmental impact of the Merced Falls Project. 
210

Our Analysis

As noted above, the Merced Falls Project area experiences many of the

environmental effects of the upstream Merced River Project because of its proximity and 

operational dependence on the upstream Merced ID facilities. While Merced Falls’ 

incremental contribution to environmental effects may be minor, compared to those 

upstream projects, PG&E’s participation in a committee would require little effort and 

would be valuable to ensure the timeliness, efficacy, and consistency in the application of 

any operational and environmental measures required of Merced ID or PG&E in the 

Merced Falls Project area and downstream. 

The NMFS recommendation that PG&E be responsible for implementing the 

Ecosystem Adaptive Management Process seems to reiterate the purposes of a technical 

advisory committee, previously discussed. Major functions of such a committee include 

review of information pertaining to environmental measures that may be included in a 

new license, including those that pertain to enhancement of anadromous fish habitat, and 

developing recommendations for future actions to be considered by other stakeholders. 

The Commission would ultimately determine if any conditions of a new license need to 

be adjusted based on recommendations from PG&E and other stakeholders to more 

effectively achieve the stated goals of environmental measures.

Instream Flows

PG&E proposes to continue operating the project run-of-river, where outflow 

equals inflow to the project.

California DFW [10j recommendation 3, parts A-D] recommends that PG&E 

calculate water year types annually and then implement and adaptively manage a flow 

schedule based on that water year type calculation. California DFW recommends that 

PG&E coordinate with Merced ID regarding implementation of its recommended 

instream flows. We note that the recommended flow schedule is identical to the flow 

schedule California DFW recommended for the Merced River Project. NMFS [10j 

recommendation 1] recommends that the Merced Falls Project pass through flows 

provided by Merced ID, such that the inflow equals outflow. NMFS further recommends 

that when diversions are occurring out of PG&E’s reservoir, outflow should equal inflow 

minus the amount of flow being diverted.

PG&E states that it does not alter the quantity or timing of flow in the Merced 

River, nor does control or have the rights to gage the non-project diversions located at the 

Merced Falls impoundment. For these reasons, PG&E states that the recommended flow 

conditions are unnecessary and unwarranted.

Our Analysis

The Merced Falls Project does not alter the timing or quantity of flow. It is 

currently operated and proposed to continue to operate as a run-of-river facility, 

completely dependent on inflow from the upstream Merced River Project facilities. As 
211

such, NMFS’ minimum instream flow recommendation is identical to proposed 

operation, and therefore, redundant. California DFW recommends an identical flow 

schedule to the flow schedule it recommends for the Merced River Project. Because the 

Merced Falls Project does not propose to alter flows in the Merced River, any flow 

schedule prescribed to the upstream project would continue downstream, unmodified by 

the Merced Falls Project. For this reason, any flow prescription for the Merced Falls 

Project is unwarranted. However, we note that the intent of California DFW’s 

recommendation was most likely to underscore the need for coordination between 

Merced ID and PG&E in the operation of both projects. We address that 

recommendation in the above sections, Coordinated Operation between the Merced River 

and Merced Falls Projects.

Water Temperature

Water temperature data collected from 1998 to 2008 in the Merced Falls Project 

impoundment ranged between 49oF and 60oF (9.4oC and 15.5oC). Downstream of 

Merced Falls dam, temperatures generally met or exceeded state standards, ranging from 

57oF (13.8oC) to just over 60oF (15.5oC). The lower Merced River is listed under CWA 

section 303(d) as impaired for temperature. Under current conditions, warm water 

temperatures reduce habitat suitability for Chinook salmon and steelhead downstream of 

Crocker-Huffman diversion dam, particularly for spawning.

PG&E proposes to implement a long-term water quality monitoring program for 

periodic (10 year intervals) assessment of water temperature and DO downstream of the 

project dam.

Identical to its recommendation for the Merced River Project, California DFW 

[10(j) recommendation 4] recommends that PG&E prepare a long-term water temperature 

management plan in conjunction with Merced ID. The plan would include: 

(1) developing a long-term strategy for meeting seasonal temperature objectives for 

Chinook salmon and O. mykiss ranging from 13.0°C (55.4°F) to 18.0°C (64.4°F) during 

the time frames included in the recommendation; (2) a feasibility study on submerged 

pipes capable of delivering at least 200 cfs to a location downstream of Crocker-Huffman 

diversion dam; (3) measures to prolong and stabilize the irrigation delivery season; 

(4) measures to restore the natural channel morphology, floodplain habitats, and riparian 

forest in the approximately 10-mile reach downstream of the Crocker-Huffman diversion 

dam; (5) provisions to provide coldwater refugia when water temperatures exceed 

objectives for more than 14 days; and (6) evaluating the effects on instream flow releases 

of implementing alternatives, and the estimated funding and schedule needed for the 

alternatives. California DFW [10(j) recommendation 6(2)] also recommends that PG&E 

continuously monitor water temperatures between inflow into the Merced Falls 

impoundment and outflow into the Merced River downstream of the project.

FWS [10j recommendation 2] recommends that PG&E coordinate and cooperate 

with Merced ID for restoration of shaded riverine habitat and riparian floodplain in the 
212

lower Merced River. FWS recommends that PG&E participate in temperature modeling 

to determine the thermal contribution of the Merced Falls Project to warming in the lower 

Merced River and bear a commensurate share of the costs of downstream restoration

based on the results of that modeling.

Identical to its recommendation for the Merced River Project, NMFS [10(j) 

recommendation 8] recommends that water temperature and flows be measured at ten

locations ranging from RM 62.0 to a location between Shaffer Bridge and the confluence 

with the San Joaquin River. NMFS states that measuring flow at temperature monitoring 

stations is important because temperature is related to flow and having information about 

both would better enable interpretation of the monitoring results given the many 

diversions that occur in the lower Merced River.

PG&E states that existing information indicates that the Merced Falls Project has 

an insignificant effect on warming in the project impoundment. Therefore, PG&E 

believes that measures related to water temperature management, monitoring, or 

mitigation are unwarranted.

Our Analysis

As previously discussed, the Merced River Project is the primary influence on 

water temperatures in the main channel of the Merced River downstream to Shaffer 

Bridge during the off-irrigation season (November through February) and exerts 

significant influence on temperatures during the irrigation season. Because of the low 

residence time of water in the Merced Falls impoundment, little warming occurs. 

Modeling studies estimated that the Merced Falls impoundment warmed only 0.54oF in 

the month of July—within the bounds of error reported by the study. Because existing 

information indicates that Merced Falls Project has a relatively insignificant thermal 

influence on the Merced River, PG&E should bear minimal responsibility for the 

implementation or funding of any potential temperature management, monitoring, or 

mitigation programs. PG&E’s proposed long-term monitoring program would identify

any potential unforeseen effects on water quality parameters (temperature and DO) 

important to aquatic biota. We analyze the effect of Merced ID’s Merced River Project 

on water temperature in the lower Merced River above, in section 3.3.1.2. 

Fish Population Monitoring

Recent surveys of resident fish species found in the project impoundment and in 

the Merced River, summarized in the affected environment section, provide baseline 

conditions of species diversity and relative abundance. Resident fish species found in 

project-affected waters are largely maintained by various stocking programs or natural 

reproduction in both reservoirs and riverine habitats. PG&E proposes to conduct annual 

semi-qualitative fish surveys in the reach between Merced Falls dam and CrockerHuffman diversion dam (Merced Falls reach) during the fall for the purpose of 

monitoring fish populations.
213

California DFW [10j recommendation 6] recommends that PG&E develop an 

annual monitoring plan and conduct O. mykiss surveys in the Merced Falls reach during 

the spring and summer to determine abundance, size distribution, spawning distribution, 

and summer distribution. Specific methodology of the monitoring plan would be 

developed in consultation with a technical advisory committee. California DFW also 

recommends that PG&E continuously monitor water temperatures between inflow into 

the Merced Falls impoundment and outflow into the Merced River downstream. 

NMFS [10j recommendation 4] recommends that PG&E should develop and 

implement an anadromous/resident fish monitoring plan in the Merced Falls reach in 

consultation with a technical advisory committee. The goals and timing of NMFS’ 

recommended plan are similar to those recommended by California DFW. The primary 

differences include NMFS’ recommendation to (1) conduct an annual pre-spawning 

mortality survey; (2) conduct carcass surveys, including data collection and analysis of 

scales, otoliths, length, sex, wire tags, and fecundity data; (3) conduct annual juvenile 

emergence and outmigration monitoring using two RSTs; (4) establish counting weirs to 

estimate Central Valley Chinook salmon and Central Valley steelhead escapement and 

provide data on the percentage of females and migration timing; and (5) conduct otolith 

analysis annually to estimate the contribution of naturally produced fry-, parr-, and smoltsized migrants to the adult population. NMFS [10j recommendation 5] recommends that 

PG&E consult with the technical advisory committee annually regarding the presence of 

special-status species in the area, and if newly-listed species are determined to be affected 

by the project, providing the committee with a draft biological evaluation or biological 

assessment.

PG&E notes that the Merced Falls reach is characterized by high flows, typically 

in excess of 2,000 cfs, throughout the spring and summer. PG&E states that these high 

flows would greatly limit the efficacy of standard fish population sampling methods, such 

as snorkel surveys and backpack electrofishing, because of the deep, swift, and unwadeable conditions.

Our Analysis

Monitoring fish populations in the Merced Falls reach could form the basis for 

establishing immediate and long-term protection strategies. Given the seasonally high 

spring and early summer flows in the Merced Falls reach, certain sampling techniques 

would not only be limited in their efficacy, but also dangerous to those responsible for 

conducting the sampling. While fall sampling efforts would ensure safer and more 

effective sampling conditions, specific data needs, such as spawning distribution or 

summer distribution, may not be fulfilled, because the timing of discrete events in the life 

cycle of the species of interest may not coincide with fall sampling. Consultation with a 

technical advisory committee could resolve the necessity for specific data needs, such as 

spawning distribution, or summer distribution, with regard to local site conditions, and 

would assist in any potential adaptation of sampling techniques to address local site 

conditions. We note that NMFS’ additional recommendations 1-5 listed above are 
214

identical to recommendations for the Merced River Project, and are primarily intended to 

gather monitoring data on anadromous species. As previously discussed, CrockerHuffman diversion dam (RM 52.0), located downstream of the Merced Falls Project,

represents the upstream barrier to resident and anadromous fish in lower Merced River. 

Therefore, monitoring these species in the Merced Falls reach, using the recommended

techniques, would be unnecessary at this time. Participation in a technical advisory 

committee, in conjunction with annual monitoring, would keep PG&E informed about

the potential future introduction of special-status species in the project area and the 

adaptation of any management programs to avoid the potential for the project to 

contribute to take of a listed species. We discuss fish monitoring in the lower Merced 

River in the Merced River—Fish Population Monitoring section.

Spawning Habitat Enhancement

Availability and composition of river gravels influences suitability of spawning 

habitat for anadromous and resident fish. For example, salmonids deposit their eggs in 

redds created within gravel. Coarse gravel also provides substrate for growth of algae 

and invertebrates, both of which are important components of the aquatic food web.

PG&E proposes no specific measures to address enhancing spawning habitat 

through gravel augmentation. The Water Board [preliminary WQC condition 3] specifies 

that PG&E develop a gravel augmentation plan in consultation with California DFW, 

FWS, and NMES, and submit the plan to the Water Board’s Deputy Director within 1 

year of license issuance. The Water Board also specifies that the amount of gravel 

augmented should be consistent with the amount of gravel annually trapped behind 

Merced Falls dam. No further details were provided about the content of the plan. 

NMFS [10(j) recommendation 2] recommends that Merced ID add 2,500 tons of 

coarse sediment to the Merced Falls reach. Following the initial large-scale gravel 

augmentations, an annual maintenance augmentation would be added to the river reach. 

Details of gravel-augmentation particle-size ranges, locations, and configurations in the 

river reaches would be developed in consultation with a technical advisory committee 

and coordinated with LWD enhancement actions.

The Conservation Groups recommends that PG&E provide a $50,000 annual 

payment to Merced ID for gravel augmentation.

PG&E states that the New Exchequer and McSwain dams prevent the transmission 

of gravel through McClure and McSwain reservoirs to the Merced Falls impoundment, 

and that no tributaries entering the Merced Falls impoundment that would contribute 

gravel. Additionally, Merced ID noted a 100 acre-foot difference in bathymetry data 

from 1972 and 2008 in its study of sediment trapped by Merced Falls dam. PG&E 

suggests that this data limitation is significant enough to question the accuracy of the 

estimate of sediment trapped by Merced Falls. PG&E concludes that no measures related 

to gravel augmentation are warranted.
215

Our Analysis

As previously discussed, pre-application studies indicated that, in conjunction with 

Merced ID’s New Exchequer and McSwain dams, the Merced Falls dam has cut-off 

access to historical spawning grounds in the upper reaches of the Merced River and 

captured sediment that would otherwise move downstream to the lower reaches where 

limited spawning habitat remains. Coarse-sediment entrapment behind the dams inhibits 

replenishment of riverine gravels considered vital for maintaining geomorphic features 

(i.e., gravel bars and riffles) and, therefore, suitable spawning opportunities in the lower 

reaches.

The two Merced ID project dams have collectively intercepted the majority of 

sediment that has contributed in part to bed coarsening, channel narrowing and 

simplification, and spawning-habitat loss in downstream reaches. Merced ID estimated 

annual sediment capture behind New Exchequer dam to be 727,000 tons per year, with an 

estimated bedload33 fraction accounting for 36,000 to 73,000 tons per year. Merced ID 

estimated sediment deposited behind McSwain dam to be 29,000 tons per year, with an 

estimated bedload fraction amounting to 1,500 to 2,900 tons per year. Merced ID 

estimated that the Merced Falls dam traps an average of only approximately 0.65 to 13 

tons of sediment per year. Taken together, the sediment supply delivered annually to the 

downstream reaches has been substantially reduced. However, the incremental effect of 

the Merced Falls project on sediment supply in the Merced Falls reach and lower Merced 

River appears to be several orders of magnitude less than that of the upstream Merced 

River project dams. 

While the study conducted by Merced ID estimated that the Merced Falls dam 

traps an average of 0.31 acre-feet of sediment annually, the study authors noted that there 

was some amount of measurement error due to the differing precision of data collected in 

1972 versus 2008. As such, the accuracy of this estimate is questionable. Regardless, we 

note that the banks of the Merced Falls impoundment are armored, the water level does 

not fluctuate dramatically, and there are no tributaries that enter the impoundment. 

Therefore, coarse sediment supply in the Merced Falls reach is likely very limited –

further confirming the project’s minor role in the sediment dynamics in the Merced Falls 

reach and the lower Merced River. 

We analyze the benefits of coarse gravel augmentation above, in the Merced 

River—Spawning Habitat Enhancement section. We acknowledge the benefits of such a 

program to aquatic species in the lower Merced River; however, our analysis indicates 

that while the Merced Falls dam may trap some coarse sediment, the New Exchequer and 

 

33 Bedload is assumed to account for 5 to 10 percent of the total sediment load 

(Stillwater Sciences 2001), and is roughly equivalent to the fraction of sediment 

accounted for by gravel-sized materials.
216

McSwain dams are the primary sediment-trapping mechanisms responsible for the lack of 

coarse sediment in the Merced Falls reach and the lower Merced River. For these 

reasons, PG&E should bear minimal responsibility for the implementation or funding of 

any potential gravel augmentation program(s). 

As described in the Merced River—Environmental Effects section above, a gravel 

augmentation plan, developed by Merced ID with input from a technical advisory

committee, would consider the appropriate sources, quantities, composition, and 

augmentation sites of gravels to place in the lower Merced River reaches, in addition to 

the Merced Falls reach, to ultimately benefit spawning habitat in the Merced Falls project

area and downstream. 

Managing Large Woody Material

LWM provides habitat structure in streams and can influence sediment storage and 

channel morphology through its effects on flow, water velocity, and sediment transport. 

LWM provides cover and holding habitat for fish, serves as substrate for the growth of 

algae and invertebrates (which are important components of the aquatic food web), and 

affects patterns of sediment deposition and scouring. Loss of LWM can result in reduced 

complexity of aquatic habitat and reduced carrying capacity for aquatic biota. 

PG&E proposes to continue performing periodic intake cleaning, wherein woody 

debris lodged against the intake is raked off, placed on a debris chute, and passed 

downstream. PG&E also notes that woody debris can continue downstream periodically 

when project gates are opened.

Identical to its recommendation for the Merced River Project, NMFS [10(j) 

recommendation 3] recommends that in conjunction with Merced ID, PG&E implement 

LWD34 enhancements in the four river reaches between Crocker-Huffman diversion dam 

and Shaffer Bridge (RMs 52.0–32.8). Specifically, NMFS recommends that PG&E 

should be responsible for adding LWD to the Merced Falls reach, based on consultation 

with the technical advisory committee. PG&E and Merced ID would routinely count and 

acquire LWD from project reservoirs and roads, and from nearby dredge tailings where 

sediment harvesting would occur. Boat surveys of the upper reaches of Lake McClure 

would be conducted within weeks of any large peak flow (i.e., greater than 1.5-year 

return interval). Collection and storage of LWD would avoid reducing the size or 

structural complexity of individual pieces, and stockpiles would be secured to minimize 

illegal firewood cutting, theft, or other non-designated consumptive uses. A spatial 

inventory of existing LWD in these reaches would be created and housed within a GIS 

database. The inventory would be updated annually to account for manually placed 

 

34 NMFS defines LWD as structurally sound logs, with or without root wads, that 

are equal to or greater than 3-feet long and equal to or greater than 8-inches in diameter at 

5 feet from the large end.
217

LWD pieces, and comprehensively throughout the reaches during water years with a 

high-flow event of at least 4,000 cfs. Annual reports on status of LWD management and 

monitoring would be provided to the Commission and used for adaptive management.

PG&E states that the primary issue regarding LWD is restricted movement 

through upstream Merced ID reservoirs. PG&E notes that the Merced Falls Project has a 

very limited potential to collect LWD that would otherwise move into the Lower Merced 

River.

Our Analysis

The Merced Falls project area consists primarily of annual grasses, with a 

relatively small percentage of woody vegetation that could contribute to the recruitment 

of LWM and LWD. Thus, the recruitment of LWM and LWD in the reach downstream 

of Merced Falls and the lower Merced River depends primarily on upstream sources. As 

previously discussed, pre-application studies indicated that LWM is uncommon at the 

New Exchequer dam, most likely because LWM transported into Lake McClure (most 

often during storm flows) sink or wash up on the reservoir shoreline before reaching the 

dam. Loss of LWM due to storage in Lake McClure is unavoidable. LWM input from

the adjacent oak woodlands downstream of Lake McClure is also limited, and hardwood 

recruited to stream channels tends to be relatively small and short-lived in the channel. 

For these reasons, the breadth and scale of the LWM management activities 

recommended by NMFS are unwarranted, given the project’s minimal effects.

However, PG&E’s current LWD/LWM management practices do not effectively 

document the quantity or timing of LWD removal and therefore, it is difficult to 

determine the biological significance of its placement back into the Merced River 

channel. Furthermore, the success of any LWD/LWM management program

implemented by the upstream Merced River Project for the benefit of the lower Merced 

River would depend on coordination and communication with the downstream Merced 

Falls Project. Therefore, development of a LWM and LWD management plan in 

consultation with the technical advisory committee would ensure that management and 

monitoring of collected and placed LWM satisfies biological needs and regulatory 

requirements and consistency with any upstream LWM/LWD management program.

Fish Passage and Canal Screening

The Merced Falls dam has a non-operational fish passage facility. The facility 

was decommissioned after construction of the upstream Merced River project dams 

eliminated suitable habitat for anadromous species upstream of the Merced Falls dam. 

PG&E does not propose any measures relating to fish passage. As previously discussed, 

Crocker-Huffman diversion dam (RM 52.0), located downstream of the Merced Falls 

project, represents the upstream barrier to resident and anadromous fish in lower Merced 

River. Crocker-Huffman diversion dam is equipped with a fish ladder that has been nonoperational since 1971 and would require replacement or retrofit to meet current 

standards for fish passage. 
218

The Water Board [preliminary WQC condition 4] specifies that if fish passage 

resumes at Crocker-Huffman diversion dam, PG&E consult with NMFS, CDFW, and 

FWS to determine if passage should resume at Merced Falls dam. In the event that 

passage is recommended after consultation, the preliminary condition specifies that 

PG&E develop a fish passage plan in consultation with the same parties. 

FWS [10(j) recommendation 1] recommends PG&E, in coordination with Merced 

ID, develop a salmonid conservation, rescue, and passage plan to include: (1) planning, 

permitting, design, scheduling, costs, construction implementation, and monitoring of 

anadromous and resident salmonid passage at Crocker-Huffman diversion dam; 

(2) cooperating screening at any conveyance facilities out of the Merced Falls reservoir 

pool; (3) cooperating with California DFW in trapping and hauling local wild fish when 

temperatures in the lower Merced River are expected to be stressful; (4) planning for 

opening of the existing fish ladder on Merced Falls dam; conducting an analysis of the 

measures that would need to be taken to bring the existing fish ladders up to NMFS 

standards; and (5) providing annual progress reports. 

The Conservation Groups recommend that PG&E reopen the fish ladder at Merced 

Falls, based upon the “reasonably foreseeable” future reoperation of the fish passage 

facility at the downstream Crocker-Huffman diversion dam.

PG&E states that it is willing to work on mutually agreeable solutions to fish 

passage; however, it does not provide details regarding a proposal for fish passage. 

Regarding canal screening, PG&E notes that a 1923 deed granted Merced ID a right-ofway easement for Merced ID’s northside canal, the only facility that conveys water out of 

the Merced Falls impoundment. PG&E states that given the terms of the deed, it cannot 

require such screens at the northside canal.

Our Analysis

As previously discussed, Crocker-Huffman diversion dam is considered a barrier 

to upstream anadromous fish movement in the Merced River. Therefore, at this time, 

reoperation of the fish ladder at Merced Falls dam would provide no benefit to 

anadromous species in the Merced River. As previously discussed, the Crocker-Huffman 

diversion dam and any associated features are not project features of either the Merced 

River or the Merced Falls Projects. We find that participation in a technical advisory 

committee, as described above, would facilitate the sharing of information regarding the 

status of anadromous fish passage at Crocker-Huffman, and therefore, the potential 

necessity of reevaluating passage scenarios at Merced Falls dam. Should fish passage be 

successfully restored upstream of the Crocker-Huffman diversion dam at some point in 

the future, the Commission’s standard reopener could be used to address any necessary 

changes to project facilities or environmental measures to accommodate anadromous 

species. Therefore, the Water Board’s specification of a plan to accommodate the 

passage of anadromous species in the project area is unnecessary.
219

PG&E’s study of entrainment at the project estimated that 87 fish are entrained 

annually into northside canal. Therefore, entrainment of fish into the northside canal 

likely represents a negligible effect on the overall abundance of the fish assemblage. As 

such, FWS’s recommendation to screen water conveyance facilities out of the Merced 

Falls reservoir pool would provide only minor enhancement to existing fish populations. 

Furthermore, we note that PG&E is not proposing any operational changes to the project 

that could increase canal entrainment. Therefore, canal screening would not mitigate for 

any potential project effect. 

3.3.1.3 Cumulative Effects 

Direct and indirect (cumulative) effects of the proposed hydroelectric project 

operation are intertwined. Consequently, some cumulative effects are previously 

discussed in section 3.3.1.2. In such cases, we summarize those effects here rather than 

repeating the entire effects analysis.

Water Quantity

Water diversions from the Merced River began well before operation of the 

Merced River Hydroelectric Project began in 1967. The Robla Canal Company first 

began diversions from the Merced River in 1870 and the Merced Falls diversion dam was 

constructed in 1901. Crocker-Huffman diversion dam was constructed in 1910 and the 

original Exchequer dam was constructed in 1926 for the purpose of facilitating water 

storage primarily for irrigation purposes. Merced ID is required to operate the project for 

flood control purposes in compliance with the rules and regulations of the Corps, which 

also enables the capture of high spring flows for water supply purposes. Therefore, 

during the spring, flows in the Merced River are substantially lower than they would be 

under unregulated conditions. During the irrigation season, which typically extends from 

March through October, diversions from the Merced River into irrigation canals can 

range from just under 200,000 acre-feet to nearly 700,000 acre-feet, but typically range 

from 400,000 to 500,000 acre-feet. Existing information reported in the Commission’s 

April 1, 2011, study plan determination indicates that during the irrigation season, nonjurisdictional withdrawals account for up to 52 percent of the average annual unregulated 

discharge from the watershed, limiting the available water supply for instream flow 

needs. Our review of annual canal diversions from 1940 through 2010 shows no clear 

trend in diversions before and after New Exchequer dam was completed in 1967. Some 

water diverted for irrigation purposes may return to the Merced River via agricultural 

returns. We find no evidence that hydroelectric project operation has had a direct bearing 

on the amount of water that remains in the Merced River during the irrigation season. 

Flows in the lower Merced River outside of the irrigation season are more directly 

influenced by hydroelectric project operation.

A reasonably foreseeable future cumulative effect on water quantity in the Merced 

River and downstream reaches of the San Joaquin River is the outcome of the ongoing 

proceeding to enhance river flows in these reaches and the Sacramento-San Joaquin 
220

Delta. In its comments and draft preliminary WQC conditions filed with the Commission 

on July 22, 2014, the Water Board states that its release of the 2012 Draft Substitute 

Environmental Document in Support of Potential Changes to the Water Quality Control 

Plan for the Bay Delta: San Joaquin River Flows and Southern Delta Water Quality may 

have an effect on how Merced ID manages water resources in Lake McClure. The draft 

Substitute Environmental Document recommends 35 percent of unregulated flow (i.e., 

inflow to Lake McClure) for the Merced River from February through June, and the final 

document may require instream flows that range from 25 to 60 percent of unregulated 

flows according to the Water Board. 

Water Quality

The results of Merced ID’s water temperature modeling indicate that during the 

March through October irrigation season, releases from the project can result in lower 

water temperatures downstream of Crocker-Huffman diversion dam, a beneficial 

cumulative effect. However, this cooling effect diminishes with distance downstream of 

the diversion dam primarily because of the increasing effect of ambient meteorology, and 

is negligible downstream of Shaffer Bridge. Larger early-season releases of water for 

environmental or irrigation purposes reduces the available cold water pool within Lake 

McClure, which directly affects the availability of cold water later in the season.

Merced ID monitored DO in the lower Merced River in 2011, 2012, and 2013. 

The 2011 monitoring results showed that downstream of the project to the confluence of 

the San Joaquin River, DO concentrations decreased between Shaffer Bridge and River 

Road, but generally met Basin Plan objectives in both the summer and the post-irrigation 

season. However, in 2012 and 2013, the Basin Plan objective for DO was not met during 

part of each day throughout each summer monitoring period. Basin Plan objectives were 

met during the fall post-irrigation season during 2012 and 2013. Merced ID water quality 

monitoring during 2010 shows that nutrient levels in water released from the project are 

low and not present in sufficient quantities to cause nuisance conditions related to algal 

blooms or decreased water clarity and therefore unlikely to contribute to downstream 

decreased DO. A likely contributor to instances of DO in water downstream of CrockerHuffman diversion dam not meeting Basin Plan objectives is nutrient input from 

agricultural runoff and irrigation return flows. However, our review of the DO data from 

August 2004 through January 2009 presented in figures 3-18 and 3-19 indicates that 

water in McSwain reservoir at the powerhouse intake location often was below the Basin 

Plan objective of 8 mg/L. This was not the case for DO monitoring results from March 

2010 through February 2011 shown in figure 3-20. Although the hydroelectric projects 

may play a role in the DO regime of the Merced River downstream of the CrockerHuffman diversion dam, establishing a causal relationship to either the Merced River or 

Merced Falls project would be difficult because of the multiple factors that influence DO.

Water quality in the Merced River downstream of Crocker-Huffman diversion 

dam can also be affected by increases in total suspended solids associated with erosion, 

mining, and habitat restoration efforts. Recommended erosion and sedimentation control 
221

measures at both the Merced River and Merced Falls Projects would minimize 

hydroelectric project effects on total suspended solids in the lower Merced River. Any 

continuation of gravel and aggregate mining in the lower Merced River would result in 

increased total suspended solid concentrations. Project-related instream habitat 

enhancement measures such as gravel augmentation have the potential to increase total 

suspended solid concentrations, but implementation of protective BMPs would minimize 

any such water quality affects. Non-project-related instream habitat enhancement 

measures also have the potential to increase total suspended solids concentrations. 

Requiring protective BMPs in such cases would be outside the Commission’s 

jurisdiction, but within the jurisdiction of other agencies such as the Water Board. 

Aquatic Habitat for Chinook Salmon and Central Valley Steelhead

Actual and potential spawning and rearing habitat for Chinook salmon and Central 

Valley steelhead exists in the lower Merced River, primarily between Crocker-Huffman 

diversion dam and Shaffer Bridge. A number of cumulative factors have contributed to 

the degradation of this habitat including: (1) numerous (estimates range from 170 to 240) 

non-project water withdrawals in the lower Merced River; (2) extensive aggregate mining 

both in the floodplain and the channel, which have created in-channel or captured mining 

pits that serve as habitat for introduced predators on rearing salmonids; (3) flow accretion 

and sedimentation from Dry Creek, a tributary to the Merced River; (4) extensive 

development of non-project levees; and (5) backwater effects of the San Joaquin River 

(Commission’s April 1, 2011, study plan determination). Under existing conditions, 

dams at the two upstream hydroelectric projects contribute to the habitat degradation by 

interrupting the downstream transport of gravel that may be suitable for spawning, and 

LWM that may enhance rearing habitat in the lower Merced River. Some enhancement 

of the thermal regime for spawning and rearing habitat can be achieved by cold pool 

releases from Lake McClure, but the finite volume of available cold water limits the 

duration of the benefit during most water years. 

Many factors influence the suitability of aquatic habitat in the lower Merced 

River. As discussed in detail in section 3.3.1.2, Environmental Effects, requiring 

hydroelectric project licensees to address factors that could enhance spawning and 

rearing habitat that have a nexus to the continued operation of the projects would be a fair 

approach to partially addressing project-related effects. Other cumulative non-project 

factors would need to be addressed by other entities for the available spawning and 

rearing habitat to reach its full potential given the competing demands for available 

water.
222

3.3.2 Terrestrial Resources

3.3.2.1 Affected Environment

Merced River Project

Vegetation 

Cover Types—In 2010 and 2011, Merced ID characterized botanical communities

using the CALVEG35 systems in areas within the existing project boundary and an area of 

at least 300 feet from the NMWSE of project reservoirs—Lake McClure and McSwain 

reservoir—or to the project boundary, whichever was greater, and 0.25 mile around 

project facilities including recreation facilities (vegetation study area). The botanical 

communities are composed primarily of upland vegetation alliances with minimal areas 

of wetland, riparian, or littoral habitats.

Four botanical communities dominate upland areas in the vegetation study area: 

blue oak, chamise, annual grasses and forbs, and agriculture. There are also subdominate areas of gray pine and smaller inclusions of lower montane mixed chaparral, 

interior live oak, and riparian mixed hardwood. 

The blue oak vegetation alliance consists of open blue oak woodlands within a 

grassland matrix. This alliance typically occurs on well-drained, gentle slopes and is one 

of the most common vegetation communities in the Central Valley ecological province. 

In addition to blue oak, other tree species include gray pine, ponderosa pine, valley oak, 

and California buckeye. Shrub species include wedgeleaf ceanothus and chamise. 

Annual grasses, including wild oats, cheatgrass, and needlegrass, dominate the ground 

layer (Forest Service, 2009).

The chamise vegetation alliance occupies drier sites on upper ridge locations. 

Dense, monotypic stands of chamise, a tall chaparral shrub species, dominate the 

vegetation community. Scrub oak also occurs in low density. Sparse trees, including 

blue oak, gray pine, and interior live oak may also be present along the fringe of chamise 

stands (Forest Service, 2009).

The annual grasses and forbs alliance is the most common vegetation community 

in the Central Valley ecological province. This alliance typically occurs between 

urban/agricultural developments and foothill woodlands. Dominant species include 

western needlegrass, cheatgrass, purple owl’s clover, filaree, wild oats, and devil’s 

 

35 The CALVEG system is the method Forest Service uses to classify existing 

vegetation in Region 5. More information about the CALVEG system can be found at 

http://www.fs.fed.us/r5/rsl/projects/classification/system.shtml.
223

lettuce. Vernal pools, depression areas that hold water in the spring but are dry in 

summer, also occur within this alliance. Vernal pools frequently support plant species 

that are rare in the surrounding area. Common species in these areas include sedges, 

rushes, bulrush, brome, fescue, bluegrass, reedgrass, false hellebore, and shooting star

(Forest Service, 2009).

The gray pine alliance forms sparse to prominent open stands throughout the 

Central Valley at lower elevations up to about 5,200 feet. This community type is very 

common in the Ranges and Foothills sections and less so in the Valley section. In 

addition to gray pine, this community includes blue oak, interior live oak, and minor 

amounts of ponderosa pine. Shrubs, including chamise and wedgeleaf ceanothus are 

common low-elevation shrubs associated with the gray pine community (Forest Service,

2009).

The lower montane mixed chaparral alliance is a mixture of low-elevation 

chaparral species such as whiteleaf and common manzanitas, wedgeleaf and lemmon 

ceanothus, scrub oaks, chamise, silk-tassel, birchleaf mountain mahogany, California 

buckwheat, and other shrub species below productive coniferous and hardwood sites. No 

single species is dominant in the mixture (Forest Service, 2009).

The interior live oak alliance is often located above blue oak stands, generally 

below about elevation 4,400 feet. Other common species include Fremont cottonwood, 

white alder, and upland trees as canyon live oak, California buckeye, Douglas-fir, and 

gray pine (Forest Service, 2009). 

Riparian areas in the Central Valley are a mixture of hardwoods with some shrubs 

rather than areas of monotypic species. Typical hardwoods species mixtures include 

willows, valley oak, Fremont cottonwood, California sycamore, and white alder. Blue 

oak is a closely associated upland hardwood that may occasionally be found in this 

mixture (Forest Service, 2009).

Agricultural lands in the Central Valley include vineyards, orchards, pastures, and 

field crops.

Vegetation along the shorelines of the lower half of Lake McClure predominantly 

consists of blue oak and annual grasses and forb communities. From Arnold Bay east to 

Bagby recreation area, the shoreline is dominated by chamise. The shorelines of the arm 

of Lake McClure east from Highway 49 to the upstream end of the project boundary are 

composed of a mixture of vegetation communities, including lower montane mixed 

chaparral, chamise, interior live oak, gray pine, annual grasses and forbs, and a few small 

areas of riparian mixed hardwoods. The vegetation communities around McSwain 

reservoir are almost exclusively blue oak and annual grasses and forbs, with a few small 

areas of gray pine and interior live oak.

Vegetation around Crocker-Huffman diversion dam and Merced ID’s wildlife 

refuge water delivery facilities is generally limited to herbaceous weeds, annual grasses, 
224

milk thistle, wild mustard, and water speedwell. These species are also present at the 

perimeter of most agricultural fields in the surrounding area and often occupy entire 

fields; they are ubiquitous throughout the vicinity and not unique to the area at or near 

project facilities. Based on our review of aerial photography in the license application 

and supporting reports, there also is riparian woodland in the vicinity of CrockerHuffman diversion dam.

Currently, Merced ID’s management of vegetation within the project boundary is 

limited to application of herbicides on the faces of project dams, along project roads, and 

in campgrounds.

Riparian Habitats and Wetlands—In 2010, Merced ID conducted proper 

functioning condition assessments of six riparian habitat sites and three wetlands sites 

collaboratively selected with relicensing participants to represent the range of riparian 

habitat and wetlands that the project has potential to affect. In addition to the proper 

functioning condition assessments, Merced ID performed a descriptive analysis of the 

named drainages occurring within the project boundary on USGS 7.5-minute quadrangle 

maps.

In preparation for fieldwork and analysis, Merced ID collected and reviewed 

available information pertinent to establishing an understanding of the capability36 and 

potential37 of the riparian habitat and wetland sites. Merced ID reviewed FWS National 

Wetland Inventory maps, which show the distribution, extent, and class of wetlands 

based on aerial photographs. Merced ID reviewed low elevation helicopter video 

imagery for each study site and performed ground-truthing reconnaissance. In addition, 

Merced ID collected historical aerial photographs of the sites to examine changes over 

time, such as variation in lateral movement or changes in vegetation coverage (e.g., forest 

development following disturbance), and for comparison with current field conditions. 

Merced ID determined that all six riparian habitat study sites (Sherlock Creek, 

Lake McClure upstream of Bagby recreation area, Maxwell Creek, Piney Creek, Cotton 

Creek, and Merced Falls reach) and three wetland study sites (McSwain reservoir, 

Merced Falls reservoir and Crocker-Huffman diversion dam impoundment) exhibited 

conditions consistent with a rating of Properly Functioning. The sites had welldeveloped riparian and wetland plant communities relative to site capability and 

 

36 Capability is defined as “the highest ecological status an area can attain given 

political, social, or economic constraints, which are often referred to as limiting factors.”

37 Potential is defined as “the highest ecological status a riparian-wetland area can 

attain given no political, social, or economic constraints, and is often referred to as the 

potential natural community.”
225

potential, and exhibited channel characteristics indicating resilience to high-flow events. 

Descriptive analysis indicated that riparian vegetation was present and vigorous at 9 of 12 

of the major tributaries surveyed (Solomon Gulch, David Gulch, Flyaway Gulch, Hell’s 

Hollow, Scotch Gulch, Whites Gulch, Wheeler Gulch, Willow Creek, and Picture Gallery 

Gulch). Riparian habitat was not present at Rocky Gulch, Rancho del Oro Gulch, or 

Temperance Creek.

Noxious and Invasive Weeds—Merced ID does not have a formal control program

for noxious and invasive plants. However, at the request of the California Department of 

Transportation, Merced ID conducts some targeted spraying of yellow starthistle near the 

Bagby recreation area. Merced ID also conducts targeted spraying along McSwain 

reservoir. Additionally, vegetation management conducted as part of project operation 

and maintenance activities may indirectly target some occurrences of invasive weeds.

To identify invasive weeds with the potential to occur in the vegetation study area, 

Merced ID: (1) compiled a list of regionally known species from the Sierra-San Joaquin 

Noxious Weeds Alliance; (2) queried the BLM about invasive weeds of concern; and 

(3) queried the California Department of Food and Agriculture (California DFA) for 

invasive weed listings at state and federal levels. Based on these sources, Merced ID

determined that 31 invasive weeds have a reasonable potential to occur within the 

vegetation study area.

In 2010, Merced ID performed surveys for these invasive weeds and others that 

may occur. Italian thistle and tocalote were the most common invasive weed species, 

ubiquitous in grasslands within the project boundary. Specific locations for these species 

were not recorded. For the other 10 invasive weed species located, a total of 323 invasive

weed occurrences were found within the vegetation study area (table 3-16).

Table 3-16. Occurrences of noxious and invasive plants identified on the Merced River 

Project vegetation study area (Source: Merced ID, 2012a, as modified by 

staff).

Common Name Scientific Name

2010 California 

DFA Ratinga

Number of 

Occurrences

Tree of heaven Aianthus altissima C 2

Giant reed Arundo donax B 2

Italian thistle Cardus tenuiflorus C Too many to count

Iberian starthistle Centaurea iberica A 1

Tocalote Centaurea melitensis C Too many to count

Yellow starthistle Centaurea solstitalis C 12

Bermudagrass Cynodon dactylon C 31
226

Common Name Scientific Name

2010 California 

DFA Ratinga

Number of 

Occurrences

Edible fig Ficus carica Not Rated 70

Klamath weed Hypericum perforatum C 170

Perennial 

pepperweed

Lepidium latifolium B 1

Medusahead grass Taeniatherum caputmedusaeC 32

Puncturevine Tribulus terrestris C 2

Note: California DFA – California Department of Food and Agriculture

a California DFA rating:

A = Eradication, containment, rejection, or other holding action at the state-county 

level. Quarantine interceptions to be rejected or treated at any point in the state.

B = Eradication, containment, control, or other holding action at the discretion of the 

California DFA commissioner. State endorsed holding action and eradication only 

when found in a nursery.

C = Action to retard spread outside of nurseries at the discretion of the commissioner;

reject only when found in a crop seed for planting or at the discretion of the 

commissioner.

Wildlife

The project and surrounding area supports a diversity of habitats and associated 

wildlife species that reflect wide variations in topography and soils and are typical of the 

western foothills of the central Sierra Nevada. Based on a review of California DFW’s 

California Wildlife Habitat Relation system, Merced ID identified 23 reptile, 12 

amphibian, 218 bird, and 85 mammal species that have a potential to occur in the vicinity 

of the project. 

Reptiles in the project vicinity include western terrestrial (or mountain) garter 

snake, western aquatic (or Sierra) garter snake, common garter snake, western 

rattlesnake, western fence lizard, western sagebrush, and southern alligator lizard. These 

species occur in a variety of habitats ranging from riverine to woodlands, forests, and 

grasslands. Most are active during the summer and inactive during the winter.

Common bird species expected to occur in the project vicinity include raptors such 

as redtailed hawk and American kestrel; songbirds including dark-eyed junco and spotted 

towhee; woodpeckers such as downy woodpecker and northern flicker; and owls 

including great horned owl and barn owl. These birds are found in a variety of habitats 

ranging from streamside riparian habitats and wet meadows to hardwood dominated 
227

woodlands common throughout the project. Seasonally, some birds are only present 

between March and July for breeding, while others may be year-round residents.

Common mammal species in the vicinity of the project, such as mule deer, bats, 

and squirrels like the California ground squirrel are most often associated with grassland 

habitats. Some of the common mammals like mule deer are migratory, and move from 

summer habitat at higher elevations to wintering habitat along the foothills.

Sensitive Plant Species

Following consultation with California DFW and BLM and a review of the 

California Native Plant Society’s Inventory of Rare and Endangered Plants database, 

Merced ID identified 40 sensitive38 plants with potential to occur in the vicinity of the 

project. In 2010 and 2011, Merced ID performed surveys for these special-status and 

California ESA-listed plants. Surveys were conducted following the botanical survey 

protocol section of California Department of Fish and Game’s (now California DFW) 

Protocols for Surveying and Evaluating Impacts to Special Status Native Plant 

Populations and Natural Communities. The study included the area surrounding all 

project facilities (e.g., powerhouses and switchyards, dams, reservoirs, access roads, and 

recreation facilities) within the existing project boundary and in the immediate area of the 

project’s seven minor wildlife refuge water delivery facilities. 

Merced ID recorded a total of 377 occurrences (i.e., either a single plant or a 

distinct geographic population of plants) of 10 different special-status plants: 165 

occurrences on federal land administered by BLM, 168 occurrences on land owned by 

Merced ID, and 44 occurrences on owned by private entities. Table 3-17 summarizes the 

special-status plant occurrences by land ownership and describes the general habitat for 

each species. No California ESA-listed plants were encountered during Merced ID’s 

survey.

 

38 Sensitive plant species include California state-listed threatened and endangered 

species, BLM-listed sensitive species, and species included in the California Native Plant 

Society’s Inventory of Rare and Endangered Plants database.
228

Table 3-17. Special-status plant species identified in the Merced River Hydroelectric Project study area (Source: Merced 

ID, 2012a, as modified by staff).

Common Name/

Scientific Name

Habitat Description and Location 

Within the Project Statusa

Number of Occurrences by Land 

Owner

Public 

(BLM)

Merced 

ID Private

Mariposa clarkia

Clarkia biloba ssp. australis

Oak woodlands and annual grasslands, 

recorded throughout the project area

BLM-S, 

CNPS 1B.2 62 31 15

Beaked clarkia

Clarkia rostrata

Oak woodlands and annual grasslands, 

recorded throughout the project area

BLM-S, 

CNPS 1B.3 20 112 19

Mariposa cryptantha

mariposae

Serpentine habitat in and around the 

Bagby recreation area

BLM-S, 

CNPS 1B.3 -- -- 1

Tansy-flowered woolly 

sunflower

Eriophyllum confertiflorum 

var. tanacetiflorum

Cismontane woodland and lower 

montane coniferous forests (CNPS,

2013a)

CNPS 4.3

6 1 --

Stinkbells

Fritillaria agrestis

Clay and sometimes serpentine soils in 

chaparral, cismontane woodland, 

pinyon and juniper woodland, and 

valley/foothill grassland (CNPS,

2013b)

CNPS 4.2

1 -- --

Serpentine bluecup

Githopsis pulchella ssp. 

serpentinicola

Serpentine habitat in and around the 

Bagby recreation area

CNPS 4.3

2 1 1

Peak rush-rose

Helianthemum scoparium

Chaparral understories in and around 

the Horseshoe Bend recreational area

CNPS 3.2 65 1 2
229

Common Name/

Scientific Name

Habitat Description and Location 

Within the Project Statusa

Number of Occurrences by Land 

Owner

Public 

(BLM)

Merced 

ID Private

Foothill jepsonia

heterandra

Rocky, metamorphic soils in 

cismontane woodland and lower 

montane coniferous forest (CNPS,

2013c)

CNPS 4.3

5 8 3

Northern California black 

walnut

Juglans californica var. 

hindsii

Riparian woodlands along rivers and 

streams, occasionally in somewhat drier 

slopes, valleys, and canyons; on 

rocky/gravelly, well-drained soil 

(NatureServe, 2013).

CNPS 1B.1

-- 1 --

Shaggyhair lupine

Lupinus spectabilis

Serpentine habitat in and around the 

Bagby recreation area

BLM-S, 

CNPS 1B.2 4 3 3

Notes: Special-status:

BLM-S = Bureau of Land Management Sensitive Plants

CNPS 1A = California Native Plant Society list presumed extinct in California

CNPS 1B = California Native Plant Society list endangered in California and elsewhere

CNPS 2 = California Native Plant Society list rare/threatened/endangered in California only

CNPS 3 = California Native Plant Society list plants requiring further information

CNPS 4 = California Native Plant Society limited distribution, watch list

a A “.1” after the CNPS rating indicates that this species is seriously endangered in California, a “.2” after the CNPS 

rating indicates this species is fairly endangered in California, and a “.3” after the CNPS rating indicates that this species 

is not very endangered in California.
230

Sensitive Wildlife Species

Special-status wildlife species include those protected by the state of California as 

endangered or threatened, candidate for listing, California species of special concern, 

California fully protected species, and BLM sensitive species. Federally listed threatened 

or endangered species and any applicable designated critical habitat for a listed species 

are discussed in section 3.3.3, Threatened and Endangered Species. 

Merced ID conducted a search of federal and state databases, including the 

California Natural Diversity Database and California Wildlife Habitat Relationship 

System, and consulted with California DFW, FWS, and BLM, to identify special-status 

species with potential to occur in the vicinity of the project. The search determined that 

29 special-status species could potentially occur within 0.25 mile of the project boundary. 

This included 3 amphibians, 2 reptiles, 14 birds, and 10 mammal species. Merced ID

reviewed habitat preferences and habitat types present within the project vicinity to 

identify species with potential habitat in vicinity of the project. Table 3-18 presents 

sensitive wildlife species known to occur in the project vicinity or with suitable habitat in 

the project vicinity.

Following consultation with stakeholders and Commission staff during the 

Integrated Licensing Process, Merced ID conducted surveys for special-status wildlife 

species known to occur in the project boundary or within 0.25 mile of the project 

boundary. Specifically, Merced ID conducted surveys for wintering and nesting bald 

eagles, limestone salamanders, sensitive bats, and western pond turtles. 
231

Table 3-18. Sensitive wildlife species known to occur or with potential habitat that occurs in or within 0.25 mile of the 

Merced River Project boundary (Source: Merced ID, 2012a,d,e, as modified by staff).

Common Name (Scientific 

Name) Status Habitat

Known to Occur within 0.25 

mile of the Project Boundary

Coast horned lizard 

(Phrynosoma cronatum)

BLM-S, SSC Occurs in valley foothill hardwood 

woodlands, conifer forests, riparian 

areas, and annual grasslands. 

No recorded occurrences within 

5 miles of the project.

Western pond turtle BLM-S, SSC Occurs in permanent ponds, lakes, 

channels, backwaters, and pools of 

streams; aquatic habitats with warm, 

shallow water with cover for hatchlings; 

terrestrial sites for nesting; and sites

with suitable basking substrates such as 

rocks, logs, banks, root masses, and 

emergent vegetation for both juveniles 

and adults.

Observed at 3 basking survey 

sites at Lake McClure and 1 site 

at McSwain reservoir; 12 

incidental observations at Lake 

McClure; 3 at McSwain 

reservoir; and 1 in Merced River 

between PG&E’s Merced Falls 

dam to the non-project CrockerHuffman diversion dam.

Foothill yellow-legged frog

(Rana boyli)

BLM-S

SSC

Occurs on small to large streams and 

rivers with pools and low-gradient riffles 

(small streams are probably nonbreeding habitat). Breeding sites usually 

in shallow, slow-flowing areas near the 

shore with coarse substrates (cobbles 

and boulders). Infrequent in habitats 

where introduced fish and American 

bullfrogs are present. 

Tadpoles were observed at 

Sherlock Creek, which flows 

into Lake McClure.
232

Common Name (Scientific 

Name) Status Habitat

Known to Occur within 0.25 

mile of the Project Boundary

Limestone salamander 

(Hydromantes brunus)

ST, FP Occurs on moss-covered outcroppings 

of limestone and other types of rock, and 

talus rubble, generally in oak woodlands 

with scattered foothill pine, and less

frequently in chaparral. Lives under 

ground for much of the year with surface 

activity most likely during cool, wet 

periods between November 1 and 

April 15.

Yes, surveys identified presence 

at 6 sites along the eastern arm 

of Lake McClure. Portions of 

BLM designated Limestone 

Salamander Area of Critical 

Environmental Concern exist in 

the project boundary.

Western spadefoot

(Spea hammondii)

BLM-S,

SSC

Occurs in grasslands, oak woodlands, 

and occasionally chaparral. Breeds in 

vernal pools and other ponds that dry 

seasonally (rarely in permanent ponds), 

and occasionally in intermittent streams.

Not observed during relicensing 

studies. No recorded 

occurrences within 2 miles of the 

project.

American white pelican 

(Pelecanus 

erythrorhynchos)

SSC Habitat includes rivers, lakes, reservoirs, 

estuaries, bays, and open marshes. May 

occur in the project during migration.

No recorded occurrences within 

5 miles of the project.

Bald eagle (Haliaeetus 

leucocephalus)

SE, FP Often found near water bodies such as 

lakes, rivers with adequate fish 

populations.

Yes, known to nest and winter at

the project. Over three winter 

survey periods, Merced ID’s 

bald eagle surveys documented a 

total of 13 sightings at Lake 

McClure and 3 sightings at 

McSwain reservoir. Nesting 

surveys documented six nests at 

Lake McClure and one at 

McSwain reservoir.
233

Common Name (Scientific 

Name) Status Habitat

Known to Occur within 0.25 

mile of the Project Boundary

Burrowing owl (Athene 

cunicularia)

BLM-S,

SSC

Nest in abandoned burrows dug by small 

mammals such as ground squirrels, as 

well as larger mammals such as foxes 

and badgers. If burrows are unavailable, 

burrowing owls may dig their own 

burrow in soft soil, or use pipes, 

culverts, and/or nest boxes.

No recorded occurrences within 

5 miles of the project.

Black-crowned night heron 

(Nycticorax nycticorax)

BLM-S Nest in dense-foliaged trees, dense fresh 

or brackish emergent wetlands, dense 

shrubbery or vine tangles, and usually 

near aquatic or emergent feeding area.

No recorded occurrences within 

5 miles of the project.

Golden eagle 

(Aquila chrysaetos)

BLM-S

FP

Occurs in sparse woodlands, grasslands, 

savannas, lower successional forest 

stages, and shrubland. Cliffs, large 

trees, and man-made structures 

(e.g., electric transmission towers) with 

a commanding view are used for 

nesting.

No recorded occurrences within 

5 miles of the project.

Loggerhead shrike (Lanius 

ludovicianus)

SSC Preferred habitats include open-canopied 

valley foothill hardwood, valley foothill 

hardwood-conifer, valley foothill 

riparian, pinon-juniper, juniper, desert 

riparian and Joshua tree habitats.

No recorded occurrences within 

5 miles of the project.

Long-eared owl 

(Asio otus)

SSC Require dense riparian and live oak 

thickets with small densely canopied 

trees.

No recorded occurrences within 

5 miles of the project.
234

Common Name (Scientific 

Name) Status Habitat

Known to Occur within 0.25 

mile of the Project Boundary

Northern harrier (Circus 

cyaneus)

SSC Occurs in meadows, grasslands, open 

rangelands, desert sinks, fresh and 

saltwater emergent wetlands.

No recorded occurrences within 

5 miles of the project.

Purple martin (Progne 

subis)

SSC Uncommon to rare local summer 

resident of various wooded, lowelevation habitats comprised of montane 

hardwood, valley foothill and montane 

hardwood-conifer, and riparian habitats.

No recorded occurrences within 

5 miles of the project.

Short-eared owl 

(Asio flammeus)

SSC Winters in the Central Valley and 

western Sierra Nevada foothills. Prefers 

open grasslands with no trees.

No recorded occurrences within 

5 miles of the project.

Swainson’s hawk (Buteo 

swainsoni)

SE Typical breeding habitat consists of trees 

within mature riparian forest, lone trees 

and oak groves, and mature roadside 

trees. It forages in native grasslands, 

lightly-grazed dryland pasture, and 

suitable grain or alfalfa fields that are 

adjacent to nesting habitat.

No recorded occurrences within 

5 miles of the project.

Tricolored blackbird 

(Agelaius tricolor)

BLM-S

SSC

Occurs in herbaceous wetland areas as 

well as cropland and hedgerow habitats. 

Tricolored blackbirds have been found 

to breed in fresh-water marshes 

consisting of cattails, tule, bulrushes, 

and sedges.

No recorded occurrences within 

5 miles of the project.

Yellow-breasted chat 

(Icteria virens)

SSC Found in thickets of willow and other 

brushy vegetation in riparian areas near 

No recorded occurrences within 

5 miles of the project.
235

Common Name (Scientific 

Name) Status Habitat

Known to Occur within 0.25 

mile of the Project Boundary

watercourses for cover.

Yellow warbler (Setophaga 

petechia)

SSC Occurs in riparian deciduous habitats 

with cottonwoods, willows, alders, and 

other small trees and shrubs found in 

low, open-canopy woodland.

No recorded occurrences within 

5 miles of the project.

American badger (Taxidea 

taxus)

SSC Found most abundantly in drier open

stages of most shrub, forest, and 

herbaceous habitats, with friable soils. 

This species’ diet consists mostly of 

rodents: rats, mice, chipmunks, pocket 

gophers, and ground squirrels.

No recorded occurrences within 

5 miles of the project.

Fringed myotis

(Myotis thysanodes)

BLM-S Roosts in caves, mines, buildings, and 

crevices. Uses open habitats, early 

successional stages, streams, lakes, and 

ponds as foraging areas (California 

WHR, 2013a).

Yes, recorded acoustically 

during surveys.

Pallid bat 

(Antrozous pallidus)

BLM-S

SSC

Arid deserts and grasslands, often near 

rocky outcrops and water. Less abundant 

in evergreen and mixed conifer 

woodland. Usually roosts in rock crevice 

or building, less often in caves, tree 

hollows, mines (California WHR,

2013b).

Yes, recorded acoustically and 

captured during surveys.
236

Common Name (Scientific 

Name) Status Habitat

Known to Occur within 0.25 

mile of the Project Boundary

Spotted bat

(Euderma maculatum)

BLM-S

SSC

Prefers to roost in rock crevices. 

Occasionally found in caves and 

buildings. Prefers sites with adequate 

roosting habitat, such as cliffs. Feeds 

over water and along washes. May move 

from forests to lowlands in autumn 

(California WHR, 2013c).

Yes, recorded acoustically 

during surveys.

Townsend’s big-eared bat 

(Corynorhinus townsendii)

BLM-S, 

SSC

Requires caves, mines, tunnels, 

buildings, or other human-made 

structures for roosting. Prefers mesic 

habitats. Gleans from brush or trees or 

feeds along habitat edges (California 

WHR, 2013d).

Yes, recorded acoustically 

during surveys.

Western long-eared myotis

(Myotis evotis)

BLM-S Roosts in buildings, crevices, spaces 

under bark, and snags. Caves are used 

primarily as night roosts. Feeds along 

habitat edges, in open habitats, and over 

water (California WHR, 2013e).

Yes, recorded acoustically 

during surveys.

Western mastiff bat 

(Eumops perotis)

BLM-S

SSC

Suitable habitat consists of extensive 

open areas with abundant roost locations 

provided by crevices in rock outcrops 

and buildings (California WHR, 2013f).

Yes, recorded acoustically 

during surveys.
237

Common Name (Scientific 

Name) Status Habitat

Known to Occur within 0.25 

mile of the Project Boundary

Western small-footed 

myotis (Myotis ciliolabrum)

BLM-S Seeks cover in caves, buildings, mines, 

crevices, and occasionally under bridges 

and under bark. Prefers open forest and 

woodland stands in arid uplands as well 

as brushy habitats. Streams, ponds, 

springs, and stock tanks are used for 

drinking and feeding (California WHR,

2013g).

Yes, recorded acoustically and 

captured during surveys.

Western red bat 

(Lasiurus blossevillii)

SSC Roosts primarily in trees, less often in 

shrubs. Roost sites often are in edge 

habitats adjacent to streams, fields, or 

urban areas. Prefers edges or habitat 

mosaics that have trees for roosting and 

open areas for foraging (California 

WHR, 2013h).

Yes, recorded acoustically 

during surveys.

Yuma myotis (Myotis 

yumanensis)

BLM-S Roosts in buildings, mines, caves, or 

crevices. The species also has been seen 

roosting in abandoned swallow nests and 

under bridges. Distribution is closely 

tied to bodies of water, which it uses as 

foraging sites and sources of drinking 

water. Open forests and woodlands are 

optimal habitat (California WHR,

2013i).

Yes, recorded acoustically and 

captured during surveys.

Notes: BLM-S – BLM sensitive species; FP – California fully protected; SE – California endangered; ST – California 

threatened; SSC – California species of special concern
238

Merced Falls Project

Vegetation 

Cover Types—In 2010 and 2011, PG&E characterized the botanical communities

within the existing project boundary, and an area of at least 200 feet from the NMWSE of 

the Merced Falls impoundment, including areas that could be affected by maintenance

and operation. This vegetation study area includes upland, riparian, wetlands, and littoral 

habitats. Specific cover types identified and discussed below. 

PG&E reviewed digital aerial photography, in conjunction with the USGS Merced 

Falls 7.5-minute quadrangle. Visible breaks and differences in the type of vegetation 

cover were identified and polygons were drawn around the visibly different areas. 

Vegetation series were assigned to these polygons and series from the Manual of 

California Vegetation were used to describe existing vegetation (Sawyer and KellerWolf, 1995). This initial vegetation map was then ground-truthed and refined during the 

2010 field surveys. 

Two botanical communities dominate upland areas in the vegetation study area: 

California annual grassland series and ruderal vegetation. Sub-dominate communities 

include valley oak, white alder, fremont cottonwood, blackberry thickets and blackberry 

thickets with sedges, black willows, blue oaks, interior live oak, Ailanthus, bulrush-cattail 

and bulrush, mosquito fern, and emergent aquatics.

The most dominant cover type in the vegetation study area is California annual 

grassland series, an extensive and variable series composed of non-native and native 

annual species. Common non-native species in the California annual grassland include 

slender wild oat, soft chess, and ripgut brome. The California annual grassland supports 

some non-dominant native species such as fiddleneck, yellow Mariposa lily, and purple 

clarkia.

The ruderal series is similar to the California annual grassland series and plants of 

this series often intergrade with plants of the California annual grassland. These habitats 

are dominated by short-statured, non-native grasses and forbs, and noxious weeds are 

mostly dominant with few to no native herbs, although some occasional late-blooming 

native bulbs do occur. The ruderal areas are disturbed areas around dwellings, heavily 

used roads and recreation areas, and also livestock pastures. Dominant species in the 

ruderal areas include ripgut brome, Jim-hill mustard, and prickly lettuce.

The valley oak series is a riparian forest series that occurs on the northwest to 

north shores of the impoundment. On the northwest shore, it intergrades with the 

Fremont cottonwood series. The overstory of the valley oak series is dominated by 

medium to large valley oaks. Other white alder, black walnut, interior live oak, 

Gooding’s black willow, and Fremont cottonwood are common and tree of heaven also 

occurs in this series. The understory varies from dense to sparse, and is either dominated 

by herbs or woody shrubs and vines, depending on the amount of available water and 
239

light. Annual grasses are common as are California pipevine, Pacific rush, and 

Himalayan blackberry.

The white alder series, a riparian forest series, presents along the northwest side of 

the immediate impoundment edge. Portions of white alder series are also present 

surrounding an inlet on the southeast side of the impoundment, and as inclusions around 

ponds within the mine tailings. These areas typically have a dense overstory dominated 

by white alder, as well as valley oak, interior live oak, or Fremont cottonwood. These 

habitats are often wetter than those dominated by valley oak. Sandbar willow, red 

willow, and stinging nettle occur in the understory. Common herbaceous species include 

western lady’s fern, Santa Barbara sedge, and dense sedge.

Blackberry thickets, including blackberry thickets with sedges, are dominated by 

thick stands of Himalayan blackberry that often form monocultures but can also be mixed 

with other riparian forest understory species. This series occurs in areas on the south side 

of the impoundment. Stands are co-dominated by dog rose, with a cover of hydrophytic 

herbs and herbaceous emergent aquatics occur along the impoundment edge. Common 

species include tufted hairgrass, spike-rushes, and meadow fescue.

The Fremont cottonwood series of riparian forest has an overstory dominated by 

Fremont cottonwood with representations of other riparian trees such as white alder, 

black walnut, Valley oak, Gooding’s black willow, and arroyo willow. These areas are 

generally somewhat moister than the valley oak series with which they intergrade. The 

understory is similar between these two series, often consisting of Pacific rush, and dense 

Himalayan blackberry and California grape.

Two areas dominated by Godding’s black willow occur in the vegetation study

area and adjacent lands. These riparian forests are very similar to the valley oak and 

Fremont cottonwood series with the exception that Godding’s black willow is the 

dominant overstory tree.

The blue oak series is a riparian series that occurs in one small area north of the 

boat launch, on the northeast side of the impoundment. Blue oak trees are dominate and 

the understory consists of herbaceous species also common in the California annual 

grasslands.

The interior live oak series occurs at some rock outcrops on the southeast side of 

the impoundment. The herbaceous understory is similar to that of the California annual 

grassland, except different native species grow on the rocks than in other places in the 

vegetation study area. Canyon dudleya, lax woodsorrel, and glassy onion are present in 

this habitat.

A tree of heaven stand occurs in a small area on the north side of the 

impoundment, opposite the Hornitos Road turnoff. The understory consists of

herbaceous species common in California annual grasslands and ruderal vegetation.

A few areas with shallow standing permanent water are dominated by perennial 

rooted emergent aquatics. The bulrush series is dominated by a near monoculture of 
240

bulrush, otherwise known as hard-stemmed tule. The bulrush-cattail series is mixed 

bulrush and broad-leaved cattail.

The mosquito fern series occurs at two small ponds on the southwest side of the 

impoundment that have permanent standing water and little disturbance. These ponds are 

covered in a layer of mosquito fern mixed with duckweed. These ponds are surrounded 

by mine tailings, and may have been old mine ponds.

Emergent aquatics occur on the northernmost portion of the vegetation study area, 

where a small perennial or long-running intermittent stream runs into the Merced Falls 

impoundment. It flows through annual grasslands at the northern tip of the project area 

and supports a small area of emergent vegetation including barnyard grass, fringed 

willowherb, and cliestogamous spike primrose.

In addition to the open water, other areas with little or no vegetation occur in the 

project area, including developed habitats, rock outcrops, and mine tailings. 

Developed habitats, on the north side of the project area include substations, 

parking lots, and residential areas that have been largely modified by human activity and 

are generally managed for no vegetation or landscaped vegetation. The most common 

plant species occurring in the developed areas include bladderpod, oleander, and 

redwood.

Rock outcrops are present on the northeast side of the impoundment, along the 

access road to the McSwain powerhouse. These rock outcrops support a sparse covering 

of many species common to the California annual grassland. However, some native 

species were observed on these rock outcrops, including pink spineflower, white-whorled 

lupine, and phacelia. 

There is a section of mine tailings on the southwest edge of the project area and 

immediate vicinity with numerous human-placed cobbles and similar rocks. The 

composition of the vegetation in the mine tailings area is similar to the California annual 

grassland and is composed of non-native and native forbs. However, vegetation cover in 

the mine tailings area is sparse.

Noxious and Invasive Weeds—PG&E does not have a formal program to control 

noxious and invasive plants at the Merced Falls Project. However, it conducts periodic 

weed control (usually twice per year) at the dam and River’s Edge Fishing Access area to 

minimize the risk of spreading noxious weeds and invasive plants through accessing the 

project. In 2010, PG&E performed surveys for noxious and invasive weeds. 

Prior to conducting field surveys, PG&E developed a candidate list species by 

reviewing the Federal Weed List, the California DFA list of A- and B-rated weeds, and 

the California Invasive Plant Council’s Inventory of noxious weeds, and cross referenced 

the potentially occurring weeds with known plants within Merced and Mariposa 

Counties. A few species were added to the candidate list from the most-recent yearly 

agricultural treatment reports for Mariposa and Merced Counties, and the Sierra-San 
241

Joaquin Noxious Weed Alliance’s Field Guide to Invasive Non-Native Weeds of 

Mariposa, Madera, and Fresno Counties).

The 2010 botanical survey found 11 noxious weed species within the vegetative 

study area and surrounding lands a total of 303 invasive weed occurrences were found 

within the vegetation study area (table 3-19). The most abundant weeds were yellow 

star-thistle and tocalote; Italian thistle and Klamathweed were also widespread and 

abundant. A large stand of milk thistle occurs on the southeast shore, and several stands 

of Himalayan blackberry and a large stand of tree of heaven occurs on the north shore.

Table 3-19. Occurrences of noxious and invasive plants identified in the Merced Falls 

Project vegetation study area (Source: PG&E, 2012, as modified by staff).

Common Name Scientific Name

Number of

Occurrences 

(Points and 

Polygons)

Approximate

Acreage

a

(polygons)

Estimated 

Number of

Plants

Tree of heaven Ailanthus

altissimus 14 0.9 600

Italian thistle Carduus 

pycnocephalus 24 2.2 200,000

Tocalote Centaurea 

melitensis 22 8.7 790,000

Yellow starthistleCentaurea 

solstialis 37 10.4 1,550,000

Bull thistle Cirsium vulgare 21 small amounts 120

Fennel Foeniculum 

vulgare 10 small amounts 140

Klamathweed Hypericum 

perforatum 54 1.2 183,000

Himalayan

blackberry

Rubus armeniacus

(=R. discolor) 39 3.8

thickets – not 

available

Milk thistle Silybum marianum 70 0.4 15,000

Medusahead Taeniatherum 

caput-medusae 1 small amounts 500

Woolly mullein Verbascum thapsis 11 small amounts 100
242

Wildlife

The project area, located in the Lower Merced Basin, supports habitats and 

associated wildlife species typical of the topography and soils and of the transition zone 

between the Central Valley and the foothills of the Sierra Nevada Mountains. The 

project area contains predominately open water habitat (i.e., the Merced Falls 

impoundment), providing habitat for a variety of aquatic species and waterfowl. Riparian 

and wetland habitat occurs along the shoreline. However, most wildlife species are 

associated with riparian and upland habitats located above the mean high water mark of 

the impoundment. The terrestrial habitats in the project area include primarily disturbed 

areas such as historic dredge tailings, roadways, and a mixture of annual grasslands and 

oak woodlands.

PG&E identified 2 reptiles, 3 amphibians, 15 birds, and 10 mammals potentially 

occurring in the project area by reviewing FWS’ website for federally endangered and 

threatened species, California DFW’s online California Natural Diversity Database, 

online records located at University of California, Berkeley, Museum of Vertebrate 

Zoology, and California Academy of Sciences’ Herpetology Records. For special-status 

species, searches were generally focused on the USGS 7.5-minute quadrangle on which 

the project is located (Merced Falls), and four surrounding quadrangles including 

Hornitos, Yosemite Lake, Haystack Mountain, and Indian Gulch, although some searches 

were conducted by county (Merced and Mariposa). 

Common resident bird species in the project area include American crow, western 

scrub-jay, American robin, and cliff swallows. Common waterfowl include the Canada 

goose, pied-billed grebe, and mallard and wading birds such as great blue heron. 

Common mammals include pocket gopher and gray fox, as well as bat species such as 

canyon bat, Townsend’s big-eared bat, Western mastiff bat, pallid bat, and Myotis

species. 

Sensitive Plant Species

Following consultation and a review of the USGS quadrangle map in which the 

Merced Falls Project is located plus eight adjacent quadrangles; available information 

from California Native Plant Society’s Online Inventory of Rare and Endangered 

Vascular Plants of California, FWS’ website and the California Natural Diversity 

Database; FWS critical habitat maps; and herbarium specimens and photographs from 

Mariposa and Merced Counties, PG&E identified 11 sensitive39 plants with potential to 

 

39 Sensitive plant species include federally-listed endangered and threatened 

species and candidate species proposed for federal listing, California state-listed 

threatened and endangered species, and species included in the California Native Plant 

Society’s Inventory of Rare and Endangered Plants database.
243

occur in the project area. In 2010 and 2011, PG&E performed surveys for these specialstatus plants. 

None of the 11 species identified as potentially occurring in the project area were 

observed during the 2010 and 2011 surveys; however, two special-status plant species, 

gypsum-loving larkspur and foothill jepsonia, were observed and mapped. Although not 

state- or federally-listed, both species are identified as uncommon in the state by the 

California Native Plant Society. PG&E documented 48 individuals of gypsum-loving 

larkspur on the southeast side of the impoundment in the California annual grassland 

series, adjacent to a rocky outcrop in the interior live oak woodland, and 86 individuals of 

foothill jepsonia on the southeast side of the impoundment in rocky outcrops within the 

interior live oak woodland. In addition, one blue elderberry shrub of suitable size to 

support the federally threatened valley elderberry longhorn beetle was observed and 

mapped on the northeast side of the impoundment during the 2010 survey.

Sensitive Wildlife Species

PG&E identified a list of sensitive wildlife species40 potentially occurring in the 

project area, including 46 plants, 15 birds, 10 mammals, 3 amphibians, 2 reptiles, and 1 

fish species. In 2010 and 2011, PG&E conducted surveys to document sensitive wildlife 

species and potential habitat for sensitive wildlife species, including unique features of 

habitats. PG&E documented nine state special-status species, including five classified as 

Species of Special Concern, two classified as Fully Protected, and two on the state’s 

Watch List (table 3-20). 

 

40 Sensitive wildlife species include federally-listed endangered and threatened 

species and candidate species proposed for federal listing, California state-listed 

threatened and endangered species, and species included in the California Native Plant 

Society’s Inventory of Rare and Endangered Plants database, and species designated as 

California Species of Special Concern by California Department of Fish and Game (now 

California DFW). Federally listed threatened or endangered species and any applicable 

designated critical habitat for a listed species are discussed in section 3.3.3, Threatened 

and Endangered Species. 
244

Table 3-20. Sensitive wildlife species known to occur or with potential habitat 

occurring within the Merced Falls Hydroelectric Project area (Source: 

PG&E, 2012, as modified by staff).

Common Name 

(Scientific Name) Status Habitat

Occurrences in 

Project Area

Western pond turtle

Actinemys 

marmorata

SSC Permanent and seasonal 

aquatic habitats; basking 

habitats; females require 

terrestrial habitat for nesting 

Observed basking in 

the Hornitos Bridge 

cove.

Bald eagle 

(Haliaeetus 

leucocephalus)

SE, FP Open water such as lakes, 

rivers with adequate fish 

populations

Five sightings 

observed on protocol 

surveys in winter

and spring. No 

nesting in 2011.

Osprey

Pandion haliaetus

WL Open water such as lakes and 

rivers with adequate fish 

populations

Three active nests on 

impoundment.

Yellow-breasted

chat

Icteria virens

SSC Thickets of willow and other 

brushy vegetation in riparian 

areas near watercourses for 

cover

Adult male singing

on southwest side of 

Hornitos Bridge, in

riparian brush.

Double-crested

comorant

Phalacrocorax

auritus

WL Open water with ample fish 

populations 

Observed foraging on 

impoundment.

Townsend’s bigeared bat

Corynorhinus

townsendii

SSC Caves, mines, tunnels, 

buildings, or other humanmade structures for roosting;

prefers mesic habitats; gleans 

from brush or trees or feeds 

along habitat edges

(California WHR, 2013d)

Documented 

roosting in mill 

ruins. Visually 

detected.
245

Common Name 

(Scientific Name) Status Habitat

Occurrences in 

Project Area

Pallid bat

Antrozous pallidus

SSC Arid deserts and grasslands, 

often near rocky outcrops and 

water; less abundant in 

evergreen and mixed conifer 

woodland; usually roosts in 

rock crevice or building, less 

often in caves, tree hollows, 

mines (California WHR, 

2013b)

Documented 

roosting in mill 

ruins. Visually 

detected.

Western mastiff bat

Eumops perotis

SSC Extensive open areas with 

abundant roost locations 

provided by crevices in rock 

outcrops and buildings 

(California WHR, 2013f)

Acoustically

detected.

Ringtail

Bassariscus astutus

FP Various riparian habitats, and 

in brush stands of most forest 

and shrub habitats 

Observed at night in 

switchyard.

Notes: FP – California fully protected; SE – California endangered; WL – California 

watch list;

41 SSC – California species of special concern

3.3.2.2 Environmental Effects

Merced River Project 

Vegetation Management

Under a new license, operation and maintenance of the project and construction of 

any new facilities could disturb vegetation resources from excavation, grading, topsoil 

stripping, or other similar activities. Such disturbances are expected to occur in 

association with improvements to recreation resources, facility maintenance, and 

treatment of invasive weeds. Vegetation and soil disturbance could alter composition of 

existing vegetation communities or increase the potential for invasive weed colonization. 

These changes could also affect wildlife habitat quality.

 

41 California DFW defines Watch List Species as taxa that were previously SSCs,

which no longer merit SSC status or do not meet SSC criteria, but for which there is 

concern and a need for additional information to clarify status.
246

To minimize potential effects of project operation and maintenance on vegetation, 

Merced ID proposes to implement its Vegetation Management Plan, as filed with the 

final license application and amended on September 22, 2014. The plan includes specific 

measures for revegetation, general vegetation management, and reporting. The plan also 

includes measures to protect sensitive species and the valley elderberry longhorn beetle. 

These components of the plan are discussed below under in Section 3.3.3.1, Threatened 

and Endangered Species.

As described in the Vegetation Management Plan, Merced ID would consider the 

need for revegetation activities in areas including all sites where treatment of invasive 

weeds covers more than 0.25 acre, construction sites subject to ground disturbance, and 

erosion control sites. Merced ID would evaluate the need for revegetation at such sites 

based on three criteria: (1) native vegetation cover is less than 30 percent of the surface 

area (excluding areas where natural vegetation cover is below 30 percent); (2) erosion is 

evident or there is a height potential for erosion; or (3) the potential for natural 

revegetation is limited based on vegetation in the surrounding area. If any of these 

criteria are met, Merced ID would develop a revegetation plan for the site.

Once Merced ID determines whether revegetation of a site is necessary, it would 

develop a site-specific revegetation plan. The revegetation plan would include: (1) a site 

assessment to record existing soil, topography, water availability, and vegetation 

characteristics; (2) identification of suitable species and planting methods; and (3) an 

implementation schedule. For sites larger than 0.5 acre, the revegetation plan would also 

include a site design, soil treatments, and an invasive weed control strategy. Merced ID

would submit all revegetation plans to BLM for approval. 

The Vegetation Management Plan includes a description of proposed revegetation 

methods. Merced ID would determine planting and site preparation methods on a siteby-site basis. Proposed methods would include soil treatments at sites where compaction 

is a concern. In these areas, Merced ID would remove the top 6 to 12 inches of top soil 

and store this soil to be used for planting following completion of the disturbance 

activities. On BLM land, Merced ID proposes to use seed mixes that contain only native 

species and meet BLM standards. Merced ID would use custom seed mixes on larger 

sites and would cover all seed with mulch. Merced ID would typically plant larger sites 

with a mixture of native trees, shrubs, and forbs but would use salvaged plants from the 

site whenever feasible. Merced ID would handle all plant materials as little as possible 

and protective features would be installed where necessary. Merced ID would complete 

seeding, planting, and restoration of disturbed areas, including topsoil piles and berms, 

within 90 days following completion of construction or ground-disturbing activities, or as 

soon as feasibly possible.

Merced ID would annually monitor disturbed sites where revegetation is deemed 

unnecessary for a minimum of 3 years or until success criteria are met. Merced ID would 

annually monitor revegetated sites until success criteria are met and attained for 1 year. 

If revegetated sites do not meet success criteria after 3 years, Merced ID would 
247

implement additional remedial measures, including additional seeding and planting. If 

after 2 years, the success criteria for these sites are still not met, Merced ID would consult 

with BLM to develop strategies to address the issues at the site. Success criteria for all 

sites would include: 

1. native vegetation cover comprises more than 60 percent of the surface area of 

the site, compared to similar sites on the adjacent undisturbed area;

42

2. no List A invasive weeds are present; 

3. List B and C invasive weeds and other undesirable plant species would meet 

the following standards for acceptable revegetation: 

 if the area adjacent to the project site contains less than a 25 percent cover 

of undesirable species, revegetation will be considered acceptable when 

the cover of undesirable species on the project site does not exceed 5 

percent; 

 if the area adjacent to the project site contains a 25 to 50 percent cover of 

undesirable species, revegetation will be considered acceptable when the 

cover of undesirable species on the project site does not exceed 10 percent; 

 if the area adjacent to the project site contains more than a 50 percent 

cover of undesirable species, revegetation will be considered acceptable 

when the cover of undesirable species on the project site does not exceed 

25 percent; 

4. there is no evidence of significant erosion, rills are less than 3 inches deep 

and deeper, or excessive rilling is not observed; 

5. desirable vegetation appears vigorous and self-sustaining and plants have the 

opportunity to complete their annual life cycles; Merced ID would evaluate 

this objective by observing the size, color, and vigor of the plants and noting 

the presence of new growth shoots, flowers, seeds, litter build-up, and 

seedlings; 

6. adequate diverse vegetation is present; and 

7. the site contains a mixture of native species similar to the adjacent 

undisturbed area.

Additionally, the Vegetation Management Plan includes descriptions of general 

vegetation maintenance activities, such as the routine clearing of vegetation around 

project facilities, removal of hazardous trees, and maintenance of recreation areas. The 

 

42 For example, if the surrounding area has 30 percent native vegetative cover, the 

site needs to have 18 percent cover, which is 60 percent of 30 percent.
248

plan includes specific protocols for applying herbicides and requires prior approval from 

BLM before applying such herbicides on federal land. The plan also requires prior 

landowner approval for hazard tree removals. At recreation areas, the plan calls for 

maintenance to ensure the ground is bare around campfire sites and vegetation 

maintenance, such as native planting and tree trimming, to promote campground 

aesthetics.

The Vegetation Management Plan also includes provisions for reporting activities

to document herbicide applications, revegetation efforts, and the results of revegetation 

monitoring. Merced ID would present these reports to BLM during its proposed annual 

meetings, which would also provide opportunities for Merced ID, BLM (and other 

invited agencies and stakeholders that chose to attend the meeting) to discuss the need for 

potential revisions to the Vegetation Management Plan over the term of a new license.

BLM [preliminary 4(e) condition 9] specifies that Merced ID develop a vegetation 

and non-native invasive plant management plan to protect terrestrial resources. 

Requirements relating to non-native invasive plant management are discussed below 

under Noxious Weeds and Invasive Plants. The general objectives of BLM’s plan 

regarding vegetation management include:

 conserving and restoring habitats to support long-term viability of native 

species, sensitive species, and the associated natural diversity of these 

habitats; 

 ensuring safe and effective operation of the facilities by maintaining safe 

access to facilities, protecting worker and public health and safety, and 

reducing fire hazards; and

 managing public lands in accordance with the Federal Land Policy and 

Management Act of 1976. 

Our Analysis

Proposed enhancements at existing project recreation areas and construction of the 

proposed new Mack Island recreation site, treatment of invasive weeds, and maintenance 

of project facilities would entail removal of existing vegetation and soil disturbance. 

These activities have potential to alter existing vegetation community composition or 

structure within the project boundary. Implementation of Merced ID’s proposed 

Vegetation Management Plan would identify areas where project operation and 

maintenance activities have the potential to affect existing vegetation and provide 

guidance for revegetation measures in these areas. Revegetation and subsequent 

proposed monitoring would help ensure existing native vegetation communities are 

restored following project-related disturbance and minimize the potential for erosion of 

exposed soils. Modifying the plan to include details about the specific BMPs to be 

implemented would provide the agencies with information to evaluate the effectiveness 

of the BMPs and would allow Merced ID to implement additional BMPs, if necessary, to 
249

further protect terrestrial resources. We further discuss measures to control erosion in 

section 3.3.1.2, Aquatic Resources. 

General vegetation management protocols identified in the plan include preapproval for herbicide use on federal land and guidelines for vegetation management at 

recreation sites and would also minimize potential for adverse effects on native 

vegetation. Merced ID’s proposed Vegetation Management Plan is consistent with the 

goals, objectives, and methodologies outlined in the components of BLM’s management 

plan that are specific to vegetation management. Implementing Merced ID’s plan for 

vegetation management would reduce project-related effects on terrestrial vegetation. 

Additionally, implementation of the proposed plan, which is consistent with BLM’s plan, 

would ensure the project is compliant with federal laws and policies.

Invasive Weeds

Project operation and maintenance activities including road grading and vegetation 

control could result in the removal of existing vegetation and soil disturbance, thereby 

increasing the potential for the spread of invasive weeds. Additionally, project vehicles 

may transport invasive weed seeds from one area to another, and the rise and fall of the 

reservoir water levels can also carry seeds from invasive weeds along the shoreline and 

distribute them in other areas suitable for colonization.

To minimize the spread of invasive weeds, Merced ID proposes to implement its 

Invasive Species Management Plan, as filed with the final license application and 

amended on September 22, 2014. The plan presents protocols for annual employee 

training, provisions for reviewing weed lists, and measures to prevent the spread of 

weeds into and within the project boundary. Prevention measures include cleaning 

vehicles and equipment prior to entering the project, revegetating disturbed areas with 

native vegetation (as described in the Vegetation Management Plan), using weed-free 

materials for erosion control, and limiting travel through weed-infested areas. The plan 

also calls for conducting surveys for invasive weeds on all public land within the project 

boundary. These surveys would occur during the first year of a license and every 5 years 

thereafter. The plan also outlines weed control measures for all California DFA A- and 

B-listed weeds on public land. Merced ID would also treat new occurrences of five 

C-listed species (tree-of-heaven, Scotch broom, Russian thistle, Spanish broom, and 

puncturevine). Weed treatments would be consistent with BLM guidelines for invasive 

weed control. Following treatment, Merced ID would annually monitor treated 

populations and would implement additional control measures until three consecutive 

surveys show no sign of the treated species present. Finally, the plan includes provision 

for annual reporting to BLM to present results of surveys and weed treatments that 

occurred during the previous year.

In preliminary 4(e) condition 9, BLM specifies that Merced ID develop a 

vegetation and non-native invasive plant management plan to protect terrestrial resources. 

The objectives of BLM’s invasive plant management plan are to:
250

 control invasive species using early detection, rapid response, and 

prevention measures; 

 prevent, eliminate, and/or control undesired non-native vegetation or other 

invasive species using an integrated pets management approach that 

combines biological, cultural, physical, and chemical tools to minimize 

economic health and environmental risks; and 

 implement federal acts and laws, BLM policies and strategies, and other 

efforts to meet the goals of eradicating and controlling invasive species on 

BLM lands. 

California DFW’s 10(j) recommendation 10 recommends that Merced ID develop 

a plan for integrated pest management and pesticide use notification to control 

undesirable woody and herbaceous vegetation in addition to aquatic plants, insects, and 

rodents to minimize the use of pesticides. California DFW recommends that the plan 

include the following specific details: locations of use, herbicides proposed for use, 

application rates, dose and exposure rates, and safety risk and time frames for application. 

The plan should include an exception for when unexpected outbreaks of pests require 

control measures that were not anticipated at the time the report was submitted. In that 

case, Merced ID would submit and emergency notification of use to the appropriate 

agencies. 

BLM [preliminary 4(e) condition 40] specifies that Merced ID request approval 

prior to using pesticides to control undesirably woody and herbaceous vegetation, aquatic 

plants, and other pests on BLM lands. The plan allows for exceptions in the event of 

unexpected outbreaks.

Merced ID proposes to obtain written approval from BLM before using pesticides 

and herbicides on lands administered by BLM.

Our Analysis

Under a new license, continued operation and maintenance of the project would 

include vegetation management, road grading, and vehicle traffic. Construction 

associated with modified or new project facilities could also result in ground-disturbing 

activities. These activities would expose soils and remove existing vegetation, creating 

suitable sites for weed establishment. Operation of project vehicles has the potential to 

spread seeds from existing populations to new areas within the project.

Merced ID’s proposed Invasive Species Management Plan includes appropriate 

measures (e.g., vehicle washing, use of weed-free materials, revegetation activities) to the 

limit potential for weed introduction and dispersal within the project boundary. The plan 

also stipulates that Merced ID would conduct surveys every 5 years to determine the 

location of invasive weeds and use BLM-approved treatment measures to treat existing 

weed populations. Proposed treatment and monitoring measures are likely to control or 
251

eradicate these populations. However, with the exception of the Iberian starthistle 

population located on private land, Merced ID’s proposed survey and treatment activities 

are limited to BLM-managed land within the project boundary. Existing populations on 

Merced ID land would be left untreated, and no surveys would be conducted to identify 

new populations on Merced ID and private land.

The majority (more than 70 percent) of the existing invasive weed populations 

identified during surveys were located on Merced ID land with a high frequency of the 

invasive weed populations occurring in the immediate vicinity of project recreation areas. 

Because the majority of these invasive weed populations are C-listed species, they may 

not require treatment. However, during its invasive weed survey, Merced ID identified a 

population of perennial pepperweed (a B-listed species) on its land, and there is no 

proposed treatment for this population. Since the majority of project activities with 

potential to introduce or spread invasive species would occur on Merced ID land, 

excluding these areas from survey and treatment measures would be counter-productive. 

Failing to monitor these areas would increase potential for establishment of A- and 

B-listed species. Untreated populations would increase the potential for invasive weeds 

to spread to surrounding areas, including BLM-managed land.

Merced ID’s proposed Invasive Species Management Plan would reduce the 

potential for the introduction and spread of invasive weeds resulting from project 

activities. Proposed treatment and monitoring of A- and B-listed species on BLM land 

would reduce potential for these populations to spread and would reduce potential effects 

of these species on native plants that are not able to outcompete invasive weeds and avoid 

mono-cultures that are less suitable for wildlife habitat compared to diverse communities 

of native plants. Modifying the proposed Invasive Species Management Plan to stipulate 

that the measures in the plan apply to all land within the project boundary, including 

treatment measures for the existing population of perennial pepperweed on Merced ID

land would further reduce invasive weeds and would more directly address projectrelated effects from invasive weeds. Modifying the plan to include specifics on the 

BMPs that Merced ID proposes to implement would keep the agencies apprised about the 

proposed BMPs and allow the BMPs to be evaluated and/or adjusted based on their

effectiveness as necessary, thereby further reducing potential effects of invasive plant 

management on other terrestrial and aquatic resources. 

Merced ID’s Invasive Species Management Plan is consistent with the goals, 

objectives, and methodologies outlined in the components of BLM’s recommended

management plan that are specific to vegetation management. 

Integrating a component for pest management and pesticide use notification into 

the Invasive Species Management Plan to address agency requirements of notification 

prior to use would further protect both terrestrial and aquatic resources from the effects of 

herbicides used to control undesirable vegetation and other pesticides. We recommend 

including a provision in the plan to describe incidents for which pesticide use without 

prior notification would be allowed. Implementing the plan and measures discussed 
252

above would also ensure the project is compliant with laws and policies regarding 

pesticide use. 

Protection of Sensitive Plants and Wildlife 

Project operation and maintenance activities, such as road grading and vegetation 

control, modification of existing facilities, and construction of new project facilities could 

remove existing vegetation, disturb soils, and change microsite habitats. These activities 

have potential to disturb sensitive plants, disturb habitat for sensitive wildlife, or directly

injury or disturb sensitive wildlife in the immediate vicinity of these activities. Specific 

effects on the bald eagle and limestone salamander are discussed in the following 

subsections.

Merced ID’s proposed Vegetation Management Plan includes several measures to 

reduce potential effects on sensitive plants and wildlife. In areas with known sensitive 

resources, Merced ID would: (1) flag sensitive areas prior to conducting any vegetation 

management or ground-disturbing activities; (2) emphasize the use of manual weed 

control methods, where feasible; (3) use unspecified BMPs; and (4) provide annual 

employee training including identification of key special-status species and the locations 

of sensitive resources to be avoided. Merced ID’s proposed Recreation Facilities Plan, as 

filed with the final license application and amended on September 22, 2014, also includes 

provisions for avoidance of known sensitive plant and wildlife populations in the 

planning of the future placement of major rehabilitation or capital improvement projects. 

For any future developments planned outside the project boundary, Merced ID would 

consult with BLM during the planning process and evaluate the need for additional 

surveys for sensitive plants and wildlife. Merced ID also proposes, as part of its Invasive 

Species Management Plan, to emphasize protection of sensitive plants when selecting 

control measures for invasive weeds in proximity to sensitive resources.

In preliminary 4(e) condition 9, BLM specifies that Merced ID conduct botanical 

surveys to provide baseline information on existing rare plants in the project area, 

identify potential adverse project effects on rare plants, and develop measures to reduce 

these effects. According to the condition, the plant surveys generally would be valid for 

5 years or until new information is obtained via BLM guidance. 

Our Analysis

Continued operation of the project under a new license would include some 

activities that, if conducted near sensitive plant species, could affect these resources. 

These activities include application of herbicides to invasive weeds, vegetation 

management in recreation areas or around project facilities, road grading, or any other 

activities with potential to disturb soil or vegetation. Implementation of Merced ID’s 

proposed Vegetation Management Plan, Invasive Weed Management Plan, and 

Recreation Facilities Plan would reduce potential for adverse effects on sensitive plants 

and sensitive wildlife habitat. However, Merced ID’s plans do not include any predisturbance surveys for areas where new disturbance could affect potential habitat. Over 
253

the term of a new license, there is potential for sensitive species to colonize new areas

and that species would be added to sensitive species lists. Therefore, we agree with BLM 

preliminary 4(e) condition 9 to conduct botanical surveys prior to disturbance. 

Consultation with BLM, California DFW, and FWS during the planning phases for any 

new disturbance would identify the need for pre-disturbance surveys and determine 

which methodology should be employed. Implementing surveys, if needed, and 

developing protection measures for any sensitive species in the disturbance area, would 

further reduce potential effects. 

Additionally, Merced ID’s proposed Vegetation Management Plan and Invasive 

Weed Management Plan state that Merced ID would employ BMPs in sensitive areas to 

protect sensitive species; however, Merced ID does not provide any detail about what 

BMPs it would implement, making this measure unenforceable, and we are unable to 

analyze the benefits of these unspecified measures. By revising the proposed Vegetation 

Management Plan and Invasive Weed Management Plan to provide details about the 

specific BMPs it proposes to implement, Merced ID would improve these plans and 

would likely reduce potential effects on sensitive species. Providing these details informs 

the agencies of the proposed BMPs and allows for the effectiveness of the BMPs to be 

assessed and revised if necessary to further reduce potential project effects on sensitive 

species.

Protection of Bald Eagles

Operation and maintenance activities, such as invasive weed control, facility 

maintenance, road maintenance, and construction, could create noise near active bald 

eagle nests and winter roosting sites. Recreation users including hikers and boaters could 

cause similar disturbance. Vegetation management activities could also result in the 

removal of nest trees or roost trees. Bald eagles can be sensitive to increased noise 

during the nesting period, and such disturbance could result in nest abandonment or 

reduced nesting success. The National Bald and Golden Eagle Protection Act and the 

Migratory Bird Treaty Act prohibit such disturbances.

To minimize potential project effects on bald eagles, Merced ID proposes to 

implement its Bald Eagle Management Plan, as amended, filed on September 22, 2014. 

The plan includes provisions to conduct bald eagle surveys at 4-year intervals, starting 

the first year of any new license issued for the project. Survey areas would include all 

lands within 0.25 mile of the project boundary. During each survey, Merced ID would 

collect data related to early spring territory occupancy, late spring nesting behavior, and 

reproduction success in summer. Merced ID would use the survey results to delineate 

protection buffers around each bald eagle nest site. Protection buffers would include all 

land within the project boundary that is within 1,000 feet of the nest.

Within the protection buffers, Merced ID would prohibit operation and 

maintenance activities that could result in bald eagle disturbance, such as weed control, 

facility maintenance, and road maintenance and construction, from January 1 through 
254

August 1. However, Merced ID may request an exception if a nest appears to be 

unoccupied, but the buffer is still in place. Merced ID would consider any emergency 

work conducted within nest buffers to be exempt from the timing restriction and would 

notify agencies of any emergency actions within a minimum of 48 hours, or as soon after 

the emergency as is reasonably possible. If a tree containing an eagle nest is identified as 

a hazard tree, because it is dead or dying and has potential to fall on or near project 

recreation facilities, powerhouses, switchyards, or other project features, it would be 

removed outside the nesting period and BLM and California DFW would be consulted.

To minimize the potential for bald eagle disturbance related to recreation 

activities, Merced ID would post public information notices at campgrounds and boat 

launch facilities. Notices would remain in place from January 1 through August 1 each 

year to: (1) inform the public about bald eagle nests occurring within the project vicinity; 

(2) describe the legal protections for bald eagles; (3) describe what recreationists can do 

to help protect nesting bald eagles (e.g., stay at least 1,000 feet from nests and observe 

birds from a distance); and (4) provide California DFW’s contact information to report 

injured birds.

In preliminary WQC condition 5, the Water Board specifies that Merced ID

prepare a monitoring plan for bald and golden eagles consistent with the most current 

National Bald Eagle Management Guidelines provided by FWS that includes goals and 

objectives, measurable criteria, a monitoring and reporting schedule, a plan for corrective 

measures if goals are not achieved, and minimum monitoring requirements. BLM 

preliminary 4(e) condition 10 specifies that Merced ID implement a bald eagle 

management plan and to consult with BLM, California DFW, FWS, and the Water Board 

before submitting the plan for Commission approval. FWS [10(j) recommendation 9]

recommends that Merced ID consult with resource agencies within 1 year of license 

issuance, before implementing the revised Bald Eagle Management Plan, which would 

include the edits made to the plan by FWS and filed with its recommendation. 

Our Analysis

Operation and maintenance activities (including invasive weed control, facility 

maintenance, road maintenance, and construction) and recreation activities (such as 

hiking and boating) would conflict with bald eagle protection laws if these activities 

adversely affect nesting bald eagles. Merced ID’s proposed buffer distances and timing 

restrictions are consistent with the National Bald Eagle Management Guidelines (FWS, 

2007). These measures would provide protection for nesting bald eagles and would 

reduce potential effects related to project operation and maintenance activities. Posting 

public notifications to inform recreationalists about the presence of bald eagle and 

protection measures would also reduce potential effects on nesting bald eagles.

However, Merced ID’s proposed plan does not include any protection measures 

for winter roost sites. In addition to nest trees, winter roost trees are also important 

habitat. Roost trees are typically taller than the surrounding tree canopy, providing a 
255

view over the landscape and foraging areas. Removal of these trees would degrade 

winter eagle habitat in the project boundary. The National Bald Eagle Management 

Guidelines (FWS, 2007) include the following recommendations to protect foraging areas 

and roost sites: 

1. minimize potentially disruptive activities and development in the eagles’ 

direct flight path between nests and roost sites and important foraging areas;

2. locate long-term and permanent water-dependent facilities, such as boat 

ramps and marinas, away from important eagle foraging areas; and 

3. avoid recreational and commercial boating and fishing near critical eagle 

foraging areas during peak feeding times (usually early to mid-morning and 

late afternoon), except where eagles have demonstrated tolerance to such 

activity. 

Revising Merced ID’s proposed Bald Eagle Management Plan to protect winter 

roost trees from vegetation management and future construction activities would reduce 

potential for degrading these areas. Including information about roost sites on public 

information boards would also help reduce disturbance to roosting and foraging eagles.

Additionally, Merced ID’s proposed Bald Eagle Management Plan states that 

emergency activities would be exempt from the timing restrictions. However, Merced ID

does not provide any description of what would constitute an emergency activity. This 

omission leaves the statement open to interpretation and reduces enforceability. Revising 

the plan to clearly describe what kinds of activities would be considered emergencies, 

and why these activities would supersede bald eagle protection would add to the quality 

of the plan and better protect bald eagles.

In its amended proposal filed on September 22, 2014, Merced ID states that it 

revised the Bald Eagle Management Plan, based on FWS’ 10(j) recommendation. 

However, we find inconsistencies between Merced ID’s proposal and FWS’ 

recommended plan. Merced ID’s proposal to conduct nesting surveys within 0.25 mile of 

the reservoir shorelines every 4 years is inconsistent with FWS’ recommendation to 

annually conduct nesting, wintering, and night roost surveys within 1 mile of the 

reservoir shorelines. Other inconsistencies include, but are not limited to, buffer 

distances around active nests and protective measures for wintering bald eagles. 

Increasing the frequency of surveys would result in data that are representative of the 

bald eagles nesting, wintering, and roosting in the project area, as opposed to data 

collected infrequently, which can cause difficulty in drawing conclusions if the data are

collected during a year when eagle use of the habitat in the project area is atypical. 

Overall, implementing the plan with the specific measures required by FWS would result 

in an eagle protection plan that affords more protection to bald eagles, thereby 

minimizing project effects on bald eagles nesting, wintering, and roosting in the project 

area. 
256

Protection of Limestone Salamanders

Project operation and maintenance activities including invasive weed control, 

vegetation management, road or trail maintenance, and recreation activities could disturb 

limestone salamander if these activities occur close to occupied habitat. 

To minimize potential effects on the limestone salamander, Merced ID identified 

and mapped suitable habitat for this species in the project area (Merced ID, 2012d). 

Merced ID also proposes to implement its Limestone Salamanders Sensitive Areas 

Management Plan, filed with the final license application. The plan includes measures 

to: (1) flag sensitive areas prior to any vegetation management or ground-disturbing 

activities; (2) conduct any necessary treatment of invasive weeds near limestone 

salamander habitat between April 16 and October 31 and manually remove weeds, if 

possible; (3) use unspecified BMPs; and (4) provide annual employee training, including 

the identification of key special-status species and of locations of sensitive resources to 

be avoided. Additionally, Merced ID would not authorize any minerals mining or the use 

of explosives in areas with potential habitat for limestone salamander. Merced ID would 

avoid sensitive areas during any vegetation maintenance and road or trail construction 

and also avoid the use of toxic fire retardants within 500 feet of suitable habitat. If roads 

or trails are needed to meet recreation commitments or to access locations to combat 

wildfire under emergency circumstances, Merced ID would consult with BLM and 

California DFW and make every effort to minimize disturbance. Further, the plan 

includes provisions for annual reporting to BLM and California DFW on any activities 

conducted in limestone salamander habitat.

In preliminary 4(e) condition 15, BLM specifies that Merced ID obtain its 

approval before submitting and implementing the plan, conduct studies of limestone 

salamanders every 7 years beginning in year one of license issuance, and inventory all 

suitable but unconfirmed habitats on BLM lands for the presence of limestone 

salamanders. In addition, BLM disagreed with some of Merced ID’s other proposed 

measures in its proposed plan. In response, Merced ID amended its proposal on 

September 22, 2014, to be consistent with BLM preliminary 4(e) condition 15. 

California DFW [10(j) recommendation 8] specifies that the Limestone Salamander 

Sensitive Areas Management Plan provide mapping of known occurrences of limestone 

salamanders and sensitive habitat, avoid sensitive areas, hold annual meetings with 

California DFW and BLM to review activities that may affect sensitive areas, and 

identify BMPs to be implemented as part of the plan. 

Our Analysis

The majority of habitat within the project boundary suitable for limestone 

salamander occurs on the southern bank of the east arm of Lake McClure. This area 

contains limited roads and trails and project-related activities are expected to be 

infrequent. In most cases, known habitat areas are difficult to approach because of steep 

slopes, rocky terrain, and unstable rocky banks, making these areas unsuitable for most 
257

project-related activities. Additionally, salamanders are likely to be deep below the 

surface during the summer, when most project maintenance is expected to occur. 

However, because of the rocky nature of the surface habitats, construction of roads or 

trails in these areas would cause substantial habitat degradation by disturbing or shifting 

loose rocks or causing rockslides that could injure salamanders occurring in the narrow 

spaces between rocks. A short recreation trail between Shepherd’s Point and Sherlock 

Creek also traverses BLM-managed land designated as Limestone Salamander areas of 

critical environmental concern (ACECs). Hikers on this trail could create similar habitat 

disturbances. Additionally, there is potential that fluctuating reservoir levels would 

inundate occupied salamander habitat. 

Implementation of Merced ID’s proposed Limestone Salamanders Sensitive Areas 

Management Plan would limit project-related activities in proximity to mapped limestone 

salamander habitat, consistent with California DFW’s recommendation. In the unlikely 

event project activities are necessary, Merced ID would conduct these actions between 

April 16 and October 31, the period during which salamanders are likely to be 

underground and unaffected by most surface activity. Merced ID would also protect 

mapped sensitive areas from future project-related development. Implementation of the 

Limestone Salamanders Sensitive Areas Management Plan would reduce project effects 

on limestone salamanders. Because the plan does not specify which BMPs would be 

implemented, this measure is unenforceable and impossible to analyze. We agree with 

California DFW’s recommendation that Merced ID should identify the BMPs that would 

be implemented as part of the plan. By revising the proposed Limestone Salamanders 

Sensitive Areas Management Plan to provide details about the specific BMPs it proposes

to implement, Merced ID would improve the plan and would likely reduce potential 

effects on sensitive species. Consulting with agencies would allow for agency comments 

on the BMPs, ensuring that only BMPs consistent with agency policies and requirements

would be included in the plan. Consultation would also ensure consistency of the plan 

with laws protecting this species, which is state endangered, fully protected, and BLM 

sensitive. 

Results of the limestone salamander survey (Merced ID, 2012d) indicate that 

while reservoir elevations occasionally inundate suitable habitat for limestone 

salamanders, these inundations rarely occur during periods when the salamanders are 

above ground. During rare periods when high water levels coincide with above-ground 

activity, it is likely that salamanders would be able to relocate upslope to avoid 

submersion. Therefore, project operation is expected to have minor effects on this 

species and no protection measures would be necessary.

The presence of hiking trails in limestone salamander habitat create potential for 

rock slides or trampling that could cause injury to limestone salamanders. We expect 

potential for injury to be small because hikers tend to stay on the trails in areas that are 

difficult to traverse. However, if a new license requires modifications to existing trails or 

construction of new trails in suitable habitat, potential for injury could increase,

especially during trail construction. Siting these features outside of suitable habitat, if 
258

possible, would further reduce potential effects on limestone salamander and be

consistent with California DFW’s recommendation to avoid sensitive habitat areas.

Protection of Western Pond Turtles

Project operation and maintenance, particularly those activities that cause water 

level fluctuations, could affect habitat for basking and nesting, as well as habitat for 

juvenile western pond turtles. Traffic associated with project maintenance and 

recreation, and maintenance activities such as pesticide applications, also may affect the 

species.

Merced ID amended its proposal to include measures for the western pond turtle, 

consistent with BLM preliminary 4(e) condition 16. Merced ID proposes to document

western pond turtles incidentally observed on lands administered by BLM while 

conducting other environmental work, record relevant data including GPS locations, and 

develop written reports to be submitted annually to BLM [consistent with BLM

preliminary 4(e) condition 1] and the Commission. Merced ID also proposes to train 

project staff to identify western pond turtles. BLM preliminary 4(e) condition 16 

includes objectives for the conservation of special-status species, habitat maintenance or 

improvement, and proactive conservation measures to minimize the likelihood of and 

need for federal listing of the species. 

Our Analysis

We agree with Merced ID’s proposed measures and acknowledge that Merced 

ID’s proposed measures accomplish BLM’s objectives regarding conservation of the 

western pond turtle. Because a project nexus exists, we recommend revising the proposal 

to record incidental observations of western pond turtles in the entire project area, rather 

than limiting the data collection to just BLM lands. Under the proposal, Merced ID 

would submit reports to BLM and the Commission. Because the species is of special 

status to the state of California (i.e., as a species of special concern) and FWS (as a 

species of concern), we recommend including these agencies in the reporting 

requirements, and developing a protection plan that would include both the proposed 

measures and measures recommended by other agencies that would minimize project 

effects on western pond turtles. 

Protection of Special-status Bats

Human presence and noise caused by human activity around project facilities 

could adversely affect bats roosting in project facilities. To protect bats from projectrelated effects, Merced ID amended its proposal to include measures for bat management. 

Under its amended proposal, Merced ID would document all known bat roosts in project 

facility structures within 1 year of license issuance and report relevant information to

BLM and California DFW. Merced ID would put humane exclusion devices in place 

when bats are absent from roosts (i.e., November through February) to prevent bats from 
259

occupying structures, and reevaluate the potential for bat roosts in project facilities every 

3 years.

BLM [preliminary 4(e) condition 12] specifies that Merced ID inspect and 

document all known bat roosts occurring in any project structure that may be used as a 

roosting structure within 1 year of license issuance, and report results of structure 

inspections to BLM (for inspections of structures occurring on BLM lands) and 

California DFW (for all structure inspections). BLM also specifies that Merced ID place 

exclusion devices at locations where bats or signs of bats are present where staff would 

have a routine presence. The exclusion devices would be placed at the structures when 

bats are absent, from November 1 through February 28, after inspecting the structures to 

prevent trapping any overwintering bats. BLM also specifies that project facilities be 

reevaluated every 3 years. 

Our Analysis

Merced ID’s proposed measures to manage bats are consistent with the measures 

contained in BLM preliminary 4(e) condition. We agree that these measures would 

protect bats by excluding them from project facilities, and, as a result, roosting bats 

would not be disturbed by project staff entering the facility or visiting other project 

structures on a regular basis. However, the proposed measures lack specific details about 

the type and design of the exclusion devices, measures for success, and other details that 

are necessary to evaluate the effectiveness of the measures. While we agree with the 

reporting requirements that would have Merced ID report to BLM about structures used 

by bats on BLM lands, and to California DFW with all information obtained from 

inspections of bat roosts at all project facilities, we assert that the well-documented 

occurrence of nine special-status bat species in or near project facilities warrants 

involvement of other agencies as well, particularly since some of these species are 

identified by FWS as species of concern. We recommend that any report made to BLM 

and California DFW also be made to FWS and the Commission, and to the Water Board 

to the extent required by its policies and procedures for special-status species. We find 

that the proposed measures should be included in a protection plan that would also 

contain specific details about the exclusion devices, locations where the devices would be 

installed, how success of the exclusion devices would be defined, and mitigation 

measures to be implemented if exclusion devices are unsuccessful. The plan should also 

include a schedule for implementation and filing reports. By developing and 

implementing a protection plan for special-status bats, project effects on bats could be 

better qualified and quantified. 

Merced Falls Project

Vegetation Management

PG&E proposes to continue to operate the project in a run-of-river mode, where 

flows are determined by releases made by the upstream Merced River Project. PG&E 

proposes no changes to its vegetation maintenance activities, which currently include 
260

vegetation trimming and clearing and herbicide spraying along project access roads, near 

gages, around the dam, and around some areas of the impoundment. Because of the 

abundance of noxious weeds and invasive plants on private lands surrounding the project,

and the infrequency of weed management activities, PG&E does not propose a formal 

management plan for the control of undesirable vegetation.

The Water Board comments that the Basin Plan pertains to all levels of pesticide 

use and includes herbicides. Preliminary WQC condition 2 specifies that PG&E develop 

a pesticide use plan within 6 months of license issuance, in consultation with the Water 

Board, BLM, California DFW, FWS, and NMFS. California DFW [10(j)

recommendation 7] recommends an integrated pest management and pesticide use 

notification plan to control undesirable woody and herbaceous vegetation, aquatic plants, 

insects, and rodents. FWS’ comments about the effects of rodenticide and pesticide use 

are discussed in section 3.3.3.2, Threatened and Endangered Species and section 3.3.3.3, 

Cumulative Effects. 

Our Analysis

No changes in flows and no resulting effects on vegetation would occur because 

PG&E proposes no changes to project operation. Project operation and maintenance 

activities, including road grading and vegetation control could result in the removal of 

existing vegetation and soil disturbance, thereby increasing the potential for the spread of 

invasive weeds. Additionally, project vehicles may transport invasive weed seeds from 

one area to another, and the rise and fall of the reservoir water levels can also carry seeds 

for invasive weeds along the shoreline and distribute them in other areas suitable for 

colonization. Under a new license, visitors would continue to access the project at the 

dam, the River’s Edge Fishing Access area, and the gages. Project access is a potential 

source for the introduction, establishment, and spread of noxious weeds and invasive 

plants. 

PG&E’s semi-annual treatment of noxious weeds and invasive plants would 

continue to control the spread of existing noxious weeds and invasive plants and would 

also reduce the establishment of additional species of noxious weeds and invasive plants

from private lands adjacent to the project area. 

A formal plan detailing the methods, locations, timing, frequency of control 

treatments, and target species would allow PG&E to manage undesirable vegetation more 

effectively. The potential effects on other species could be determined by reviewing 

details of a management plan for noxious weeds and invasive plants, which would reduce 

effects on sensitive species and state and federally listed species, as discussed below. 

Integrating the use of rodenticides and insecticides into the plan for the control of 

undesirable vegetation would be consistent with agency conditions and 

recommendations, and would further reduce potential effects on sensitive species and 

state and federally listed species. 
261

Protection of Sensitive Plants and Wildlife 

Project operation and maintenance activities, such as vegetation control, could 

remove existing vegetation, disturb soils, and change microsite habitats. These activities 

have the potential to disturb sensitive plants, disturb habitat for sensitive wildlife, or 

directly injure or disturb sensitive wildlife in the immediate vicinity of these activities. 

Specific effects on the bald eagle are discussed in the following subsection, and specific 

effects on the elderberry shrub and the valley elderberry longhorn beetle, California redlegged frog, and San Joaquin kit fox are discussed in section 3.3.3, Threatened and 

Endangered Species.

PG&E does not propose a formal vegetation management plan to reduce potential 

effects on sensitive plants and wildlife, nor does it propose changes to project operation 

or maintenance activities. Under a new license, PG&E would continue to control 

vegetation about twice a year around the powerhouse, gages, the River’s Edge Fishing

Access area, particular areas of the impoundment, and along access roads. 

As noted above, the Water Board indicates that the Basin Plan pertains to all levels 

of pesticide use and includes herbicides. Preliminary WQC condition 2 specifies that

PG&E develop a pesticide use plan within 6 months of license issuance, in consultation 

with the Water Board, BLM, California DFW, FWS, and NMFS. California DFW [10(j)

recommendation 7] recommends an integrated pest management and pesticide use 

notification plan to control undesirable woody and herbaceous vegetation, aquatic plants, 

insects, and rodents. 

FWS comments that the burrowing owl, a BLM sensitive species, has been known 

to occur in the project vicinity. FWS points out that because burrowing owls occur in 

ground squirrel burrows, they are vulnerable to rodent control methods such as burrow 

fumigation and burrow collapse. FWS’ comments about the effects of rodenticide and 

pesticide use are also discussed in section 3.3.3.2, Threatened and Endangered Species

and section 3.3.3.3, Cumulative Effects. 

Our Analysis

Continued operation of the project under a new license would include some 

activities that, if conducted near sensitive plant species, could affect these resources. 

These activities include vegetation management activities such as application of 

herbicides to noxious weeds and invasive plants, vegetation trimming, recreation 

activities, or any other activities with potential to disturb soil or vegetation. 

Although none of the eleven sensitive plant species identified as potentially 

occurring in the project area were observed during the surveys, two other special-status 

plant species identified as uncommon by the California Native Plant Society, gypsumloving larkspur and foothill jepsonia, were observed and mapped on the southeast side of 

the impoundment. Although the abundance of these two species suggests that they are 

thriving under current project operation and maintenance activities, it is difficult to assess
262

effects on these species. Because PG&E does not propose changes to project operation 

and maintenance activities, the current status of these species is not expected to change. 

Sensitive plants, as well as sensitive wildlife, could be adversely affected by the 

control of undesirable vegetation. The development of a formal plan for the control of 

noxious weeds and invasive plants would disclose the details of the locations, timing, and 

frequency of treatments so agencies could determine potential effects on sensitive plants 

and wildlife. Consultation with agencies during the development of the plan would 

ensure consistency with state and federal laws and compliance with laws protecting 

sensitive plants and wildlife that occur within the project area. Therefore, the 

development of a formal plan for the control of noxious weeds and invasive plants could 

reduce effects of the control measures on sensitive species.

Commonly used control measures for rodents and insects could directly or 

indirectly affect sensitive plants and wildlife. Integrating a component on rodenticides 

and insecticides into the control plan for noxious weeds and invasive plants would ensure 

that all pest management activities and methods are considered and evaluated by agencies 

for their potential effects on sensitive species, and that the plan is consistent with the 

Basin Plan and other comprehensive plans listed in section 5.4, Consistency with

Comprehensive Plans. 

Protection of Bald Eagles

Operation and maintenance activities, such as vegetation management activities 

and facility and road maintenance, could create noise near active bald eagle nests and 

winter roosting sites. Recreation users, including hikers and boaters could cause similar 

disturbance. Vegetation management activities could also result in the removal of nest 

trees or roost trees. Bald eagles can be sensitive to increased noise during the nesting 

period, and such disturbance could result in nest abandonment or reduced nesting 

success. The National Bald and Golden Eagle Protection Act and the Migratory Bird 

Treaty Act prohibit such disturbances.

A bald eagle nest and bald eagles were documented within the project area during 

2010 and 2011. PG&E does not propose any measures to minimize potential project 

effects on bald eagles or their roost trees within the project area. PG&E does not propose 

construction activities within the project area, nor does PG&E propose any changes to 

project operation and maintenance activities. 

Preliminary WQC condition 5 specifies that PG&E develop a monitoring and 

conservation plan for bald eagles, consistent with the most current guidelines provided by 

FWS. FWS [10(j) recommendation 5] recommends a bald eagle management plan, either 

to be implemented in concert with Merced ID or to be developed and implemented by 

PG&E. In its reply comments, PG&E opposes some aspects of FWS’ recommended 

survey protocols and protection and mitigation measures, such as the implementation of 

buffer zones, and argues that buffer zones should be site- and project-specific. 
263

Our Analysis

Without proposed measures for the protection of bald eagles from project 

operation, maintenance, and recreation activities, the project could conflict with bald 

eagle protection laws if these activities adversely affect nesting bald eagles. The National 

Bald Eagle Management Guidelines (FWS, 2007) include recommendations to protect 

bald eagle nests during breeding season from ORV use, motorized watercraft, and nonmotorized recreation and human activities such as fishing and hiking within 330 feet 

from the nest. 

The removal of overstory trees within 330 feet of a nest is prohibited during any 

season. Similarly, bald eagles could be adversely affected without proposed measures to 

protect winter roost trees, which are necessary components of bald eagle habitat. Roost 

trees are typically taller than the surrounding tree canopy, providing a view over the 

landscape and foraging areas. Removal of these trees would degrade winter eagle habitat 

in the project boundary. The National Bald Eagle Management Guidelines (FWS, 2007) 

include the following recommendations to protect foraging areas and roost sites: 

1. minimize potentially disruptive activities and development in the eagles’ 

direct flight path between nests and roost sites and important foraging areas; 

2. locate long-term and permanent water-dependent facilities, such as boat 

ramps and marinas, away from important eagle foraging areas; and 

3. avoid recreational and commercial boating and fishing near critical eagle 

foraging areas during peak feeding times (usually early to mid-morning and 

late afternoon), except where eagles have demonstrated tolerance to such 

activity. 

Requiring a plan to protect bald eagle nests from operation and maintenance 

activities and recreation activities would reduce project-related effects on nesting bald 

eagles. Also requiring protection of winter roost trees from vegetation management and 

future construction activities would reduce potential habitat degradation. 

All survey protocols and protection and mitigation measures should be consistent 

with the guidelines provided in the National Bald Eagle Management Guidelines, rather 

than site- or project-specific. Implementing survey protocols and protection and 

mitigation measures inconsistently could conflict with the National Bald and Golden 

Eagle Protection Act and the Migratory Bird Treaty Act. Therefore, requiring 

consultation with FWS, California DFW, and BLM prior to developing the plan would

ensure that appropriate survey protocols and protection and mitigation measures are 

proposed to reduce project-related effects on bald eagles during and outside the nesting 

season. Consultation would ensure consistency with FWS’ most current guidelines and 

compliance with the National Bald and Golden Eagle Protection Act and the Migratory 

Bird Treaty Act. 
264

3.3.3 Threatened and Endangered Species

3.3.3.1 Affected Environment

Merced River

Aquatic Species

Central Valley Steelhead—Steelhead (O. mykiss), the anadromous life history 

form of rainbow trout, historically migrated up the Merced River well past the site of 

present-day Lake McClure and are believed to have spawned and reared in the Sierra 

Nevada as far upstream as Yosemite National Park based on water temperature, known 

barriers to upstream passage, and other factors (Lindley et al., 2006). O. mykiss currently 

found in and upstream of project reservoirs and in the Merced River between Merced 

Falls dam and Crocker-Huffman diversion dam are considered resident rainbow trout 

because they are not the progeny of anadromous parents. 

O. mykiss found in the Merced River downstream of Crocker-Huffman diversion 

dam have the potential to be anadromous and are therefore considered by NMFS to 

belong to the California Central Valley steelhead DPS. This DPS is federally listed as 

threatened (71 FR 834; January 5, 2006) and critical habitat includes the Merced River 

downstream from Crocker-Huffman diversion dam, the San Joaquin River, and the 

Sacramento-San Joaquin Delta (70 FR 52488; September 2, 2005). Steelhead43 in the 

lower Merced River belong to the Southern Sierra Nevada Diversity Group of the Central 

Valley steelhead DPS. Populations of naturally reproducing Central Valley steelhead 

have been experiencing a long-term decline in abundance throughout their range with 

populations in the Central Valley and southward experiencing the most severe declines. 

Adult steelhead enter the San Joaquin River Basin as early as late September and 

spawn primarily from December through March. Egg incubation can extend through 

May, and juvenile rearing and outmigration occur year-round. Spawning occurs in riffles 

and pool tails with abundant gravel ranging in size from 0.4 to 1.8 inches (median 

particle size, or D50) and low fine sediment concentrations. Recommended water 

temperatures44 are < 18°C for adult immigration and < 13°C for spawning, incubation, 

and emergence. Steelhead fry and juveniles rear in a wide range of hydraulic conditions, 

generally occupying areas with rocky substrates and overhead cover. Water temperatures 

 

43 Throughout the remainder of this section, we refer to O. mykiss that occur 

downstream of Crocker-Huffman diversion dam as steelhead, even though some may be 

resident rainbow trout.

44 Water temperature thresholds referenced in this section are based on 

recommendations found in EPA (2003), and criteria are given as the 7-day average of the 

daily maximum temperatures.
265

of < 16°C are recommended for rearing, and temperatures of < 14°C are recommended 

for smolting.

Modeled spawning habitat suitability for steelhead in the lower Merced River 

downstream of Crocker-Huffman diversion dam varies with flow (see figures 3-28, 3-31, 

and 3-34). The greatest amount of suitable habitat is predicted to occur between RM 42.0 

and 52.0, which corresponds with the reach containing most of the suitable spawning 

gravel. Downstream of this 10-mile reach, substrate in the lower Merced River is 

predominantly cobble embedded in sand, which is not suitable for steelhead spawning 

and provides poor steelhead rearing habitat. 

Water temperature has been identified as a primary limiting factor for steelhead 

production in many Central Valley streams. Merced ID compared water temperature 

monitoring data collected from 1991 through 2010 at seven locations between RM 52.0

and RM 13.0 with EPA’s (2003) recommended 7-day average daily maximum water 

temperature criteria for salmonids to evaluate the frequency with which the criteria were 

exceeded for each steelhead life stage. Merced ID’s conclusions regarding existing 

conditions were: 

 During the upstream migration period, the 18°C criterion for adult 

steelhead migration was exceeded 58 to 100 percent of the time in 

September and 12 to 68 percent of the time in October between RM 46.3 

and RM 13.0. From November through February, water temperatures 

were below the 18°C criterion at all times and locations, except during 

November at RM 52.0 (>18°C 2 percent of the time) and RM 46.3 (>18°C 

1 percent of the time).

 During the December through March spawning and incubation period, the 

13°C criterion to protect spawning, incubation, and fry emergence life 

stages was evaluated at locations from RM 52.0 downstream to RM 41.9. 

In December, the 13°C criterion was exceeded 1 to 14 percent of the time 

from RM 52.0 to RM 41.9. In January the criterion was exceeded only at 

RM 41.9 (12 percent of the time). In February and March, the 13°C 

criterion was exceeded at all locations 5 to 97 percent of the time.

 During the year-round steelhead juvenile rearing period, the 16°C rearing 

criterion was exceeded about 20 percent of the time at RM 52.0, 37 to 53 

percent of the time between RM 46.3 and RM 33.0, and 61 percent of the 

time at RM 13.0. 

 During the March through May steelhead smoltification period, the 14°C 

smoltification criterion was exceeded 20 percent of the time at RM 52.0, 

57 to 82 percent of the time between RM 46.3 and RM 41.9, 77 percent of 

the time at RM 33.0, and 94 percent of the time at RM 13.0.

Population data for steelhead in the lower Merced River are lacking. Good et al., 

(2005) report incidental captures of juvenile steelhead during RST monitoring in 2002, 
266

but none were captured during outmigration monitoring using RSTs in 2007 (S.P. Cramer 

and Associates, 2007). The 110 O. mykiss observed in the lower Merced River during 

seasonal fish monitoring in 2006 through 2008 ranged in size from the 0 to 1 inch (0 to 

25 mm) size class to the 15.8 to 16.7 inch (401 to 425 mm) size class, and likely ranged 

up to age 4+. Only 37 of these 110 fish were observed downstream of Crocker-Huffman 

diversion dam and therefore were possibly anadromous steelhead (Stillwater Sciences, 

2008).

Steelhead populations in the Merced, Tuolumne, Stanislaus, and Calaveras Rivers 

are the only remaining representatives of the Southern Sierra Nevada diversity group, but 

currently none of these populations are considered to be viable (i.e., at low risk of 

extinction). NMFS’ recovery plan for the DPS of Central Valley steelhead characterizes 

the Merced River as a Core 2 watershed, in which steelhead populations have a moderate 

risk of extinction (NMFS, 2014). Core 2 watersheds have lower potential to support 

viable populations of steelhead because of lower abundance or amount and quality of 

habitat. NMFS lists the risk of extinction in the Merced River as uncertain.

Priority 1 Merced River recovery actions for steelhead presented in NMFS (2014) 

are as follows:

 Develop a program to reestablish steelhead in historic habitat upstream of 

Crocker Huffman, Merced Falls, McSwain, and New Exchequer dams. 

The program should include feasibility studies, habitat evaluations, fish 

passage design studies, and a pilot reintroduction phase prior to 

implementation of the long-term program.

 Supplement flows provided pursuant to the Davis-Grunsky Agreement and 

the Merced River Project license with water acquired from willing land 

owners and water districts to provide additional instream flow.

 Develop a Merced River steelhead team to help guide collection and 

evaluation of baseline data to address hypotheses for why resident 

O. mykiss are more abundant than anadromous O. mykiss in the Merced 

River.

 Evaluate whether pulse flows in the Merced River are beneficial to adult 

steelhead immigration and juvenile steelhead emigration; if pulse flows are 

determined to be effective, implement the most beneficial pulse flow 

regime.

 Identify floodplain and side channel projects to improve river function and 

increase habitat diversity in the Merced River.

 Develop a long-term gravel management plan to increase and maintain 

steelhead spawning habitat downstream of Crocker-Huffman, Merced 

Falls, and New Exchequer dams.
267

Priority 2 Merced River recovery actions for steelhead presented in NMFS (2014) 

are as follows:

 Manage release from Lake McClure to provide the most beneficial flow 

and water temperatures for all steelhead life stages.

 Prioritize Merced River diversions based on their level of entrainment and 

screen those with the highest benefit to cost ratio.

 Work with water rights holders in the Merced River Watershed to provide 

flows that protect steelhead.

 Develop ramping rate criteria for the Merced River that protect

anadromous fishes.

 Continue to supply spawning-sized gravel to landowners for construction 

and maintenance of wing dam diversion structures in the Merced River.

 Evaluate the potential benefits and feasibility of installing a water 

temperature control device on New Exchequer dam to most efficiently use 

the volume of cold water in the reservoir.

 Federal, state, and local agencies should use their authorities to develop 

programs and projects that focus on retaining, restoring, and creating 

riparian corridors within their jurisdiction in the Merced River Watershed.

 Permanently protect Merced River riparian habitat through easements 

and/or land acquisition.

 Increase monitoring and enforcement of illegal rip rap applications in the 

Merced River.

 Implement studies designed to quantify the impact of predation on 

steelhead in the Merced River. If the studies identify predator species 

and/or locations contributing to low steelhead survival, then evaluate 

whether predator control actions can be effective in minimizing predation 

on steelhead in the Merced River; continue implementation if effective.

 Implement programs and measures designed to control predation in the 

Merced River, including actions to isolate “ponded” sections in the river.

Vernal Pool and Conservancy Fairy Shrimp—Fairy shrimp are generally 

restricted to seasonal aquatic habitats where predatory fish do not occur. Female fairy 

shrimp of all species carry their eggs in a ventral brood sac. The eggs either are dropped 

to the pool bottom or remain in the brood sac until the mother dies and sinks. When the 

pool dries, the eggs dry and remain dormant in the dry pool bed until rains and other 

environmental stimuli cause them to hatch. Resting fairy shrimp eggs are commonly 

referred to as cysts and are capable of withstanding heat, cold, and prolonged desiccation. 
268

When the pools refill, some, but not all, of the cysts may hatch. The cyst bank in the soil 

may contain cysts from several years of breeding.

The vernal pool fairy shrimp occupies a variety of different vernal pool habitats—

from small, clear, sandstone rock pools to large, turbid, alkaline, grassland valley floor 

pools. Although the vernal pool fairy shrimp has been collected from large vernal pools, 

including one exceeding 25 acres in area, it tends to occur primarily in smaller pools, and 

is most frequently found in pools measuring less than 0.05 acre in area in grass or mudbottomed swales or basalt depression pools in unmowed grasslands. The vernal pool 

fairy shrimp typically occurs at elevations from 30 feet to 4,000 feet, although two sites 

in the Los Padres National Forest have been found to contain the species at an elevation 

of 5,600 feet. The species is typically found in pools with low to moderate amounts of 

salinity or total dissolved solids. 

The Conservancy fairy shrimp (Branchinecta conservatio) is active from early 

November to early April. This species primarily inhabits relatively large (1 acre to 

7.5 acres), cool-water, sparsely vegetated, vernal pools with moderately turbid water. In 

addition to vernal pools, Conservancy fairy shrimp may be found in alkaline pools or 

vernal lakes. The Conservancy fairy shrimp occurs on basin rim, high terrace, and 

volcanic mud flow landforms. Conservancy fairy shrimp and vernal pool fairy shrimp 

may co-occur; however, they have rarely been collected from the same pool at the same 

time.

Vernal pool fairy shrimp and Conservancy fairy shrimp are federally listed as 

threatened and endangered, respectively. Neither species is state-listed in California. In 

2006, FWS designated critical habitat for four vernal pool crustaceans and eleven vernal 

pool plants, including these two species of fairy shrimp. In its designation, FWS created

35 critical habitat units. Primary constituent elements of critical habitat include: 

(1) vernal pools with underlying restrictive soil layers that hold water for a minimum of 

18 days but do not promote development of obligate wetland vegetation; (2) continuous 

or intermittent flowing surface water that connects pools to other pools; (3) sources of 

detritus within the pools for foraging; and (4) living and dead plant material in the pools 

that provide shelter for fairy shrimp (71 FR 7118–7316). Critical habitat unit 21B for 

vernal pool fairy shrimp overlaps about 1 acre of land in the project study area.

45

 This 

area is a 656-feet by 79-feet section of the existing Lake McClure Road, which is 

adjacent to PG&E’s Merced Falls reservoir. The road does not contain any of the 

primary constituent elements of vernal pool fairy shrimp critical habitat. The nearest 

critical habitat for Conservancy fairy shrimp is critical habitat unit 6, which is 

 

45 The fairy shrimp study area consisted of project-affected areas with potentially 

suitable habitat, such as vernal pools or other appropriate seasonally flooded habitats, 

within the project boundary, and the section of the Merced River from PG&E’s Merced 

Falls dam to Crocker-Huffman diversion dam.
269

approximately 0.25 mile southwest of the project boundary surrounding McSwain 

reservoir, and overlaps critical habitat unit 22 for vernal pool fairy shrimp.

In 2010, Merced ID reviewed aerial imagery, national wetland inventory maps, 

and conducted field reconnaissance to identify areas in the project study area with 

potential to support fairy shrimp. Based on the review, Merced ID conducted site 

assessments at 44 sites. Merced ID assessed the suitability of sites as potential vernal 

pool fairy shrimp habitat based on of the following components: (1) seasonal standing 

water (i.e., continuous for at least 19 days), (2) water depth of 0.1 feet or greater for more 

than 45 days under optimal conditions, and (3) location within the known range or 

vicinity of documented vernal pool fairy shrimp occurrences. Because the Conservancy

fairy shrimp is typically associated with very large vernal pools (or playa pools46) and not 

known to occur in anthropogenic habitats, such as ditches and toe-drains, sites that 

differed from this habitat profile were considered unlikely to support Conservancy fairy 

shrimp. Merced ID also related the potential of sites to support vernal pool fairy shrimp 

and Conservancy fairy shrimp to the absence of frequent and/or excessive disturbance 

(e.g., plowing or grading). This study identified potential vernal pool fairy shrimp habitat 

at 33 of the 44 sites. None of the sites were suitable for Conservancy fairy shrimp.

Of the 33 sites identified as potentially suitable for vernal pool fairy shrimp, 

9 sites occur in areas where vegetation maintenance or recreation activities are likely to 

occur (six sites at Lake McClure and three sites and McSwain reservoir). Information 

describing these sites is presented in table 3-21. Fairy shrimp habitat surveys did not 

identify suitable habitat for Conservancy fairy shrimp. Continued operation of the 

project would have no effect on Conservancy fairy shrimp and this species is not 

discussed further.

 

46 Playa pools are large, flat, bottoms of undrained desert basins that become 

shallow lakes during wet periods.
270

Table 3-21. Summary of sites assessed for federally threatened and endangered fairy shrimp in areas of project-related 

activities (Merced ID, 2011e).

Site Name, Location

Maximum Area/ 

Maximum Depth Pool Substrate Pool Description

Site 7, Barrett Cove 

recreation area

538 square feet (50 

square meters)/1

inch (3 cm)

Organic matter, gravel Small seasonal pool fed by hillside drainage and road runoff 

(site adjoins access road into Barret Cove recreation area and 

is within the project boundary); no invertebrates observed; 

potential disturbance from vehicular traffic and roadside 

maintenance.

 Potential vernal pool fairy shrimp habitat

 Little or no potential to support Conservancy fairy 

shrimp habitat

Site 8, McClure Point 

recreation area

20 pools ranging 

from 11 square feet

(1 square meter) to 

215 square feet (20 

square meters) in 

size and 0.4 inch

(1 cm) to 1inch

(3 cm) deep

Cement, sand, and 

cobble

Approximately 20 small seasonal depressions formed in tire 

ruts on a gravel pad; ostracods observed in some of the 

depressions; vehicular disturbance likely infrequent.

 Potential vernal pool fairy shrimp habitat

 Not potential Conservancy fairy shrimp habitat

Site 9, McClure Point 

recreation area

5 square feet

(0.5 square 

meter)/8.7inches

(22 cm)

Cobbles Seasonal ditch fed by runoff from surrounding campgrounds 

(site adjoins road); no invertebrates observed; human 

disturbance likely is uncommon.

 Potential vernal pool fairy shrimp habitat

 Little or no potential to support Conservancy fairy 

shrimp habitat
271

Site Name, Location

Maximum Area/ 

Maximum Depth Pool Substrate Pool Description

Site 11, South of 

McClure Point 

recreation area

16 square feet

(1.5 square 

meters)/5 inches

(13 cm)

Organic matter, gravel Anthropogenic pool formed out of tire ruts in an unpaved 

parking area; mosquito larvae observed; vehicular disturbance 

observed in pool.

 Potential vernal pool fairy shrimp habitat

 Little or no potential to support Conservancy fairy 

shrimp habitat

Site 15, South of 

McClure Point 

recreation area

592 square feet 

(55 square meters)/ 

12 inches (30 cm)

No data Site inaccessible; remote observations only; seasonally 

ponded emergent wetland formed in a drainage fed by road 

runoff and hillside drainage (site adjoins road); human 

disturbance likely is uncommon.

 Potential vernal pool fairy shrimp habitat

 Little or no potential to support Conservancy fairy 

shrimp habitat

Site 16, South of 

McClure Point 

recreation area

242 square feet 

(22.5 square 

meters)/2 inches 

(4 cm)

Organic matter, gravel Seasonal ditch fed by runoff from adjoining road; no 

invertebrates observed; use of herbicides in pool.

 Potential vernal pool fairy shrimp habitat

 Little or no potential to support Conservancy fairy 

shrimp habitat

Site 21, Lake 

McSwain recreation 

area

39 square feet

(3.6 square 

meters)/7 inches

(18 cm)

Clay soil, organic 

matter

Swale fed by surface water discharge from upslope culverts 

and ephemeral drainage; mosquito larvae observed; site 

adjoins campground, but human disturbance likely is 

uncommon.

 Potential vernal pool fairy shrimp habitat

 Little or no potential to support Conservancy fairy 

shrimp habitat
272

Site Name, Location

Maximum Area/ 

Maximum Depth Pool Substrate Pool Description

Site 24, Lake 

McSwain recreation 

area

80 square feet

(7.5 square 

meters)/2 inches (6 

cm)

Organic matter over 

clay loam

Seasonal pool formed from a seasonal surface drainage that 

discharges to McSwain reservoir; no invertebrates observed; 

human disturbance likely is uncommon.

 Potential vernal pool fairy shrimp habitat

 Little or no potential to support Conservancy fairy 

shrimp habitat

Site 32, Lake 

McSwain recreation 

area

46 square feet

(4.3 square 

meters)/4 inches (9 

cm)

Organic matter Shallow, seasonal ditch that adjoins a paved pedestrian trail 

and is fed by hillside drainage; mosquito larvae and ostracods 

observed; site adjoins a trail but likely not frequently 

disturbed.

 Potential vernal pool fairy shrimp habitat

 Little or no potential to support Conservancy fairy 

shrimp habitat
273

Terrestrial Species

In consultation with FWS, NMFS, and other relicensing participants, Merced ID

developed a list of threatened and endangered species that potentially occur in the project 

area. Merced ID used a three-step screening process to identify threatened and 

endangered species that could be affected by the project. 

In 2010 and 2011, Merced ID performed surveys for federal and state-listed plants. 

Surveys were conducted following the botanical survey protocol section of California 

Department of Fish and Game’s (now California DFW) Protocols for Surveying and 

Evaluating Impacts to Special Status Native Plant Populations and Natural Communities. 

The study included the area surrounding all project facilities (e.g., powerhouses and 

switchyards, dams, reservoirs, access roads, and recreation facilities) within the existing 

project boundary and in the immediate area of the project’s seven minor wildlife refuge 

water delivery facilities. Individual species are discussed below. 

Layne’s Butterweed—Layne’s butterweed (Senecio layneae), also known as 

Layne’s ragwort, is a perennial herb that blooms April to August (CNPS, 2014). It grows 

in open rocky areas of gabbro and serpentine soils within chaparral plant communities at 

elevations ranging from 650 to 3,300 feet msl. Most plants do not grow well on gabbro 

or serpentine soils because they are unusually low in nutrients and high in heavy metals, 

giving those plants adapted to such soils, such as Layne’s butterweed, a competitive 

advantage over other species. Most known sites are scattered within a 40,000-acre area 

in western El Dorado County that includes the Pine Hill intrusion and adjacent serpentine 

soils (located about 80 miles northwest of the project area). 

Layne’s butterweed is federally listed as threatened, state listed as rare, and is a 

California Native Plant Society 1B.2 species (CNPS, 2014). FWS published a recovery 

plan for this species in 2002 but did not designate critical habitat (FWS, 2014a). 

Layne’s butterweed was not found during Merced ID’s surveys. All project 

features except those at the New Exchequer development are below the known elevation 

of this species. The closest known population exists in the Red Hills in Tuolumne 

County (Chinese Camp and Moccasin quadrangles) about 10 to 15 miles northwest of 

suitable habitat in the project boundary. No occurrences of Layne’s butterweed have 

been documented in Mariposa and Merced Counties. However, suitable habitat is present 

within the project boundary.

Keck’s Checkerbloom—Keck’s checkerbloom (Sidalcea keckii), also called 

Keck’s checker-mallow, is an annual herb that blooms April to June (CNPS, 2014). It 

grows in relatively open areas on grassy slopes of the Sierra foothills in Fresno and 

Tulare Counties. The species is associated with serpentine soils at elevations ranging 

from 250 to 2,150 feet msl. Serpentine soils are fairly rare, limiting the range of plants 

such as Keck’s checkerbloom that are adapted to grow on them. The species’ low 

population numbers leave it vulnerable to random environmental events including bad 

weather, disease, and damaging insect infestations. The isolation of remaining 
274

populations exacerbates these vulnerabilities by precluding re-colonization of extirpated 

populations. Limited cross-pollination between populations and loss of genetic 

variability may also be causes for concern in such small isolated populations.

Keck’s checkerbloom is federally listed as endangered and is designated by the 

California Native Plant Society as 1B.1 (CNPS, 2014). FWS designated critical habitat 

for this species in 2003, but no critical habitat exists within the project area (FWS, 

2014b). The closest critical habitat unit is in Fresno County, about 70 miles southeast 

from the project. Merced ID did not find this species during its rare plant surveys 

conducted in 2010 and 2011, although suitable habitat is present within the project 

boundary.

Chinese Camp brodiaea—Chinese Camp brodiaea (Brodiaea pallida) is a 

perennial bulbiferous herb that blooms May to June (CNPS, 2014). It grows in overflow 

channels, seeps, and springs in clays derived from serpentine soils of the foothills of the 

Sierra. This species grows in association and hydridizes with two other brodiaeas, but 

can be differentiated by the shape, color, and position of the flower parts (FWS, 1998). 

The species is known from only two occurrences near Chinese Camp in Calaveras and

Tuolumne Counties and occurs in areas located on only four quadrangles, including 

Sonora, Chinese Camp, New Melones dam, and Copperopolis, although it could be found 

in other areas where suitable habitat exists (CNPS, 2014). 

Chinese Camp brodiaea is federally listed as threatened, state listed as endangered, 

and is designated by the California Native Plant Society as 1B.1 (CNPS, 2014). No 

critical habitat rules have been published for the Chinese Camp brodiaea. 

Mariposa pussypaws—Mariposa pussypaws (Calyptridium pulchellum) is an 

annual herb that blooms April to August (CNPS, 2014). It grows in small, barren areas 

on decomposed granitic sands in annual grasslands and woodlands in the southwestern 

foothills of the Sierra Nevada (FWS, 1998) at elevations between 1,500 and 3,600 feet 

(Merced ID, 2012a). Its adaptation to a harsh, exposed setting makes it unusual as little 

else grows on these shallow, bare substrates (Merced ID, 2012a). Seven small 

populations are patchily distributed over a 750-square mile area in Fresno, Madera, and 

Mariposa Counties, collectively occupying only 14 gross acres (FWS, 1998). 

Mariposa pussypaws is federally listed as threatened and is designated by the 

California Native Plant Society as 1B.1. No critical habitat rules have been published for 

this species. This species is vulnerable to extirpations from random events because of the 

limited number and small size of population and small range of the species (FWS, 1998). 

Merced ID did not find this species during its rare plant surveys conducted in 2010 and 

2011, although it has been found in surrounding areas located on the Mariposa 

quadrangle. 

California vervain—California vervain (Verbena californica) is a perennial herb 

that blooms May to September (CNPS, 2014). It occurs at elevations between 850 to 

1,150 feet in the Red Hills and nearby Rawhide Hill in western Tuolumne County 
275

(Merced ID, 2012a). California vervain is restricted to intermittent and perennial streams 

within areas of serpentine soils (FWS, 1998). The populations are distributed over about 

90 acres within an area of 24-square miles (Merced ID, 2012a). 

California vervain is federally listed as threatened, state listed as threatened, and 

designated by the California Native Plant Society as 1B.1 (CNPS, 2014). No critical 

habitat rules have been published for this species. This species is vulnerable to 

extirpation because few populations with low numbers exist (FWS, 1998). Merced ID 

did not find this species during its rare plant surveys conducted in 2010 and 2011 

(Merced ID, 2012a), although it has been found in surrounding areas located on Chinese 

Camp quad (CNPS, 2014). 

San Joaquin Kit Fox—The San Joaquin kit fox is federally listed as endangered

and state listed as threatened (FWS, 2014c; California DFW, 2014c). No critical habitat 

rules have been published for the San Joaquin kit fox. 

Dens are an important habitat component for the San Joaquin kit fox. The kit fox 

may use numerous dens throughout the year for shelter, reproduction, and temperature 

regulation. Kit foxes may dig the den sites; modify den sites constructed by ground 

squirrels, badgers, and coyotes; or use human-made structures such as culverts and 

abandoned structures. This species historically occupied several native plant 

communities in the San Joaquin Valley, but presently occur in areas where native habitats 

only occur as remnants and are surrounded by habitat extensively modified by 

anthropogenic activities, including agriculture, oil fields, and wind energy projects 

(California DFW, 2014b; FWS, 2014d). Any habitat occupied by kit fox must support a 

suitable prey base, including nocturnal rodents, as well as diurnal rodents and insects. 

Kit fox also consume some vegetation (FWS, 2014d). Population declines are attributed 

to habitat loss and degradation caused by agriculture and urban uses of lands. Mortality 

from predation, shooting, habitat loss, and poisoning through the consumption of 

poisoned rodents contributes to population decline (California DFW, 2014b; FWS, 

2014d). 

In its license application, Merced ID notes that it eliminated the San Joaquin kit 

fox from further analysis because it does not occur in the vicinity of the project. Merced 

ID therefore did not conduct surveys for the San Joaquin kit fox. 

Valley Elderberry Longhorn Beetle—The valley elderberry longhorn beetle is 

listed as threatened. The valley elderberry longhorn beetle is associated with various 

species of elderberry (Sambucus spp.) throughout the California Central Valley and 

foothills below 3,000 feet msl. Mariposa County is within the valley elderberry longhorn 

beetle range, although no critical habitat is designated within the county. The valley 

elderberry longhorn beetle occurs within riparian vegetation communities where it feeds 

exclusively on elderberry in both adult and larval stages. Adult valley elderberry 

longhorn beetles appear to feed externally on the flowers and foliage of the elderberry. 

Adult females lay eggs in crevices in the bark of the host elderberry plant. After 
276

hatching, larvae spend 1 to 2 years feeding inside the plant. Prior to pupating, valley 

elderberry longhorn beetle larvae chew an exit hole in the elderberry trunk for the 

emerging adult, leaving boreholes in the elderberry stems.

Merced ID’s botanical surveys documented boreholes at 9 out of 101 elderberry 

populations identified in the project study area. These 9 populations occurred on the 

north shore of Lake McClure, on the Piney Creek arm of Lake McClure, in the Barrett 

Cove recreation area, and along McSwain reservoir. No valley elderberry longhorn 

beetles were observed during the elderberry surveys.

California Red-legged Frog—The California red-legged frog is federally listed 

threatened. There is no state status for this species. FWS published a Recovery Plan for 

the California Red-legged Frog (Rana aurora draytonii) (2002). The project occurs in 

the vicinity of one of the recovery units.

FWS revised critical habitat for this species in 2010. The criteria for the 

California red-legged frog critical habitat are: (1) suitable aquatic habitat, (2) associated 

uplands, and (3) suitable dispersal habitat connecting suitable aquatic habitat. At a 

minimum, critical habitat includes two or more suitable breeding locations, one of which 

must be a permanent water source, associated uplands surrounding these water bodies 

(extending to 500 feet from the water’s edge), all within 1.25 miles of one another and 

connected by barrier-free dispersal habitat of at least 500 feet in width. No critical 

habitat occurs within the project boundary. The closest critical habitat unit to the project 

is about 50 miles northwest in Calaveras County.

California red-legged frog breeding occurs from late November to late April in 

ponds, backwater pools, or creeks. Egg masses are attached to emergent vegetation such 

as cattails and bulrushes. Tadpoles remain in these aquatic habitats until metamorphosis. 

Increased siltation during the breeding season can cause asphyxiation of eggs and small 

tadpoles. Tadpoles typically metamorphose between July and September, and most 

likely feed on algae.

Outside of the breeding season, adults may disperse upstream, downstream, or 

upslope of breeding habitat to forage and seek sheltering habitat, which may consist of 

small-mammal burrows, leaf litter, and other moist sites in or near (up to 200 feet from) 

riparian areas. During wet periods, long distance dispersal of up to a mile may occur 

between aquatic habitats, including movement through upland habitats or ephemeral

drainages. Seeps and springs in open grasslands can function as foraging habitat or 

refugia for wandering frogs.

The California red-legged frog is primarily associated with perennial ponds or 

pools and slow-moving perennial or seasonal streams where water remains continuously 

for a minimum of 20 weeks beginning in the spring (i.e., sufficiently long for breeding to 

occur and tadpoles to complete development). The California red-legged frog is not 

expected to breed successfully at sites holding water less than 15 weeks. The minimum 

depth of breeding habitat is 20 inches; however, deep water pools, ponds, and lake areas 
277

are not suitable. Dense, shrubby riparian vegetation (e.g., willow, bullrush, and tule 

species), and bank overhangs are important features of California red-legged frog

breeding habitat, although they sometimes use sites that lack these features. Locations 

with the highest densities of California red-legged frogs exhibit dense emergent or 

shoreline riparian vegetation closely associated with moderately deep (greater than 

2.3 feet), still, or slow-moving water. 

Another correlate to California red-legged frog occurrence is the absence or nearabsence of introduced predators such as American bullfrog and predatory fish,

particularly Centrarchids (i.e., freshwater bass and sunfishes), which feed on the tadpoles 

at higher rates than native predatory species. Hiding cover from predators may be 

provided by emergent vegetation, undercut banks, and semi-submerged root wads. Some 

habitats that are not suitable for breeding (e.g., vernal pools, pools in intermittent streams, 

seeps, and springs) may constitute habitats for aestivation, shelter, foraging, predator 

avoidance, and juvenile dispersal.

Suitable upland habitat consists of all upland areas (riparian or otherwise) within 

500 feet of the water’s edge but not farther than the watershed boundary. This upland 

habitat is important in maintaining the integrity of California red-legged frog

aquatic/breeding habitat, as land use activities adjacent to and upstream of suitable 

aquatic habitat greatly affect the quality of aquatic/breeding habitat downstream.

Suitable dispersal habitat consists of all upland and wetland habitat that connect 

two or more patches of suitable aquatic habitat within 1.25 miles of one another. 

Dispersal habitat must be at least 500 feet wide and free of barriers such as, heavily 

traveled roads (roads with more than 30 cars per hour), moderate to high-density urban or 

industrial developments, and large reservoirs. The healthiest California red-legged frog

populations persist and flourish where suitable breeding and non-breeding habitats are 

interspersed throughout the landscape and are interconnected by un-fragmented dispersal 

habitat.

Merced ID conducted site assessments to characterize suitability of aquatic habitat 

sites for California red-legged frog breeding habitat using FWS guidelines. Assessments 

were based on the following components: (1) deep, still or slow-moving water that 

persists for a sufficient portion of the breeding season in order for larvae to reach 

metamorphosis, and (2) closely associated dense, shrubby, or emergent vegetation. The 

presence of introduced predatory fish was considered a negative site attribute that 

decreases the likelihood of California red-legged frog occurrence. Merced ID assessed 

habitat locations which were accessible on-site or viewable from an adjacent public road 

in the field. Locations not accessible or viewable in the field were evaluated from aerial 

imagery.

Neither Lake McClure nor McSwain reservoir has suitable habitat because of the 

prevalence of deep, open water, limited suitable associated vegetation, pronounced 

seasonal changes in water level (Lake McClure), and the presence of abundant predatory 

fish. The essential components of California red-legged frog breeding habitat were 
278

present or presumed to be present (based on available information from aerial photo 

interpretation) at 61 of the 336 assessment sites within 1 mile of the project boundary. 

There were no incidental observations of California red-legged frog during the licensing 

studies.

California Tiger Salamander—The California tiger salamander (Ambystoma 

californiense) is federally listed as endangered in Santa Barbara and Sonoma Counties 

and listed as threatened elsewhere. California lists this species as threatened. FWS 

designated critical habitat for the central population in 2005, encompassing 199,109 acres 

in 19 counties, including Mariposa and Merced. The nearest designated critical habitat 

units are situated about 7 miles west of Lake McClure (Central Valley unit 8) and about 6 

miles southwest of the McSwain reservoir (Central Valley unit 9).

The California tiger salamander is a terrestrial salamander that typically resides in 

existing mammal burrows in uplands until it emerges for nocturnal breeding migrations 

that mainly occur from December through February after rains fill pools and ponds. Eggs 

are laid singly or in small clusters, often attached to submerged stems and leaves, and 

hatch in 2 to 4 weeks. Larvae transform in about 4 months as pools dry in late spring or 

summer, but larvae may overwinter in permanent ponds. California tiger salamander 

may not breed at all in drought years when ponds fail to fill. Metamorphosed California 

tiger salamander disperse from natal sites to find suitable burrows and spend the majority 

of their time underground, emerging from burrows only occasionally, usually on rainy 

nights. Interpond dispersal may occur as well. California tiger salamanders have been 

observed on land as far as 1.24 miles from any potential breeding pool. California tiger 

salamander populations generally do not persist where fish, American bullfrogs, or 

predacious insects are well-established in breeding habitats. For this reason, neither Lake 

McClure nor McSwain reservoir constitutes suitable breeding habitat. Low relief areas 

surrounding the southern and western portions of Lake McClure contain areas that meet 

California tiger salamander upland habitat requirements; these primarily consist of annual 

grassland with additional areas of oak savanna along the southern shore. Suitable upland 

habitat is also present surrounding most of McSwain reservoir where low relief areas 

with annual grassland and oak savanna are prevalent. Merced ID reviewed aerial 

imagery and National Wetlands Inventory wetland maps to identify sites within 1.24 

miles of the project boundary with potential aquatic habitat for California tiger 

salamander. This review identified 69 aquatic assessment sites surrounding Lake 

McClure and 39 sites surrounding McSwain reservoir. Field reviews confirmed that six

sites at Lake McClure and nine sites at Lake McSwain meet criteria for breeding habitat. 

However, in many cases, habitat quality is low due to presence of predatory species or

short periods of water availability. 

There were no incidental observations of California tiger salamander during the 

licensing studies. Merced ID did not conduct protocol-level surveys for the California 

tiger salamander. 
279

Merced Falls

Terrestrial Species

PG&E conducted reconnaissance-level field surveys in 2010 and 2011, focusing 

on identifying potential habitat. Field surveys documented existing conditions, including 

habitat types present, quality of these habitats, and the presence of unique habitat 

features. PG&E developed a target list of threatened and endangered species by 

reviewing FWS’ list of threatened and endangered species available on its website, 

California DFW’s online California Natural Diversity Data Base, the online 

herpetological records located at the Museum of Vertebrae Zoology, University of 

California at Berkeley, and California Academy of Sciences’ online Herpetology 

Records. Searches were county-based and also based on a search of the USGS 7.5-

minute quadrangle on the Merced Falls quadrangle and four adjacent quadrangles,

including Hornitos, Yosemite Lake, Haystack Mountain, and Indian Gulch. PG&E 

checked habitat data and the closest known locations of species relative to the project 

area, and compared this information to information from its botanical surveys. Individual 

species below are discussed below. 

San Joaquin Kit Fox—The San Joaquin kit fox is federally listed as endangered

and state listed as threatened (FWS, 2014c; California DFW, 2014c). No critical habitat 

rules have been published for the San Joaquin kit fox. 

Dens are an important habitat component for the San Joaquin kit fox. The kit fox 

may use numerous dens throughout the year for shelter, reproduction, and temperature 

regulation. Kit foxes may dig the den sites; modify den sites constructed by ground 

squirrels, badgers, and coyotes; or use human-made structures such as culverts and 

abandoned structures. This species historically occupied several native plant 

communities in the San Joaquin Valley, but presently occur in areas where native habitats 

only occur as remnants and are surrounded by habitat extensively modified by 

anthropogenic activities, including agriculture, oil fields, and wind energy projects

(California DFW, 2014b; FWS, 2014d). Any habitat occupied by kit fox must support a 

suitable prey base, including nocturnal rodents, as well as diurnal rodents and insects. 

Kit fox also consume some vegetation (FWS, 2014d). Population declines are attributed 

to habitat loss and degradation caused by agriculture and urban uses of lands. Mortality 

from predation, shooting, habitat loss, and poisoning through the consumption of 

poisoned rodents contributes to population decline (California DFW, 2014b; FWS, 

2014d). 

PG&E did not conduct surveys for the San Joaquin kit fox. 

California Red-legged Frog—California red-legged frog is federally listed as 

threatened. There is no state status for this species. FWS published a Recovery Plan for 

the California Red-Legged Frog (Rana aurora draytonii) (2002). The project occurs in 

the vicinity of one of the recovery units.
280

FWS revised critical habitat for this species in 2010. Criteria for California redlegged frog critical habitat include: (1) suitable aquatic habitat, (2) associated uplands,

and (3) suitable dispersal habitat connecting suitable aquatic habitat. At a minimum, 

critical habitat includes two or more suitable breeding locations, one of which must be a 

permanent water source, associated uplands surrounding these water bodies (extending to 

500 feet from the water’s edge), all within 1.25 miles of one another and connected by 

barrier-free dispersal habitat at least 500 feet wide. No critical habitat occurs within the 

project boundary. The closest critical habitat unit to the project is about 50 miles 

northwest in Calaveras County.

California red-legged frog breeding occurs from late November to late April in 

ponds, backwater pools, or creeks. Egg masses are attached to emergent vegetation such 

as cattails and bulrushes. Tadpoles remain in these aquatic habitats until metamorphosis. 

Increased siltation during the breeding season can cause asphyxiation of eggs and small 

tadpoles. Tadpoles typically metamorphose between July and September, and most 

likely feed on algae. Outside of the breeding season, adults may disperse upstream, 

downstream, or upslope of breeding habitat to forage and seek sheltering habitat, which 

may consist of small-mammal burrows, leaf litter, and other moist sites in or near (up to 

200 feet from) riparian areas. During wet periods, long distance dispersal of up to a mile

may occur between aquatic habitats, including movement through upland habitats or 

ephemeral drainages. Seeps and springs in open grasslands can function as foraging

habitat or refugia for wandering frogs.

The California red-legged frog is primarily associated with perennial ponds or 

pools and slow-moving perennial or seasonal streams where water remains continuously 

for a minimum of 20 weeks beginning in the spring (i.e., sufficiently long for breeding to 

occur and tadpoles to complete development). The California red-legged frog is not 

expected to breed successfully at sites holding water for fewer than 15 weeks. The 

minimum depth of breeding habitat is 20 inches; however, deep water pools, ponds, and 

lake areas are not suitable. Dense, shrubby riparian vegetation (e.g., willow, bullrush, 

and tule species), and bank overhangs are important features of California red-legged 

frog breeding habitat, although they sometimes use sites that lack these features. 

Locations with the highest densities of California red-legged frogs exhibit dense 

emergent or shoreline riparian vegetation closely associated with moderately deep 

(greater than 2.3 feet), still, or slow-moving water. 

Another correlate to California red-legged frog occurrence is the absence or nearabsence of introduced predators such as American bullfrog and predatory fish, 

particularly Centrarchids (i.e., freshwater bass and sunfishes), which feed on the tadpoles 

at higher rates than native predatory species. Hiding cover from predators may be 

provided by emergent vegetation, undercut banks, and semi-submerged root wads. Some 

habitats that are not suitable for breeding (e.g., vernal pools, pools in intermittent streams, 

seeps, and springs) may constitute habitats for aestivation, shelter, foraging, predator 

avoidance, and juvenile dispersal.
281

Suitable upland habitat consists of all upland areas (riparian or otherwise) within 

500 feet of the water’s edge but not farther than the watershed boundary. This upland 

habitat is important in maintaining the integrity of California red-legged frog

aquatic/breeding habitat, as land use activities adjacent to and upstream of suitable 

aquatic habitat greatly affect the quality of aquatic/breeding habitat downstream. 

Suitable dispersal habitat consists of all upland and wetland habitat that connect two or 

more patches of suitable aquatic habitat within 1.25 miles of one another. Dispersal 

habitat must be at least 500 feet wide and free of barriers such as, heavily traveled roads 

(roads with more than 30 cars per hour), moderate to high-density urban or industrial 

developments, and large reservoirs. The healthiest California red-legged frog populations 

persist and flourish where suitable breeding and non-breeding habitats are interspersed 

throughout the landscape and are interconnected by unfragmented dispersal habitat.

The reservoir itself does not likely does not contain suitable habitat because of the 

prevalence of deep, open water, limited suitable associated vegetation, and the presence 

of predatory fish and bullfrogs, although other areas of suitable habitat exist in the project 

area. 

PG&E conducted visual encounter surveys for amphibians, including California 

red-legged frogs, and four areas were sampled by dip nets for aquatic life stages of frogs. 

Frogs were identified to species using binoculars, and under a spotlight if the survey was 

conducted during dark. No California red-legged frogs were observed during the 

surveys. 

Valley Elderberry Longhorn Beetle—The valley elderberry longhorn beetle is 

federally listed as threatened. The valley elderberry longhorn beetle is associated with 

various species of elderberry (Sambucus spp.) throughout the California Central Valley 

and foothills below 3,000 feet msl. Mariposa and Merced Counties are within the valley 

elderberry longhorn beetle range, although no critical habitat is designated within the 

counties. The valley elderberry longhorn beetle occurs within riparian vegetation 

communities where it feeds exclusively on the blue elderberry shrub in both adult and 

larval stages. Adult valley elderberry longhorn beetles appear to feed externally on the 

flowers and foliage of the blue elderberry. Adult females lay eggs in crevices in the bark 

of the host elderberry plant. After hatching, larvae spend 1 to 2 years feeding inside the 

plant. Prior to pupating, valley elderberry longhorn beetle larvae chew an exit hole in the 

elderberry trunk for the emerging adult, leaving boreholes in the elderberry stems.

During the 2010/2011 surveys, PG&E documented one blue elderberry shrub 

located on the northeast side of the impoundment. The shrub was of suitable size to 

support the valley elderberry longhorn beetle and showed signs of possible exit holes by 

the beetle. Although no beetles were observed, the presence of the valley elderberry 

longhorn beetle should be assumed, given the exit holes in the bark of the elderberry 

shrub.
282

3.3.3.2 Environmental Effects

Merced River Project 

Aquatic Species

The environmental effects of the proposed project on Central Valley steelhead 

would be similar to those on fall run Chinook salmon and relate to physical habitat 

availability, temperature management, and a flow regime that attracts adults to enter the 

Merced River to spawn and facilitates outmigration of juveniles. We discuss these 

environmental factors as they relate to Central Valley steelhead in section 3.3.1.2,

Aquatic Resources. 

Terrestrial Threatened and Endangered Species

General Protection Measures—Merced ID proposes numerous measures that 

would protect terrestrial and aquatic resources, including threatened and endangered 

species, from effects of project operation and maintenance. Two of those measures focus 

on threatened and endangered species: annual review of special-status species and annual 

employee training. 

Merced ID proposes to review special-status species lists annually, assess newly 

added species occurring on federal land, and if necessary consult with agencies to 

develop and implement protection measures. The Water Board [preliminary WQC

condition 12] specifies annual consultation to review the project status and plans, results 

of studies, necessary modifications to plans, and protection measures for newly listed 

species. In addition, the Water Board [preliminary WQC condition 13] specifies that

Merced ID review the lists of species protected by the ESA and special-status species 

within 3 months of license issuance and annually thereafter, and evaluate potential 

project effects on newly listed species. BLM [preliminary 4(e) condition 1] specifies

annual consultation to discuss the project status and plans, results of studies, review of 

non-routine maintenance, changes to project facilities, necessary modifications to plans, 

and protection measures for newly listed species. BLM [preliminary 4(e) condition 11]

specifies an annual review of special-status species list and an assessment of newly listed 

species on federal lands. It also specifies that Merced ID conduct surveys and develop 

protection measures for newly added species. FWS 10(j) recommendation 6(b) 

recommends annual consultation to review federally listed and special-status species lists. 

FWS also recommends that Merced ID develop and implement studies to assess project 

effects on newly added species and prepare a draft biological assessment. 

Merced ID proposes to provide annual employee training regarding the 

identification of special-status, non-native species and sensitive areas. BLM [preliminary

4(e) condition 3] specifies that Merced ID conduct annual employee training and 

immediate training for newly hired employees to familiarize them with special-status, 

non-native invasive plants and sensitive areas and that Merced ID provide maps, 
283

locations, and pictures of special-status species, non-native invasive plants and sensitive 

areas. 

Our Analysis

Merced ID’s proposal to conduct an annual review of federally listed and specialstatus species lists is consistent with the Water Board’s preliminary WQC condition 13

and BLM preliminary 4(e) condition 11. Annual review would identify newly listed 

species that should be evaluated as potentially affected by the project. Both the Water 

Board [preliminary WQC condition 12] and BLM [preliminary 4(e) condition 1] specify 

annual consultation to further protect federally listed and special-status species by 

reducing the possibility that newly added species could be affected by non-routine 

maintenance activities and activities included in plans. The annual consultation would 

also provide an opportunity for plans to be modified in the event of delisting of species. 

Further, the process of annual consultation would allow agencies to provide input based 

on unpublished data, gray literature, and other sources of information that may not be 

available in public databases. Although we recognize the benefits of annual review and 

consultation, the Commission typically includes in its licenses a standard license article 

with a fish and wildlife reopener provision, as discussed in section 5.1.1.3, Measures not 

Recommended by Staff.

Implementing Merced ID’s proposed measure to conduct annual training for 

employees would reduce effects of project maintenance on threatened and endangered 

species and their habitats. Including BLM’s recommendation to provide employees with 

maps, locations, and pictures of special-status species, non-native invasive plants, and 

sensitive areas would increase the probability of employees successfully avoiding 

special-status species and sensitive areas and also identifying non-native invasive plants. 

Unintentional effects of project maintenance activities would be avoided. Implementing 

the measure for employee training would reduce project effects on threatened and 

endangered species. 

Federally Listed Plant Species—Project operation and maintenance, new 

construction, and recreation activities could affect federally threatened and endangered 

plants occurring or potentially occurring in the project area. Construction of any new 

facilities would directly affect vegetation through excavation and grading. Project 

maintenance activities, including road grading, vegetation removal and trimming, and 

herbicide applications to treat invasive plants would directly affect threatened and 

endangered plants occurring in the areas where these maintenance activities would occur. 

Recreation activities, such as hiking, would affect threatened and endangered plants 

situated on or near hiking trails. 

Merced ID did not document any federally threatened or endangered plants during 

its surveys. Although Merced ID does not propose a plan specifically for the protection 

of federally listed plants, it does propose other plans with components that would protect 

these plants. Merced ID proposes to implement its Vegetation Management Plan to 
284

minimize potential effects of project operation and maintenance on vegetation, including 

sensitive plants. Merced ID’s proposed Vegetation Management Plan includes several 

measures to reduce potential effects on sensitive plants. Specific to sensitive plants, 

Merced ID would: (1) flag sensitive areas prior to conducting any vegetation 

management or ground-disturbing activities; (2) emphasize the use of manual weed 

control methods, where feasible; (3) use BMPs; and (4) provide annual employee training 

including identification of key special-status species and the locations of sensitive 

resources to be avoided. Per Merced ID’s proposed Recreation Facilities Plan, areas 

where sensitive plants occur would be avoided during improvement or new construction 

projects. As part of the Invasive Species Management Plan, Merced ID proposes to 

emphasize protection of sensitive plants when selecting control measures for invasive 

weeds in proximity to sensitive resources. Merced ID also proposes annual employee 

training to, in part, help protect sensitive plants, and annual consultation to determine, in 

part, if project activities would affect newly listed species and develop appropriate 

studies and mitigation measures. 

FWS comments that suitable habitat exists within the project for the endangered 

Keck’s checkerbloom, threatened Layne’s butterweed, Chinese Camp brodiaea, mariposa 

pussypaws, and California vervain. FWS states that there are no historical records of 

federally listed plants occurring with the project area and acknowledges that no federally 

listed plants were observed during the surveys conducted by Merced ID. FWS further 

states that Merced ID did not conduct the surveys during the peak bloom period or in the 

habitat for each plant. FWS [10(j) recommendation 6(b)] recommends annual 

consultation to identify newly listed species that could be affected by the project, the 

development of studies, and preparation of a biological assessment including protection 

measures. 

The Water Board [preliminary WQC conditions 12 and 13] specify annual 

consultation and reviews to protect newly listed federally listed and special-status 

species. BLM [preliminary 4(e) condition 1] specifies annual consultation to discuss, in 

part, necessary protection measures for federally listed species. BLM [preliminary 4(e) 

condition 3] specifies annual employee training to train employees to identify federally 

listed species. In addition, this condition specifies review of federally listed and specialstatus species and assessment of newly listed species. 

Our Analysis

Continued operation of the project under a new license would include some 

activities that could affect federally listed plant species. Proposed enhancements at 

existing project recreation areas, proposed construction of the new recreation site, and 

road grading would result in the removal of existing vegetation. Project maintenance 

activities, such as herbicide applications to noxious weeds and invasive plants and 

vegetation management in recreation areas or around project facilities could affect 

federally listed plant species and their habitats. 
285

Ideally, implementation of Merced ID’s proposed Vegetation Management Plan 

would identify areas where project operation and maintenance activities have the 

potential to affect sensitive plants and their habitats. Similarly, implementation of 

Merced ID’s proposed Weed Management Plan and Recreation Facilities Plan should 

reduce the potential for adverse effects on sensitive plants and their habitats. These plans 

have been developed and proposed based on the assumption that the respective resources 

have been identified through surveys conducted in accordance with accepted 

methodologies and protocols. Because Merced ID did not follow species-specific 

methodologies and protocols during the surveys and did not conduct the surveys at the 

appropriate times and places, the resulting data do not prove the absence of these species 

or their habitats. None of the aforementioned plans could protect federally listed plants 

and their habitats that have not yet been identified in the project area. Proceeding with 

project activities without knowing the status and location of federally listed plants in the 

project area could result in federally listed plants being adversely affected by the project. 

We recommend developing a protection plan for federally listed plants in 

consultation with FWS, the Water Board, California DFW, and BLM. The plan would, at 

a minimum, include the following for each federally listed plant species potentially 

occurring in the project area: (1) study methodologies and protocols sufficient to produce 

adequate survey results; (2) a list of peak bloom times and identifying features; (3) the 

timing and frequency of the surveys; (4) maps and written descriptions of habitat areas to 

be surveyed; (5) references to measures contained in other plans that could protect 

federally listed plants; (6) protection and mitigation measures; and (7) reporting 

requirements. 

With the development and implementation of the protection plan for the federally 

listed plants, the project is not likely to adversely affect federally threatened and 

endangered plants, including Keck’s checkerbloom, Layne’s butterweed, Chinese Camp 

brodiaea, Mariposa pussypaws, and California vervain.

Vernal Pool Fairy Shrimp—Seven of the 33 sites Merced ID identified as 

potential habitat for vernal pool fairy shrimp exist in areas where vegetation and road 

management activities could occur. Two additional sites are located near recreation areas 

where vehicle use may occur. The remainder of the 33 sites occurs outside of areas 

where project activities are expected to occur. Vegetation maintenance activities, 

including herbicide treatments in roadside ditches or swales, runoff from treated sites,

and mechanical vegetation maintenance could affect water quality in these sites. 

Pesticide applications could also affect vernal pool fairy shrimp. Vehicle use could

compact soils or alter runoff patterns, potentially changing hydrology of seasonal pools. 

Such activities could affect vernal pool fairy shrimp if they occupy these habitats.

Although Merced ID proposes measures (e.g., annual review and annual 

consultation) that could benefit fairy shrimp, it does not propose any species-specific 

measures to monitor or protect fairy shrimp in the project area. The Water Board
286

[preliminary WQC condition 6] specifies that Merced ID develop and implement a 

monitoring and conservation plan for vernal pool and Conservancy fairy shrimp. Per the 

Water Board, monitoring would be conducted annually 4 years, and thereafter every 3

years and prior to construction or ground-disturbing activities. FWS commented that 

although no documented occurrences of fairy shrimp are known in the project area, 

Merced ID did not conduct protocol level surveys. FWS notes that project area overlaps 

with about 1 acre of critical habitat for the vernal pool fairy shrimp. FWS states that 

levee breaches spill water into vernal pool critical habitat in the dry summer months, and 

the project road that transects the critical habitat is likely to cause long-term degradation 

of the habitat adjacent to the road, despite the fact that the road itself does not contain any 

primary constituent elements. 

Our Analysis

Continued operation of the project would include vegetation maintenance, road 

maintenance, and recreation activities in proximity to vernal pools with potential to 

support vernal pool fairy shrimp. These activities could change water quality or site 

specific hydrology and runoff patterns, potentially affecting any fairy shrimp that occur 

in these pools. The identified pools are largely dependent on human-modified hydrology, 

relying on runoff from roads and culverts, or spills from levees as noted by FWS, as well 

as depressions created by vehicles parking areas. While these areas may meet the 

conditions for vernal pool fairy shrimp habitat, it is unlikely that the species occurs in the 

project area, as substantiated by the FWS’ comment that no known occurrences of fairy 

shrimp are documented in the project area. However, because Merced ID did not conduct 

protocol level surveys and therefore cannot show the presence or absence of the species, 

the presence of vernal pool fairy shrimp should be assumed. 

Merced ID proposes recreation facility rehabilitation and construction activities in 

the Barrett Cove, McClure Point, and Lake McSwain recreation areas in proximity to 

pools suitable for vernal pool fairy shrimp. If occupied, disturbance to these pools could 

adversely affect this species. Merced ID could treat pools associated with study sites 7, 

8, 9, 11, 21, 24, and 32 as sensitive habitats occupied by vernal pool fairy shrimp. Where 

vernal pool fairy shrimp are either shown to be by protocol level surveys or assumed to 

be, Merced ID could implement protection measures such as flagging and avoiding 

disturbance during vegetation management and ground-disturbing activities to minimize 

project effects on the species. The Water Board’s preliminary WQC condition to conduct 

surveys would definitely determine the presence of vernal pool fairy shrimp. With 

respect to critical habitat, we acknowledge FWS’ concern that the project road 

transecting the critical habitat could cause long-term habitat degradation to adjacent 

habitat. We agree that potential degradation of adjacent habitat is an issue, and we 

recognize that the potential long-term effects would likely be realized over the term of the 

license. The fact that critical habitat for vernal pool species overlaps with the project area 

validates the need for surveys and protective measures for vernal pool fairy shrimp and 

its habitat. We recommend developing a protection plan for the vernal pool fairy shrimp 

and its habitat that would include the measures specified by the Water Board [preliminary 
287

WQC condition 6], and other measures as determined during consultation with the Water 

Board, FWS, California DFW, and BLM. 

With the development and implementation of the protection plan for vernal pool 

fairy shrimp and its habitat, the project is not likely to adversely affect the affect vernal 

pool fairy shrimp or modify its critical habitat.

San Joaquin Kit Fox—Project activities, such as maintenance activities and 

recreation, could result in noise that could disturb kit fox in the project vicinity. Pest 

control, particularly the control of undesirable rodents through the use of rodenticides and 

burrow fumigants, could adversely affect the San Joaquin kit fox by poisoning its prey. 

Merced ID did not conduct surveys for or analyze project effects on the San 

Joaquin kit fox, citing a lack of occurrence in the project vicinity. FWS states that the 

San Joaquin kit fox is known to occur on the Merced NWR, which receives mitigation 

water from the project. FWS cites its unpublished documentations of San Joaquin kit fox 

vocalizations in Mariposa County, within 4 miles of the project boundary, and notes that 

more than 300 square miles of San Joaquin kit fox habitat occurs to the north, south, and 

east of the project. 

Merced ID proposes to avoid the use of burrow fumigants and rodenticides in 

habitat of the San Joaquin kit fox as a protection measure for the species. FWS [10(j) 

recommendation 6(a)F] recommends prohibiting the unauthorized use of burrow 

fumigants or rodenticides on federal land and 10(j) recommendation 6(a)G recommends 

prohibiting the use of burrow fumigants or rodenticides in habitat of the San Joaquin kit 

fox until section 7 ESA consultation is completed or a permit is issued under section 10 

of the ESA. FWS also comments that the burrowing owl, a BLM sensitive species, has 

been known to occur in the project vicinity. FWS points out that because burrowing owls 

occur in ground squirrel burrows, they are vulnerable to rodent control methods such as 

burrow fumigation and burrow collapse.

In preliminary WQC condition 18, the Water Board specifies that Merced ID 

develop a pesticide use plan to prevent pesticides from affecting federally and state listed 

species in the project area or downstream of the project area. BLM specifies in 

preliminary 4(e) condition 40 that the use of pesticides be restricted and requires written 

approval by BLM. California DFW [10(j) recommendation 10] recommends that Merced 

ID develop an integrated pest management and pesticide use notification plan, which 

includes a provision for Merced ID to obtain approval prior to using pesticides including 

rodenticides. The plan includes an exception for unexpected outbreaks of pests requiring

control measures not anticipated at the time the report was submitted. In that case, 

Merced ID would submit an emergency notification of use to the appropriate agencies. 

Our Analysis

Merced ID does not provide information about San Joaquin kit fox in the project 

vicinity, nor does it provide information about potential project-related effects on the San 
288

Joaquin kit fox. Although Merced ID does not propose construction activities that would 

result in noise, project maintenance activities and recreation could cause noise that could 

disturb San Joaquin kit fox in the project vicinity. Because Merced ID does not provide 

information about its current or proposed use of rodenticides and burrow fumigants, we 

are unable to analyze any effects on the San Joaquin kit fox, or other animals that could 

be affected by rodent control methods such as the burrowing owl. 

Merced ID proposes to avoid the use of rodenticides and burrow fumigants in San 

Joaquin kit fox habitat, but it does not propose a protection plan, nor has it conducted 

surveys for the San Joaquin kit fox in the project area. Surveys would be necessary to 

identify habitat areas used by the San Joaquin kit fox, provide information on where to 

avoid the use of rodenticides and burrow fumigants, and where other protective measures 

may be necessary. Including the surveys as a component of a protection plan would 

allow study results to be formally documented, such that Merced ID can sufficiently 

evaluate project effects on the San Joaquin kit fox to develop appropriate protection and 

mitigation measures. 

Also, under the staff alternative, the Noxious Weeds and Invasive Plants Control 

Plan would include the staff-recommended component on pest management and pesticide 

use, which would protect the San Joaquin kit fox, and other animals potentially affected 

by pesticides. 

We recommend developing a protection plan for the San Joaquin kit fox in 

consultation with FWS, the Water Board, California DFW, and BLM. The plan would 

include: (1) study methodologies and monitoring protocols to identify San Joaquin kit 

fox habitats within the project area; (2) an assessment of potential project effects on San

Joaquin kit fox in the project area; (3) protection and mitigation measures; (4) references 

to measures contained in other plans that would protect San Joaquin kit fox; and 

(5) descriptions of any exceptions to the prohibited use of rodenticides that would be 

considered emergencies and allowed by agencies and an explanation of why the 

emergency situations would supersede protection measures for the San Joaquin kit fox. 

With the development and implementation of the protection plan for the San 

Joaquin kit fox, the project is not likely to adversely affect the San Joaquin kit fox.

Valley Elderberry Longhorn Beetle—Merced ID uses a combination of manual, 

mechanical, and chemical methods to control vegetation in the project boundary. Merced 

ID also conducts regular road maintenance on project roads, including grading, graveling, 

and paving. These project management activities could result in adverse effects on the 

valley elderberry longhorn beetle by trimming or pruning elderberry bushes that provide 

potential habitat. Merced ID also proposes a variety of rehabilitation and construction 

activities at project recreation sites. Ground-disturbing activities related to these 

activities have potential to damage or remove elderberry plants and could affect habitat 

for the valley elderberry longhorn beetle.
289

To minimize potential effects on valley elderberry longhorn beetles, Merced ID’s 

proposed Vegetation Management Plan and Invasive Species management Plan include 

several measures specific to protection of elderberry plants. These measures are: 

(1) flagging all elderberry plants with stems measuring 1 inch in diameter or larger at 

ground level prior to any project maintenance or ground-disturbing activities with 

potential to affect the plant; (2) prohibiting removal of any elderberry plants with stems 

measuring 1 inch in diameter or larger at ground level; (3) prohibiting trimming of any 

elderberry stems measuring 1 inch in diameter or larger at ground level; (4) training 

project personnel to recognize valley elderberry longhorn beetle habitat; and (5) 

prohibiting use of herbicides, insecticides, fertilizers, or other chemicals that might harm 

the beetle or its host plant within 100 feet of any elderberry plant with one or more stems 

measuring >1 inch in diameter at ground level.

The Water Board [preliminary WQC condition 11] specifics that Merced ID 

develop, in consultation with the Water Board, a conservation plan for the valley 

elderberry longhorn beetle. At a minimum, the plan would include goals and objectives, 

monitoring protocols, potential effects on the beetle, a monitoring and reporting schedule, 

mitigation measures to be implemented if the beetle is affected by the project, and 

protective measures. FWS [10(j) recommendation 6(a)] recommends that Merced ID

develop a biological assessment to evaluate effects of proposed construction of new 

project facilities or non-routine maintenance activities before such construction or 

activities are implemented and conclude consultation on the valley elderberry longhorn 

beetle. 

Our Analysis

Merced ID proposes, as part of its Invasive Species Management Plan, and 

Vegetation Management Plan to use manual and chemical methods to control vegetation 

in the project boundary. Merced ID also proposes to maintain project roads through 

surface grading and resurfacing, ditch clearing, erosion control, and culvert clearing and 

repair. These activities have the potential to disturb vegetation, and could adversely 

affect elderberry plants in the area if appropriate protection measures are not 

implemented. Merced ID’s proposed measures would ensure elderberry plants are clearly 

marked prior to maintenance and ground-disturbing activities near existing elderberry 

populations that could provide valley elderberry longhorn beetle habitat. Grounddisturbing activities would include construction related to recreation enhancements and 

other facilities that may be included in a new license for this project. Annual training 

would educate maintenance workers to recognize elderberry plants and understand their 

importance for valley elderberry longhorn beetles. Together, proposed flagging and 

training measures would minimize potential for accidental damage to elderberry plants. 

Proposed measures that prohibit removal and trimming of elderberry plants large enough 

to support valley elderberry longhorn beetles, and prohibiting use of chemicals within 

100 feet of these plants would also minimize potential for on effects valley elderberry 

longhorn beetles.
290

Over the term of the license, existing elderberry plants would increase in size and 

new elderberry plants would likely be found. Therefore, the number of elderberry plants 

of suitable size to support the valley elderberry longhorn beetle would increase and the 

distribution of the plants within the project area would likely change. It would then be 

necessary to update the proposed plan to identify elderberry plants that should be flagged 

for avoidance. Over the term of license, the Water Board’s preliminary WQC condition 

specifying that monitoring occur every 3 years would address changes in habitat for the 

valley elderberry longhorn beetle and allow for updates to the components of the 

Vegetation Management Plan and Invasive Species Management Plan concerning 

elderberry plants. Revising section 3.0 of the Vegetation Management Plan to include 

maps showing the locations of elderberry plants, both with and without signs of 

occupancy by the valley elderberry longhorn beetle, would facilitate the implementation 

of the plan and keep the information current for employee education. 

The Water Board also specifies monitoring prior to construction, and FWS [10(j) 

recommendation 6(a)A-C] recommends that Merced ID evaluate project effects on any 

federally listed and candidate species and their habitats prior to construction of new 

facilities or features and non-routine maintenance activities. We agree that monitoring 

before implementing new construction and maintenance activities would reduce project 

effects on the valley elderberry longhorn beetle and its habitat. However, as discussed in 

section 5.1.1.3, Measures not Recommended by Staff, the Commission typically includes 

a standard license article with a fish and wildlife reopener provision.

With implementation of these measures, the project is not likely to adversely 

affect valley elderberry longhorn beetles.

California Red-legged Frog—Of the 61 sites supporting potential habitat for 

California red-legged frog, 2 occur in areas of potential project effects. The first is on a 

stream below the New Exchequer dam spillway. The second is a pond connected to 

McSwain reservoir via culverts. No project-related maintenance or recreation activities 

are expected to occur in these areas. However, there is potential for project operation to 

affect water levels in these areas. Abrupt water increases in the spillway could flush 

California red-legged frog eggs, tadpoles, or sub-adults downstream to unsuitable habitat. 

Water-level fluctuations at the pond site have potential to leave eggs or tadpoles stranded 

above the water level.

FWS comments that the project overlaps with a recovery unit defined in the 

Recovery Plan for the California Red-Legged Frog (Rana aurora adraytonii) (FWS, 

2002). More specifically, the project overlaps with the Piney Creek core area. FWS

[10(j) recommendation 7] recommends that Merced ID, in consultation with FWS and 

BLM, develop and implement a watershed management and protection plan for the 

California red-legged frog in the Piney Creek core area of the recovery plan. The plan 

should include measures to control bullfrogs and reestablish populations of the California 

red-legged frog in the Piney Creek core area and reduce population-level impacts from 

the frog-killing Batrachochytrium dendrobatidus fungus. 
291

BLM specifies in preliminary 4(e) condition 1 that Merced ID consult with BLM, 

FWS, the Water Board, and California DFW to develop a management plan for the 

California red-legged frog that includes identification of areas where non-native predators 

occur, control and eradication measures for non-native species and predators, and 

identification of a habitat mosaic containing both breeding and dispersal habitat. BLM, 

in preliminary 4(e) condition 14, also specifies that Merced ID develop a management 

plan for the foothill yellow-legged frog. The plan would include provisions to monitor 

water temperature at the confluence of Sherlock Creek and the Merced River once in 

each water year type for the first 10 years, then every 5 years thereafter. In preliminary 

4(e) condition 40, BLM specifies that Merced ID avoid pesticide use within 500 feet of 

known locations of foothill yellow-legged frogs and other special-status animals and 

plants. 

The Water Board [preliminary WQC condition 10] specifies that Merced ID 

develop a monitoring and conservation plan for the California red-legged frog, foothill 

yellow-legged frog, and western spadefoot.

Our Analysis

As determined by surveys and noted by FWS in its comments, suitable habitat for 

California red-legged frog is present within the project’s affected area. Although Merced 

ID recorded no incidental observations of California red-legged frog in the project area, it

did not conduct protocol-level surveys for the frogs in the project area. 

There is limited potential for project operation to affect the California red-legged 

frog. The majority of releases from Lake McClure occur through the powerhouse into 

McSwain reservoir. Spills over the New Exchequer dam have only occurred once, 

shortly after construction of the dam. The majority of releases from Lake McClure occur 

through the powerhouse into McSwain reservoir. Spills over the New Exchequer 

spillway have only occurred once, shortly after construction of New Exchequer dam. 

The spillway is located about 0.9 mile north of the dam and the spillway channel enters 

McSwain reservoir about 0.7 mile downstream from the powerhouse. Consequently, 

there is little influence of project releases from Lake McClure to affect these areas. 

Merced ID does not propose any changes to existing maintenance or operation that would 

affect baseline conditions in these areas. 

Conversely, hydropower projects generally support bullfrogs and predatory fish. 

Sites identified in areas of project maintenance or operation are known to either support 

American bullfrog, or are accessible to predatory fish—both of which can adversely 

affect California red-legged frog and other amphibian species in the project area. In 

addition to potential effects of flows on frog reproduction, hydropower projects may also 

affect water temperature, which could affect the development time and rate of tadpoles, 

which is BLM’s concern for the foothill yellow-legged frog. Additionally, other project 

maintenance activities, such as the application of herbicides and pesticides, could 

adversely affect the California red-legged frog and other amphibians in the project area. 
292

Some of the protection measures that would be implemented for the California 

red-legged frog may benefit other species in the project area. Broadening the protection 

plan to encompass other federally listed and special-status amphibians, such as the 

foothill yellow-legged frog and western spadefoot, would facilitate consultation with 

agencies and eliminate the need for duplicate measures. Therefore, we recommend that 

Merced ID develop and implement a protection plan for federally listed and special-status 

species, including but not limited to the California red-legged frog, foothill yellow-legged 

frog, and western spadefoot. The plan should be developed in consultation with FWS, 

BLM, the Water Board, and California DFW and include the following: (1) all measures 

recommended by FWS, BLM, and the Water Board in their respective 10(j) 

recommendations and 4(e) conditions; (2) details of survey and monitoring protocols for 

each federally listed and special-status amphibian species recommended for monitoring 

by the agencies; (3) maps showing locations of species and their habitats relative to 

locations of project activities that could affect amphibians; (4) descriptions of potential

project effects on each species; (5) and protective measures sufficient to minimize project 

effects on each species. 

With implementation of these measures, the project is not likely to adversely 

affect the California red-legged frog. 

California Tiger Salamander—Project-related activities occurring in potential 

California tiger salamander habitat include vegetation management, road maintenance, 

construction or rehabilitation of recreation facilities, and recreation activities. Vegetation 

management could result in vegetation removal or trampling that could disturb existing 

burrows, and the application of rodenticides could adversely affect small mammals that 

create the burrows used by California tiger salamanders. Herbicide applications could

also affect this species. Maintenance of recreation areas, road maintenance, and projectrelated traffic have the potential to injure or kill salamanders crossing roads or migrating 

across project lands. Several potential aquatic breeding sites are used as swimming 

lagoons and there may be potential for these activities to disturb or injure salamander 

larvae.

FWS notes that seven documented occurrences of California tiger salamanders 

occurred within 5 miles of the project area. Fifteen aquatic sites within the project area 

provide potentially suitable breeding habitat, surrounded by potentially suitable upland 

habitat. FWS also commented that ESA consultation has not been concluded because 

Merced ID did not conduct protocol-level surveys for this species. FWS [10(j)

recommendation 6(a)G] recommends prohibiting the use of burrow fumigants or 

rodenticides in the habitat of California tiger salamanders. 

The Water Board [preliminary WQC condition 7] specifies the development of a 

monitoring and conservation plan to protect the California tiger salamander from the 

effects of pesticide use and recreation and construction activities.
293

Although Merced ID does not propose a protection plan for the California tiger 

salamander, it does propose to avoid the use of burrow fumigants and rodenticides in 

California tiger salamander habitat. 

Our Analysis

Proposed maintenance activities, including rodent control and vegetation 

maintenance, could affect the California tiger salamander. Merced ID’s proposal to avoid 

the use of burrow fumigants and rodenticides in habitat of the California tiger salamander 

would certainly minimize project effects from rodent control and would be consistent 

with FWS’ recommendation. Avoiding the use of herbicides in California tiger 

salamander habitat, per the staff-recommended measure for pest management and 

pesticide discussed in section 3.3.2, Terrestrial Resources, would further reduce project 

maintenance effects. In areas where vegetation trimming and removal are planned, foot 

traffic could cause burrows to collapse. Although recreational activities in these areas are 

expected to remain similar to existing conditions and there are no plans for development 

in these areas,

47 with the exception of recreation development on Mack Island, we 

consider that recreation could adversely affect this species’ burrows and habitat for eggs 

and larvae in pools in areas used for recreational hiking and recreational swimming, 

respectively. Additionally, vehicle traffic could adversely affect California tiger 

salamanders that cross roads as they migrate to breeding pools or upland foraging sites, 

or disperse to other ponds.

Although the habitat quality was reported to be low to marginal, and no incidental 

observations of California tiger salamanders were recorded during the surveys, 

assumptions about the presence or absence of this species should not be based on habitat 

surveys and incidental observations. Even with protocol-level surveys, secretive and rare 

species are difficult to detect and quantify. Therefore, the presence of this species should 

be assumed, until protocol-level surveys prove otherwise and agencies concur with 

survey results. 

Although Merced ID proposes measures and other plans that would reduce project 

effects on the California tiger salamander, we find that surveys and monitoring efforts 

would be necessary to identify the areas where protective measures would best be 

implemented, based on habitats where the salamanders occur and their migratory routes. 

Therefore, we recommend developing and implementing a protection plan for the 

California tiger salamander, including, at minimum, provisions to conduct protocol level 

surveys, identify habitats and migratory routes used, and avoid using burrow fumigants 

and rodenticides in habitat of the California tiger salamander. 

 

47 Although Merced ID proposes construction and rehabilitation at some recreation 

areas (i.e., McClure Point, Barrett Cove, Horseshoe Bend, Bagby, and McSwain), no 

potential California red-legged frog habitat occurs in the area of the proposed activities.
294

With implementation of these measures, the project is not likely to adversely 

affect the California tiger salamander.

Merced Falls Project

General Protection Measures

PG&E does not propose any general protective measures that would protect 

terrestrial and aquatic threatened and endangered species from effects of project 

operation and maintenance. 

The Water Board [preliminary WQC condition 7] specifies that PG&E conduct a 

review of lists of endangered and special-status species within 6 months of license 

issuance, and every 5 years thereafter, to identify newly listed species that could be 

adversely affected by the project. The Water Board [preliminary WQC condition 7] also 

specifies that PG&E should consult with FWS, California DFW, the Water Board, and 

NMFS to develop a species -specific study plan for any newly added species in the 

project area that could be adversely affected by the project. 

Our Analysis

The Water Board’s preliminary WQC condition 7 specifying pentennial review of 

threatened, endangered, and other special-status species would identify newly listed 

species. We agree that any newly listed species should be evaluated for potential project 

effects. We also agree that the requiring input from agencies in the development of 

species-specific study plans is appropriate, particularly since much information is 

available through unpublished data and gray literature. Although we recognize the 

benefits of pentennial review and consultation to threatened, endangered, and specialstatus species and their habitats, the Commission typically includes in its licenses a 

standard license article with a fish and wildlife reopener provision, as discussed in section 

5.1.2.3, Measures not Recommended by Staff. 

Effects on individual species are discussed below. 

San Joaquin Kit Fox—Noise caused by project maintenance activities and 

recreation could affect San Joaquin kit fox in the project vicinity. The use of rodenticides 

or other pesticides to control rodents would adversely affect kit foxes in the project 

vicinity. 

In the discussion of wildlife surveys in Appendix E1, Updated Study Report, 

PG&E states that habitat for the San Joaquin kit fox occurs within the USGS 7.5-minute 

Merced Falls quadrangle. PG&E states that an evaluation of project impacts on the San 

Joaquin kit fox is likely unnecessary because of a lack of sightings, prey base, and 

burrows and friable soils in the project area. Thus, PG& E did not indicate in its license 

application whether it proposes to use rodenticides at project facilities or any other 

pesticides to control rodents, which could ultimately affect the San Joaquin kit fox. 
295

FWS disagrees with PG&E’s reasoning for excluding an evaluation of project 

effects on the San Joaquin kit. FWS’ disagreement is based on detections of kit fox less 

than 6 miles from the project boundary with the presence of contiguous habitat from the 

detection sites to Merced Falls reservoir, and a lack of surveys for kit fox in the project 

area. FWS also comments that the lack of prey base is likely due to eradication efforts in 

the vicinity of the project and the resulting effects on burrows. FWS comments that the 

reservoir is likely a dispersal barrier for kit fox, and opening Merced Falls dam for fish 

passage may also affect kit fox dispersal. FWS comments that the use of rodenticides 

and insecticides should be addressed through ESA consultation. 

The Water Board [preliminary WQC condition 2] specifies that PG&E develop a 

pesticide use plan to protect state and federally threatened and endangered species, where 

pesticide use includes rodenticides. California DFW [10(j) recommendation 7] 

recommends an integrated pest management and pesticide use notification plan for 

undesirable vegetation, insects, and rodents. 

Our Analysis

Because PG&E did not provide information about the use of rodenticides or other 

pesticides in the project area or noise caused by project maintenance or recreation, we are 

unable to evaluate project effects on the San Joaquin kit fox. 

Conducting surveys in the project area would be necessary to document the use of 

habitat in the project area by San Joaquin kit fox. Additionally, data collected during 

surveys may provide information on the effects of the project on the dispersal of kit fox. 

Including the surveys as a component of a protection plan would allow for study results 

to be formally documented so that project effects on kit fox can sufficiently be evaluated

and appropriate protection and mitigation measures can be developed. Developing the 

plan in consultation with FWS, the Water Board, California DFW, and BLM would 

ensure that study protocols and protection and mitigation measures are consistent with 

agency guidelines. 

The use of rodenticides and insecticides affects kit foxes by poisoning its prey 

base, thereby contributing to mortality of kit fox. Other species that are vulnerable to 

rodenticides, burrow fumigants, and ultimately burrow collapse could also be affected. 

Requiring a component for pest management and pesticide use to be integrated with the 

control plan for noxious weeds and invasive plants would reduce effects of pesticides on 

kit fox as well as other species affected by rodent control methods. Including this 

component in the control plan for noxious weeds and invasive plants, would be consistent

with state and federal laws protecting threatened and endangered species, including the 

San Joaquin kit fox. 

We recommend developing a protection plan for the San Joaquin kit fox in 

consultation with FWS, the Water Board, California DFW, and BLM. The plan would 

include: (1) study methodologies and monitoring protocols to identify San Joaquin kit 

fox habitats within the project area; (2) an assessment of potential project effects on San 
296

Joaquin kit fox in the project area; (3) protection and mitigation measures; and 

(4) references to measures contained in other plans that would protect San Joaquin kit 

fox; and (5) descriptions of any exceptions to the prohibited use of rodenticides that 

would be considered emergencies and allowed by agencies and an explanation of why the 

emergency situations would supersede protection measures for the San Joaquin kit fox. 

With the development and implementation of the protection plan for the San 

Joaquin kit fox, the project is not likely to adversely affect the San Joaquin kit fox.

California Red-legged Frog—PG&E does not propose changes to project 

operation or construction activities; thus no effects on the California red-legged frog 

would be caused by project operation or construction activities. However, PG&E does 

not address the potential for the project to support bullfrogs and predatory fish, which in 

turn affect California red-legged frogs, nor does PG&E address the potential effects of 

controlling noxious weeds and invasive plants or other pests, on the California red-legged 

frog. 

PG&E does not propose any protective measures for the California red-legged 

frog because it asserts the frog does not occur in the project area. The Water Board

[preliminary WQC condition 9] specifies a frog monitoring program for the California 

red-legged frog, foothill yellow-legged frog, and western spadefoot. FWS [10(j)

recommendation 4] recommends a conservation plan for the California red-legged frog

that would include control measures for bullfrogs to reduce their effects on mortality of 

California red-legged frogs. FWS commented that Merced Falls reservoir is situated 

between two areas of potential breeding habitat for the California red-legged frog and 

that ESA consultation has not been concluded for the frog. In its reply comments, PG&E 

stated that the Water Board and FWS improperly impose conditions for California redlegged frogs because, as PG&E asserts, California red-legged frogs do not occur at 

the project. 

Our Analysis

PG&E conducted only reconnaissance level surveys and did not conduct protocol 

level surveys in areas of suitable habitat within the project area. FWS commented that 

Merced Falls reservoir has not been surveyed for California red-legged frogs, and that 

potential breeding habitat occurs 0.83 and 1.17 miles south of Merced Falls reservoir and 

also 1.13 and 1.25 miles north of the reservoir. The project area could therefore provide 

suitable habitat to frogs dispersing from the breeding areas to the north and south of the

reservoir. California red-legged frogs would be exposed to mortality risks while 

dispersing to habitat within the project area, and also when bullfrogs disperse into 

California red-legged frog habitat during routine drawdowns. Controlling predators of 

California red-legged frogs, particularly bullfrogs, has shown to be effective, based on 

information provided by FWS in its filing on July 22, 2014. 

Requiring control measures for bullfrogs to be detailed in a protection plan that 

includes surveys for California red-legged frogs, and in consultation with FWS, the 
297

Water Board, California DFW, and BLM, would ensure that survey protocols and 

protection measures are consistent with FWS and the Water Board’s recommendations, 

and that any mitigation measures are adequate. Requiring a conservation plan for the 

California red-legged frog would ensure that consultation has been completed and that 

the project would remain in compliance with the ESA. Including other federally listed 

and special-status amphibian species, such as the foothill yellow-legged frog and western 

spadefoot, in the plan per the Water Board’s recommendation, would further protect 

terrestrial resources in the project area, particularly these two species that are currently 

under review by the FWS.

It is also possible that the application of herbicides to control noxious weeds and 

invasive plants could affect the California red-legged frog and other amphibians in the 

project area. Requiring a formal plan that documents locations and timing of herbicide 

applications, relative to that of any documented occurrences of California red-legged 

frogs in the project area, would reduce potential effects of herbicides on California redlegged frogs.

With the implementation of these measures, the project is not likely to adversely 

affect the California red-legged frog. 

Valley Elderberry Longhorn Beetle—One blue elderberry shrub showing exit 

holes of the valley elderberry longhorn beetle on the bark occurs in the project area, on 

the northeast side of the impoundment. PG&E proposes no construction or maintenance 

activities that could affect habitat in the area where the blue elderberry shrub was located. 

Project maintenance activities such as vegetation maintenance, and recreation activities 

such as hiking, could affect the blue elderberry shrub. PG&E conducts weed control 

about twice yearly at the dam, at the River’s Edge Fishing Access area, and around gages 

to minimize the spread of noxious weeds.

PG&E does not propose a protection plan for the valley elderberry longhorn 

beetle. FWS commented that it considers exit holes in the bark of elderberry bushes to be 

extremely rare and to be evidence of occupation by the valley elderberry longhorn beetle. 

FWS [10(j) recommendation 3] indicates ESA consultation has not been concluded for 

this species. The Water Board [preliminary WQC condition 6] specifies a monitoring 

and conservation plan for the valley elderberry longhorn beetle.

Our Analysis

PG&E states that it proposes no construction; therefore, no maintenance activities 

would have no effect on the blue elderberry shrub and the valley elderberry longhorn 

beetle. PG&E also states that no maintenance activities would affect the blue elderberry 

shrub, because the periodic weed control would not be implemented in the near the shrub.

The presence of one blue elderberry shrub makes it reasonable to assume that other blue 

elderberry shrubs could occur in the project area over the term of a new license. It is also 

reasonable to assume that maintenance activities, such as the control of undesirable 

vegetation, and increases in recreation could occur over the term of the license. In these
298

cases, blue elderberry shrub(s) and valley elderberry longhorn beetles could be affected 

by the project. 

Marking the existing blue elderberry shrub, and consulting before implementing 

any future activities that could affect valley elderberry longhorn beetle habitat would 

minimize project effects on the valley elderberry longhorn beetle. Developing a 

protection plan for the valley elderberry longhorn beetle and its habitat would prevent 

unforeseen damage or removal of the shrub in the future, which would reduce the effects 

of the project on the valley elderberry longhorn beetle and its habitat. Consulting with 

FWS, BLM, California DFW, and the Water Board to develop the plan would ensure 

consistency of protocols and complete consultation requirements with FWS. 

Additionally, developing a formal plan for the control of noxious weeds and 

invasive plants would reduce the potential effects of vegetation management on blue 

elderberry shrubs, and integrating pest management into the plan would reduce potential 

effects of any pesticides on valley elderberry longhorn beetles. 

With the implementation of these measures, the project is not likely to adversely 

affect the valley elderberry longhorn beetle. 

3.3.3.3 Cumulative Effects

Based on our review of the license application and agency and public comments, 

we have identified the federally listed San Joaquin kit fox and California red-legged frog 

as resources that may be cumulatively affected by the proposed continued operation of 

the project in combination with other past, present, and foreseeable future activities.

San Joaquin Kit Fox

Project facilities and maintenance activities of the Merced River and Merced Falls 

Projects would result in direct and indirect effects on the San Joaquin kit fox that when 

considered in concert with other activities in the basin, would further contribute to the 

cumulative adverse effects on the San Joaquin kit fox. 

The Merced Falls Project dam could directly affect the San Joaquin kit fox by 

acting as a dispersal barrier for kit fox, despite the fact that McSwain dam and the 

Hornitos Bridge provide dispersal corridors. Project activities, particularly those 

occurring at dusk and dawn, would directly affect kit fox through disturbance. The use of 

pesticides, including rodenticides, burrow fumigants, and insecticides would have both 

direct and indirect effects on the San Joaquin kit fox. Rodenticides and insecticides 

commonly used around businesses and homes in the basin directly affect the San Joaquin 

kit fox by poisoning its prey. Rodenticides and burrow fumigants have been widely used 

in ground squirrel eradication programs in the basin, directly and indirectly affecting the 

species by poisoning the prey and reducing the prey base of the San Joaquin kit fox, 

respectively. The magnitude of the effects of pesticides is difficult to discern because of

the effects of unregulated pesticide use on private lands in the basin. As noted by FWS, 
299

the San Joaquin kit fox populations in the project vicinity are likely suppressed as a result 

of the basin-wide ground-squirrel eradication programs and predation pressure. 

Proposed measures for the Merced River Project and agency conditions and 

recommendations for both the Merced River and Merced Falls Projects impose limits and 

regulations on the use of any pesticides at the projects. These limits and regulations 

would protect San Joaquin kit fox and other species dependent on ground-squirrel 

burrows and potentially affected by the use of rodenticides and burrow fumigants. Other 

project effects would be mitigated by developing and implementing the staffrecommended protection plan for the San Joaquin kit fox and developed in consultation 

with FWS, California DFW, the Water Board, and BLM. The plan would include 

management goals and objectives and describe and assess project-related effects on San 

Joaquin kit fox. It would also identify methods to mitigate ongoing project-related 

effects. Based on the above, we conclude that implementation of the protection plan 

would reduce any project-related cumulative effects associated with operation and 

maintenance of the Merced River and Merced Falls Projects. 

California Red-legged Frog 

Hydropower projects and the associated operation and maintenance activities for

the Merced River and Merced Falls Projects would result in direct and indirect effects on

the California red-legged frog that would be further contribute to cumulative effects on

California red-legged frogs in the basin. These adverse cumulative effects would be 

compounded by undocumented activities on private lands that cannot be quantified or 

analyzed in the scope of cumulative effects. 

Reservoirs of hydropower projects typically support bullfrogs and predatory 

fishes, which directly affect California red-legged frogs through increased predation. 

Operation and maintenance activities of hydropower projects, particularly drawdowns, 

cause bullfrogs to disperse from the reservoir to habitat areas where California red-legged 

frogs occur. Therefore, drawdowns at one reservoir would adversely affect California 

red-legged frogs at the other project by possibly increasing predation pressure. This is of 

particular concern because the Merced River Project area overlaps with the Piney Creek 

core area of the Recovery Plan of the Red-legged Frog (Rana aurora draytonii). As 

such, bullfrog control measures implemented at the Merced Falls Project area would 

facilitate the objectives for controlling bullfrogs at the Piney Creek core area and the 

Merced River Project area. Moreover, bullfrog control at Merced Falls is important even 

though California red-legged frogs have not been observed in the Merced Falls Project 

area, because frogs dispersing from breeding habitats outside the project area would be 

adversely affected by bullfrogs once inside the project area. Herbicides would also affect 

California red-legged frogs, both directly at the time of application and indirectly as these 

pesticides could mobilize in water or break down to components that could also affect the 

species. 
300

Agency conditions and recommendations to protect the California red-legged frog 

at both the Merced River and Merced Falls Projects would reduce project effects on the 

this species by identifying goals and objectives, assessing project-related effects on 

California red-legged frogs, and mitigating for ongoing project effects. Developing and 

implementing a protection plan in consultation with FWS, California DFW, the Water 

Board, and BLM, and including other potentially occurring federally listed and specialstatus species, such as the foothill yellow-legged frog and western spadefoot, would 

protect other amphibian species of concern to agencies. Based on the above, we conclude 

that implementation of the protection plan would reduce any project-related cumulative 

effects in the basin associated with operation and maintenance of the Merced River and 

Merced Falls Projects.

3.3.4 Recreation Resources

3.3.4.1 Affected Environment

The regional recreation resources in the vicinity of the two projects are primarily 

associated with the Merced River extending from the crest of the Sierra Nevada 

Mountain range to the San Joaquin Valley of central California. Approximately 30 miles 

upstream of the project, the Merced River flows through Yosemite National Park, which 

is the most important regional recreation resource. Yosemite National Park annually 

receives about 4 million visitors, who enjoy sight-seeing, camping, hiking, rock climbing, 

water sports (e.g., waterskiing), and other outdoor activities (Park Service, 2013). Public 

lands managed by the Forest Service and BLM extend to the west of Yosemite National 

Park and offer opportunities for developed camping and scenic viewing along the 

designated Wild and Scenic River portion of the Merced River. Upstream of the project 

the Merced River provides whitewater boating opportunities from Yosemite National 

Park to Lake McClure. Within the park, whitewater boating is not allowed, except at one 

small area in Yosemite Valley. Proceeding downstream beyond the park boundary, the 

river has class IV to V rapids48 and it is not commonly boated until near the community 

of El Portal, at which point commercial and private whitewater boating takes place. 

Boaters typically take out about 11 miles downstream at Briceburg (see figure 3-1). 

 

48 The American Whitewater Scale of River Difficulty: Class I, Easy: fast moving 

water with riffles and small waves; Class II, Novice: straightforward rapids with wide, 

clear channels which are evident without scouting; Class III, Intermediate: rapids with 

moderate, irregular waves which may be difficult to avoid and which can swamp an open 

canoe; Class IV, Advanced: intense, powerful but predictable rapids requiring precise 

boat handling in turbulent water; Class V, Expert: extremely long, obstructed or very 

violent rapids which expose a boater to added risk; Class VI, Extreme and Exploratory: 

runs that have almost never been attempted and often exemplify the extremes of 

difficulty, unpredictability, and danger.
301

Downstream of Briceburg, the Merced River has class IV and one class VI rapids. This 

reach is about 13 miles long and boaters take out at the project reservoir near Shepherd’s 

Point, Bagby campground, and Bagby boat launch (American Whitewater, 2013). 

Upslope of the river corridor, the road system provides general access to public lands for 

dispersed recreational uses (Forest Service, 2003). 

Downstream of the project, the Merced River flows into the San Joaquin Valley 

where there are many cities, rural residences, and agricultural farms. Most land along the 

Merced River downstream of the project is privately owned but there are limited 

opportunities for fishing, walking, bicycling, swimming, and floating (University of 

California, Merced, 2013). Class I and II whitewater boating opportunities exist on the 

nearly 50-mile-long reach of the Merced River downstream of the public access point just 

below Crocker-Huffman diversion dam to the confluence with the San Joaquin River 

(American Whitewater, 2013).

Additional recreation resources in the vicinity include State Route 49 (known as 

the Golden Chain Highway) and Lake Don Pedro. State Route 49 is a 317-mile state 

highway that is eligible for state scenic highway designation. This route is popular for 

scenic driving through river canyons and the scattered small historic towns established 

during the gold rush era located in the foothills of the Sierra Nevada Mountains

(Geotourism Mapguide, 2013). State Route 49 crosses the Merced River at the upstream 

end of Lake McClure.

Lake Don Pedro, which impounds the Tuolumne River, is about 5 miles northwest 

of Lake McClure (Turlock Irrigation District, 2013). This reservoir is owned and 

operated by Turlock and Modesto Irrigation Districts together with the city and county of 

San Francisco. The reservoir is similar in size and character to Lake McClure with many 

developed facilities for popular recreation activities including boating, fishing, camping, 

water sports, swimming, picnicking, bicycling, and hiking.

Merced River Project

Project Recreation Resources

Lake McClure—At a NMWSE of 867 feet, Lake McClure extends 19 miles 

upstream from New Exchequer dam, has a surface area of 7,110 acres, and a shoreline 

length of approximately 82 miles. License article 44 requires that Merced ID make every 

reasonable effort to maintain the water surface elevation of Lake McClure as high as 

possible from April through October to be consistent with the primary purposes of the 

reservoir49 and maintain a minimum pool of no less than 115,000 acre-feet (a reservoir 

 

49 MID operates the project for flood control, water supply, recreation, 

hydropower, and environmental purposes.
302

elevation of about 640 feet), except when a drawdown is necessary to maintain minimum 

streamflow as required by license article 40. Typically, the reservoir is at its highest level 

in June or July, recedes through the summer, and falls to its lowest elevation in October 

where it remains until the reservoir begins to fill again in the spring. Figure 3-38 shows 

typical reservoir elevations that occur in different water year types. In general, the 

reservoir only achieves the maximum elevation in above normal water year types. 

During critically dry water years, the reservoir can be more than 125 feet lower than the 

maximum water surface elevation during the summer months. Three of the five boat 

ramps at the reservoir, Barrett Cove (north and south) and McClure Point, are 

functional50 year-round in all water year types. The boat ramp at Horseshoe Bend is 

functional year-round in below normal, above normal, and wet water year types. The 

boat ramp at Bagby is functional year-round in above normal and wet water year types.

The shoreline is steep and mainly undeveloped, except in the vicinity of the four 

recreation areas. Although there is public access along most of the shoreline, the steep 

shoreline is not very suitable for recreational use. The reservoir has four branch-like 

arms in the shape of a letter H (see figure 1-2). The widest arm of the reservoir is near 

the dam and the other three arms wind up narrow canyons. Merced ID reports extremely 

low boating density during peak recreation season with, on average, less than one 

watercraft per acre, regardless of water year type. Motorized boats (i.e., power boats, 

houseboats, personal watercraft) were the most common watercraft observed on Lake 

McClure; a few canoes and kayaks were occasionally observed. Boating regulations on 

Lake McClure include: (1) all boats must travel in a counterclockwise rotation on the 

reservoir; (2) waterskiing is prohibited in the reservoir arms adjacent to any of the four 

project recreation areas and in other marked, smaller arms of the reservoir; and 

(3) boaters must obey posted speed limits during the daytime and not exceed 10 miles per

hour during the nighttime (Mariposa County Code Title 12, Chapter 16). In addition, as 

part of normal operation, Merced ID installs signs and buoys where water hazards exist 

along the reservoir throughout the year to ensure public boating safety and, as necessary, 

prohibits boats from accessing portions of the reservoir at lower water levels.

 

50 Water surface is no less than 3 feet above the end of the constructed launch lane.
303

Notes: Break in water surface elevation line in this figure is because of the water year 

change (i.e., the water year runs from October 1 through September 30 of the 

following calendar year).

RA – recreation area

NMWSE – normal maximum water surface elevation

Figure 3-38. Water surface elevation of Lake McClure in different water year types

(Source: Merced ID, 2013b).

Lake McClure supports a warmwater fishery, dominated by threadfin shad and 

black bass, and a coldwater fishery of rainbow trout, Chinook salmon, and kokanee. 

California DFW manages Lake McClure primarily as a put-and-take fishery for rainbow 

trout, although in 2004 and 2005, Chinook salmon and kokanee were stocked for 

managing as a put-and-grow fishery. Black bass is the most commonly caught species in 

the reservoir, and rainbow trout is the second most commonly caught species. May 

appears to be the most popular time of the year for fishing in the reservoir.

McSwain Reservoir—At a NMWSE of 399.0 feet, McSwain reservoir extends 

6.3 miles upstream from McSwain dam, has a surface area of 310 acres, and a shoreline 

length of approximately 12.5 miles. Operated as a re-regulating afterbay for flows 

released from Lake McClure, the reservoir water surface elevation fluctuates throughout 

the year, but the water surface elevation remains fairly constant within about 7.5 feet 

(between elevation 391.5 and 399.0 feet). Unplanned outages or unexpected events 

500

550

600

650

700

750

800

850

900

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Water Surface Elevation (WSE) (ft)

Month

Critically Dry

Dry

Below Normal

Above Normal

Wet

Bagby RA

Barrett Cove RA

(south ramp)

Horseshoe Bend 

RA

McClure Pt. RA

Barrett Cove RA 

(north ramp)

NMWSE
304

occasionally cause the water surface elevation to be lower than 391.5 feet. Figure 3-39

shows typical reservoir elevations that occur in different water year types. The boat ramp 

at McSwain recreation area is functional year-round in all water year types.

Note: RA – recreation area boat ramp elevation

WSE – water surface elevation

Figure 3-39. Water surface elevation of McSwain reservoir in different water year types

(Source: Merced ID, 2012e).

The shoreline is steep and mainly undeveloped, except in the vicinity of one 

recreation area. Although the shoreline of the long and narrow reservoir is publically 

accessible, it is not very suitable for recreational use. Boating speed on the reservoir is 

restricted to 10 miles per hour on the entire reservoir (PaddlingCalifornia.com, 2013),

and Merced ID reports extremely low boating density during the peak recreation season 

with, on average, 0.5 water craft per acre. About two-thirds of the boating use consists of 

motorized boats (power boats) and one-third of the boating use consists of non-motorized 

boats (i.e., canoes, row boats, and kayaks). California DFW stocks the reservoir with 

trout and manages the reservoir as a put-and-take fishery. Anglers most commonly catch 
305

rainbow trout in the reservoir, and May appears to be the most popular time of the year 

for fishing in the reservoir.

Project Recreation Facilities

Exhibit R drawings (filed in 1963 and revised in 2007) depict the four project 

recreation areas at Lake McClure and one recreation area at McSwain reservoir. The 

recreation areas provide developed facilities for camping, picnicking, swimming, and 

launching boats. Figure 1-2 shows the location of the recreation areas, and table 3-22

lists the facilities provided at the recreation areas and their capacities. Campgrounds 

typically have flush restrooms, showers, trash receptacles, and potable water spigots 

distributed within the campground; each campsite typically has a picnic table, pedestal 

grill, food locker, and paved or gravel surfaced parking spur. Some campsites have 

water, septic, and power for recreational vehicles. Picnic areas typically have flush 

restrooms, potable water spigots, a parking area, and picnic sites with a table and pedestal 

grill. Some group picnic areas have shelters, sinks, and food preparation areas.

Swimming beaches typically have a parking area, flush restrooms, showers, and picnic 

sites each with a table and pedestal grill. Marinas typically provide a parking area, flush 

restrooms, watercraft rentals, and slips. Boat launches typically have a parking area, 

concrete surfaced launch lane(s), courtesy docks, restrooms, watercraft rentals, and slips.

Merced ID owns and operates all of the project recreation facilities. Except 

Shepherd’s Point, within the Bagby recreation area, the four recreation areas are open for 

public use year-round. When recreation use declines between Labor Day and Memorial 

Day, Merced ID closes some of the campground loops and other facilities. This strategy 

allows for operational efficiency yet maintains sufficient capacity for public use. 

Shepherd’s Point is typically open for public use from Memorial Day through October; 

the opening and closing dates depend on weather and road conditions.

Based on Merced ID’s condition and accessibility assessments, most of the 

campground loops are in poor or fair condition; very few are in fair to good condition. 

The boat launches are in fair to good condition and picnic areas are in fair condition. 

With a few exceptions (Barrett Cove [north and south], Horseshoe Bend, and Bagby boat 

launches), project recreation facilities do not comply with applicable accessibility 

guidelines.

Two recreation trails are located within the project boundary at Lake McClure 

(figure 3-40). The 6-mile-long segment of the Merced River trail on the north shoreline 

of Lake McClure follows an old railroad grade that was used for access to what is now 

Yosemite National Park. The trail crosses two drainages, David and Solomon gulches, 

and is located on both Merced ID and federal land. The trail is not maintained and is in 

poor condition (e.g., being debris-covered and eroded). The majority (approximately 59 

percent) of the segment within the project boundary—from RM 85.2 downstream to 

RM 79.4—is located below the NMWSE and is inundated when the reservoir is full or 

nearly full (Merced ID, 2011f). 
306

Table 3-22. Recreation facilities and capacities at project recreation areas (Source: 

Merced ID, 2012a).

Recreation Area Facility

Camp 

Sites

Picnic 

Sites

Parking 

Spaces

Boat 

Ramps

Lake McClure

McClure Point Campground 101 -- 14 --

Picnic area -- 8 8 --

Swimming beach -- 22 60 --

Marina -- -- 50 --

Boat launch -- -- 140 1 (3 lanes)

Barrett Cove Campground 275 -- 39 --

Swimming beach -- 13 30 --

Boat 

launch/marina

-- 6 267 2 (5 lanes)

Overflow parking -- -- 35 --

Horseshoe Bend Campground 109 1 -- --

Swimming beach -- 12 50 --

Boat launcha-- -- 49 1 (2 lanes)

Bagby Bagby 

campground

30 -- 22 --

Shepherd’s Pointb 15 -- -- --

Boat launch -- -- 31 1 (2 lanes)

On-reservoir Floating 

restrooms (3)

-- -- -- --

McSwain Reservoir

McSwain Campground 112 -- -- --

Picnic area -- 56 -- --

Swimming beach -- -- -- --

Boat 

launch/marina

-- -- 89 1 (2 lanes)

a Boat cleaning and fish cleaning stations also are provided.

b One vault restroom is available, but potable water is not provided. 
307

Figure 3-40. Trails located within the project boundary at Lake McClure (Source: Merced ID, 2012a).
308

A second trail, unnamed and approximately 3 miles long, is located mostly above 

the normal maximum reservoir elevation on the south shoreline to the east of Shepherd’s 

Point and proceeds upstream to Sherlock Creek. The trail is located on Merced ID, 

private, and federal lands and provides non-motorized trail opportunities including 

hiking, mountain biking, and equestrian use. The trail is not maintained and varies in 

width from several feet to less than 1 foot due to overgrown vegetation. It is not known 

if the trail was formally constructed or informally developed over time by shoreline users.

Recreation Activities and Use

Most visitors using McClure Point, Barrett Cove, Horseshoe Bend, and McSwain 

recreation areas are residents of nearby Merced and Stanislaus Counties. Most of the 

visitors using the Bagby recreation area are Mariposa County residents.

Lake McClure provides a setting for many water-based recreational activities. 

Lake McClure supports year-round fishing, including bass tournaments. Houseboating 

and water sports (e.g., waterskiing and wakeboarding) are also popular activities at the 

reservoir, and commercial marinas provide boat rentals and slip rentals; boat launches 

provide access to the reservoir surface. Merced ID regulates houseboating using its 

permit system. Popular land-based activities at the project include camping, picnicking, 

swimming, hiking, and walking. Overall, the two most popular activities at the reservoir 

are camping and fishing.

The 10-mile per hour boating speed limit strongly influences water-based 

recreation on McSwain reservoir. Consequently, McSwain reservoir receives more nonmotorized and low-speed watercraft use than Lake McClure. Recreation facilities at the 

reservoir provide opportunities for camping, picnicking, swimming, and boat launching.

The annual project recreation visitation in 2010 was nearly 1.9 million recreationdays.

51 Visitation at Lake McClure—1.4 million recreation-days—was three times 

greater than visitation at McSwain reservoir—482,030 recreation-days. About half of the 

visitor use at Lake McClure occurs during the non-peak season (Labor Day to Memorial 

Day); however, about 70 percent of the visitor use at McSwain reservoir occurs during 

the non-peak season. By 2050, the annual recreation visitation is projected to increase to 

about 3 million recreation-days at Lake McClure and about 1.2 million recreation-days at 

McSwain reservoir, a 132 percent increase.

In 2010, weekend campground occupancy at Lake McClure (except Shepherd’s 

Point) ranged from 28 to 33 percent. The occupancy of Shepherd’s Point in 2010 was 15 

percent on weekends. McSwain campground had the highest 2010 occupancy at 50 

percent. The weekend occupancy in 2050 is projected to range from 26 to 57 percent at 

 

51 A recreation-day is a visit by one person for recreational purposes during any 

24-hour period.
309

Lake McClure, but the weekend occupancy at McSwain campground is projected to be 

87 percent.

Weekend occupancies for day use facilities (e.g., swimming beaches and picnic 

areas) in 2010 ranged widely from 2 to 56 percent with the highest occupancy occurring 

at swimming beaches and picnic areas. Similar to overnight use, the McSwain reservoir 

day use facilities are projected to have occupancy rates higher than those at Lake 

McClure.

At Lake McClure, only three parking areas had moderate overall occupancies 

between 30 and 45 percent and moderate to high weekend occupancies between 57 and 

81 percent in 2010. These included parking areas at the boat launches at McClure Point 

and Barrett Cove (north and south boat launches) recreation areas. The remaining 

parking areas had occupancies below 20 percent overall and 43 percent on weekends. By 

2050, occupancy at these same boat launch parking areas is projected to reach 45 to 67 

percent overall and 85 to 122 percent on weekends. Occupancy at the remaining parking 

areas is projected to be less than 30 and 65 percent overall and on weekends, 

respectively.

Recreation Needs

Recreation Survey Responses—Merced ID’s recreation surveys investigated user 

satisfaction with, and needs related to, reservoir levels, recreation facilities, user conflicts 

and crowding, recreation information, access, and recreation activities. At Lake 

McClure, most visitors were satisfied with the recreation facilities, information, and 

access provided at the project. The few visitor needs identified in the survey responses 

included new or improved boating facilities (launches, parking, and docks), picnic areas, 

and restrooms. Some visitors also identified the need for trails, improvements to 

swimming areas to increase swimmer safety, higher reservoir levels to improve scenic 

quality, and more access for fishing along the shoreline.

At McSwain reservoir, most survey respondents said they had no opinion about 

making improvements to boating facilities. However, 40 percent of day use respondents 

identified the scenic quality of the shoreline and the ability to access the shoreline as 

large problems. About 30 to 40 percent of all respondents identified the need to improve 

picnic areas, restrooms, and trash receptacles, and about half of the visitors indicated the 

need to improve vehicle parking areas.

Most of the respondents to Merced ID’s survey regarding the demand for trails 

were from Mariposa County, in particular, the towns of El Portal and Mariposa, and these 

visitors reported using trails a couple of times a year. Most visitors used the Merced 

River trail for hiking or walking, mountain biking, and nature viewing, and the trail is 

most often used from December through June. About half of the respondents indicated 

that barriers or conditions prevented or impaired their use of the Merced River trail 

between Bagby and Railroad Flat. Specific problems included trail condition, high water 

levels in tributaries, overgrown vegetation, downed trees, and eroded sections of the trail. 
310

Visitors reported using alternative trails including the section of the Merced River trail 

from Briceburg to El Portal, the Burma Grade trail near Briceburg, and Hites Cove trail 

near the confluence of the South Fork Merced and Merced Rivers. Just fewer than half of 

the survey respondents indicated a need for additional non-motorized trails in the vicinity 

of the project. Specific recommendations included trails: (1) across New Exchequer 

dam; (2) that connect Merced River trail to McSwain reservoir; (3) downstream of Bagby 

recreation area in the vicinity of State Route 49 to the small arm immediately south of 

State Route 49 bridge (about 0.5 mile); (4) around McSwain reservoir; and (5) upstream 

from McSwain recreation area (approximately 1 mile).

Recreation Needs Identified by Agencies and Stakeholders—Agencies and 

stakeholders provided comments that included recommended measures during the 

relicensing proceeding. These recommendations reflect a need to reconstruct, relocate, 

and maintain the Merced River trail and an unnamed trail on the south side of the Merced 

River that is in the vicinity of Bagby near the upstream extent of the project boundary. 

Additional trail needs include constructing and maintaining a new trail extending from 

Bagby recreation area to McSwain reservoir. Other needs identified relate to existing and 

new recreation facilities, recreation and flow information, monitoring, and flow releases.

Merced Falls Project

Project Recreation Resources

The Merced Falls impoundment is approximately 1-mile long with a total surface 

area of approximately 65 acres at a normal impoundment elevation of 344 feet above msl. 

The shoreline is 2.7 miles long. The project is operated in a run-of-river mode, which 

keeps reservoir fluctuations negligible. The impoundment is open for boating and fishing 

year-round and does not require a user fee.

PG&E allows public access to all licensee-owned lands, with the exception of 

those lands that enclose project structures. According to the Recreation Resource Report 

(2010), approximately 50 percent of the 1-mile northern shoreline of the impoundment is 

available to the general public for recreational access. The southern shoreline is mostly 

private property and has only a single egress point (canoe portage trail). 

The Merced Falls impoundment also supports a recreational cold-water fishery, 

which historically has been stocked by California DFW with catchable-sized trout. 

Below Merced Falls dam to Crocker Huffman diversion dam, the Merced River 

offers approximately 3.4 miles of Class I whitewater boating. A recreational boating 

study suggested minimum flows are above 250 cfs, while the American Whitewater 

website reports that minimum flows are around 300 cfs and high boatable flows are 

around 5000 cfs (American Whitewater, 2014).
311

Project Recreation Facilities

There are several formal and informal recreation facilities located at the Merced 

Falls impoundment (see figure 3-41). 

The River’s Edge Fishing Access area is located near the dam on the northern 

shoreline of the impoundment. The site encompasses 0.5 acre, supports paved parking 

for up to eight vehicles, and includes waste receptacles and landscaping. Boat launching 

and swimming at this site are prohibited. The Merced Falls Fishing Access area is 

located on the northern shoreline at the upstream end of the impoundment and includes a 

sign, restroom, a car-top boat launch, and parking to accommodate 15 vehicles with boat 

trailers and 30 vehicles without trailers. PG&E maintains the car-top boat launch at the 

Merced Falls Fishing Access area; however, all facilities at Merced Falls Fishing Access 

area are owned by Merced ID. 

Two informal, unpaved parking areas are located on either side of the Hornitos 

Bridge on the northern shoreline of the impoundment. The bridge features a pedestrian 

path that provides access to anglers. According to the Recreation Resource Report 

(PG&E, 2011b), these 2 parking areas can accommodate approximately 8 to 12 vehicles 

and serve as a location for informal car-top boat launching. However, many of these 

parking areas are located outside of the project boundary. 

There is a 0.4-mile-long informal, partially-paved angler trail located along the 

northern shoreline of the impoundment, which accounts for most of the 0.5 mile of 

publically accessible shoreline. A user-created canoe portage trail is located on the south 

shoreline of the impoundment. The trails allows boaters to take their boats out above 

Merced Falls dam, portage around the south side of the dam, and put their boats back on 

the water directly below the dam. The canoe portage itself is between 150 and 200 yards 

depending on the exact location of take out, and portions of the trail may be located on

private property. 

Recreation Activities and Use

Total recreation days supported by the project in 2002, according the 2003 FERC 

Form 80, were 7,000 annually, with a peak weekend average of 84 recreation days. The 

more recent 2009 FERC Form 80 states that total recreation days supported by the project 

were 2,500 annually, with a peak weekend average of 120 recreation days. Results from 

the Recreation Resource Report (PG&E, 2011b) visitor counts conducted on 5 days 

between May 11, 2010, and July 14, 2010, (two weekend days and three weekdays) 

found a daily average of 20 recreation days. 

Specifically, 80 percent of visitors surveyed at the project reported visiting the site 

before. These returning visitors visited the project an average of 16 times in the past 

year. The overwhelming majority of respondents reported zip codes that came from 

nearby communities in the Central Valley, with about 40 percent of respondents from the 

vicinity of the city of Merced. 
312

Figure 3-41. Map of recreation areas at Merced Falls Project (Source: PG&E, 2012).
313

Respondents also reported engaging in a small selection of recreation activities. 

Specifically, 92 percent of respondents reported fishing as their primary activity at the 

project, 5 percent reported visiting the project for multiple activities, and 3 percent

reported their primary activity as kayaking. Other activities visitors reported engaging in 

at the project included resting/relaxing, picnicking, motor boating, and photography. 

Recreation Needs

Use counts and capacity estimates from the Recreation Resource Report (PG&E, 

2011b) included both formal and informal recreation areas at the project. Table 3-23 

displays capacity estimates for parking, number of boats on the impoundment, and 

number of anglers on the shoreline for the project. The results presented in this table are 

based on average observed daily usage and peak observed daily usage during the 

Recreation Resource Study (PG&E, 2011b). 

Table 3-23. Recreation capacity estimates for Merced Falls Project (Source: PG&E, 

2011b as modified by staff).

Facility (Area) Capacity

Vehicle

Parking

Boats on

the

Reservoir

Anglers on

Shoreline

Total site capacity

46a 20b 53c

Average total daily observed use 9 2 20

Percent utilization based on average 

total daily observed use 20 10 38

Peak total daily observed use 14 3 34

Percent utilization based on peak total 

daily observed use 30 15 64

a Estimates of physical capacity for parking at both formal and informal sites.

b Estimates of recreational capacity for the reservoir assuming that each boat requires at 

least 3 acres of space. 

c Estimates of recreational capacity for the publically accessible shoreline assuming 

that each fishermen needs at least 50 feet of linear space. 
314

Future use at the project is expected to increase primarily due to population 

increases in the area. Between 2000 and 2010, the population of Merced County 

increased by 21.5 percent, Mariposa County increased by 6.5 percent, and the state of 

California increased by 10 percent. Because the project provides few and fairly specific 

amenities, recreation activity participation may only increase moderately in proportion to 

the population growth.

The recreation facility condition assessment in the Recreation Resource Report 

(2010) states that River’s Edge Fishing Access area is in “good” condition, while the 

informal angler trail and Merced Falls Fishing Access area “need repairs.” Specifically, 

the report notes that the informal trail needs vegetation clearing and the Merced Falls 

Fishing Access area parking lot needs grading and the potholes need to be filled. 

Merced ID conducted a recreational boating study on a 3-mile reach of the Merced 

River, from Merced Falls dam to Crocker Huffman diversion dam in 2010 and 2011. A 

focus group conducted as part of this study identified access to the riverine reach below 

Merced Falls dam as problematic. Vehicle and pedestrian access to the reach below 

Merced Falls dam does not exist because of private property restrictions. Currently, 

boaters launch in the Merced Falls impoundment and portage around the south side of 

Merced Falls dam. However, because the canoe portage trail may be located on private 

property, there is a potential for trespassing issues.

3.3.4.2 Environmental Effects

Merced River Project

To address project effects on recreation resources Merced ID proposes to 

(1) implement its Recreation Facilities Plan (measure RR1); (2) provide real-time 

information (flow and reservoir levels) and parking and signage for river access near 

Crocker-Huffman diversion dam (measure RR2); (3) make a good faith effort to maintain 

the water surface elevation of Lake McClure as high as possible from April through 

October and provide a minimum pool of no less than 115,000 acre-feet, except when 

necessary to maintain minimum streamflows (measure AQR2); (4) make a good faith 

effort to operate McSwain reservoir at an elevation no lower than elevation 388 feet, 

except when necessary to maintain minimum streamflows or make repairs (measure 

AQR2); (5) annually stock Lake McClure and McSwain reservoir for recreational 

fishing; and (6) implement ORV road closures at Piney Creek within the project 

boundary.

Recreation Facilities Plan

The project provides suitable settings for various recreational activities that, if 

unmanaged, could affect environmental and cultural resources. Merced ID filed a 

Recreation Facilities Plan with the license application (Merced ID, 2012a) to address this 

project effect and to provide visitors with a quality recreation experience. In its June 13, 

2012, letter, the Commission identified several inadequacies in Merced ID’s Recreation 
315

Facilities Plan and requested Merced ID revise and refile the plan. Merced ID (2012e) 

provided some of the additional details the Commission requested, and further revised its 

Recreation Facilities Plan on August 23 and September 22, 2014. Merced ID’s 

Recreation Facilities Plan is consistent with BLM preliminary 4(e) conditions 18, 19, 20, 

and 22 to designate a licensee contact person, annually coordinate with the BLM, 

implement a recreation facilities plan, and improve existing trails and provide additional 

trail access at the project. We analyzed the measures contained in the revised Recreation 

Facilities Plan provided by Merced ID (as filed with the August 21, 2014, alternative 

conditions).

Project Recreation Areas

Merced ID proposes to continue providing recreation facilities at the five project 

recreation areas (table 3-22). Merced ID also would be responsible for all annual 

maintenance, rehabilitation, and replacement of existing and proposed recreation 

facilities. The Recreation Facilities Plan defines and provides examples and frequency of 

actions that would be within the scope of operational maintenance. 

Merced ID would rehabilitate and replace, as necessary, all existing project 

recreation facilities. All new, rehabilitated, and reconstructed facilities would be 

designed and constructed to meet accessibility guidelines for privately owned or federally 

owned facilities, as applicable. Merced ID would be responsible for all costs (e.g., 

design, contract, permits, and construction) associated with constructing and 

reconstructing facilities located on its lands.

On BLM-managed land, Merced ID would be responsible for survey, design, 

contract preparation, and administration; environmental analysis (including any required 

additional site-specific resource studies) and documentation (including permits) 

necessary for construction or reconstruction. Facilities on BLM-managed land would be 

designed to the agency’s design standards, and BLM approval would be secured prior to 

constructing or reconstructing these recreation facilities. After construction, Merced ID

would provide BLM with as-built drawings of facilities located on lands the agency 

manages.

Attachments to the Recreation Facilities Plan provide: (1) aerial photographs of 

the five existing recreation areas with labels showing site details, such as locations of 

loops, boat launches, project boundary, marinas, and swimming areas; (2) facility 

inventory and condition and accessibility assessments (relicensing study results); and 

(3) site plans for the five existing recreation areas.

Our Analysis

All recreation use at the five recreation areas identified in the Recreation Facilities 

Plan is directly related to project reservoir use. Accordingly, Merced ID appropriately 

proposes to be responsible for operating and maintaining these facilities to provide safe 

and adequate public recreation facilities. Most of the existing recreation facilities are in 

need of rehabilitation because of their condition and non-compliance with applicable 
316

accessibility requirements. Implementing Merced ID’s proposal to rehabilitate and 

replace facilities would correct public safety issues, provide recreation facilities that are 

accessible to persons with disabilities, and address an identified visitor need for improved 

recreation facilities. Securing BLM approval of facility designs, as proposed, would 

ensure these recreation facilities meet agency guidelines. 

New Project Recreation Facilities

New technologies, recreational activities and trends create a need for new types of 

recreation facilities or increased capacity. Merced ID proposes to provide the following 

additional facilities at the project recreation areas:

 McClure Point recreation area:

– concrete boat launch ramp, restroom, and paved parking area at the 

existing informal boat launch;

– aerator in the swimming area;

– up to 10 park model cabins with picnic tables and pedestal grills; 

– group day use area with shelter, picnic tables, pedestal grills, and 

restroom;

– additional sand at the existing swimming area and up to 10 additional 

picnic tables and pedestal grills; 

– up to two floating swim platforms; and

– potentially expanding the number of houseboat slips at the marina.

 Barrett Cove recreation area:

– aerator in the swimming area;

– additional sand at the existing swimming area and up to 15 additional 

picnic tables and pedestal grills;

– sand lot volleyball court and playground at the swimming area; 

– up to 12 park model cabins with picnic tables and pedestal grills; and

– potentially expanding the number of houseboat slips at the marina.

 Horseshoe Bend recreation area:

– one-mile-long, non-motorized loop trail and information board;

– aerator in the swimming area;

– additional sand at the existing swimming area and up to 10 additional 

picnic tables and pedestal grills;

– swim platform;
317

– sand lot volleyball court and playground at the swimming area;

– host site at the campground with septic system, power, and water; and

– up to 10 park model cabins with picnic tables and pedestal grills.

 Bagby recreation area:

– interpretive and educational displays at the boat launch parking area and 

campground;

– up to 12 park model cabins;

– gravel parking area with 10 spaces, including at least 2 trailer spaces, 

two-unit vault restroom, and take-out trail from the reservoir/river to the 

parking area at Shepherd’s Point primitive area;

– an upstream take-out facility, gravel parking area with 10 spaces, twounit vault restroom, and take-out trail from reservoir/river to the parking 

area at Sherlock Creek recreation area.

52

 McSwain recreation area:

– non-motorized shoreline trail between the day use area and New 

Exchequer dam (about 4.1 miles, native surfaced);

– information board at existing, native surfaced parking areas and 

directional signs on Lake McClure Road;

– up to 12 park model cabins; 

– paved bicycle lane (about 5 miles) on Lake McClure Road from County 

Road J16 to near New Exchequer dam;

– additional sand at the existing swimming area and extend beach to the 

east by up to 50 percent; and

– up to two swim platforms.

 New Mack Island non-motorized recreation area:

– non-motorized trails (paved and unpaved) for bicycle and pedestrian 

use;

– trailhead parking area with restroom;

– pedestrian bridge to Mack Island;

 

52 Merced ID proposes to develop an upstream take-out facility at Sherlock Creek 

only if BLM is able to secure public access to Mosher Road and ensures the road 

condition is suitable for vans/buses with trailers.
318

– up to 10 primitive campsites on Mack Island with shoreline trail access;

– up to two swim platforms; and

– watercraft restriction area between west shore of Mack Island and 

reservoir shoreline to the west.

 Maintain existing Merced River Trail (railroad grade trail along north 

shoreline) and provide:

– interpretive and educational display at the trailhead;

– pedestrian bridge over Merced river near Sherlock Creek recreation 

area; and

– new trail segment on the south shoreline of Merced River to the Bagby 

recreation area.53

Merced ID’s explanation of the need for new facilities follows (Merced ID, 

2012b):

 Aerators in swimming areas—No relicensing study results indicated a 

need for these improvements, but Merced ID believes these improvements 

would enhance the visitor experience.

 Designated swimming area with platforms—These facilities do not 

currently exist at McClure Point and Horseshoe Bend recreation areas 

where the steep shoreline limits suitability. These improvements would 

increase opportunities for swimming in safe locations (e.g., providing 

designated areas where boating is restricted).

 Park model cabins—These facilities do not exist at the project but are 

commonly offered at large recreation complexes. Merced ID believes 

these facilities would provide an upgraded camping opportunity that is not 

currently available at the project or other area reservoirs.

 Volleyball court and playground equipment—Providing these facilities 

would create consistency among the amenities provided at other project 

recreation areas and could more evenly distribute visitor use among the 

recreation areas.

 

53 Merced ID proposes to construct and maintain the pedestrian bridge and trail 

segment along the south shoreline only if all necessary lands have legal access through 

ownership or easements to allow public access to Bagby recreation area and BLM agrees 

to construct a bridge across the North Fork of the Merced River to allow safe public 

crossing during spring snow melt off and storm events.
319

 Non-motorized trail construction and recreation area—Relicensing study 

results indicate there is an unmet demand for non-motorized trail use at the 

project. Trails in the vicinity of Horseshoe Bend recreation area, along the 

McSwain reservoir shoreline, and at the new Mack Island recreation area 

would meet this need in the area of the project closest to the existing 

vehicle access points. These areas are also ones where the topography 

would be suitable for non-motorized trail development.

 Bicycle lane on Lake McClure Road—Visitors currently bike along the 

road, and this activity is projected to increase in the future. Providing a 

bicycle lane would improve safety for bicyclists and meet the future, 

increased demand for this activity. 

 Expanded houseboat slip capacity—Evaluating the need for and 

potentially providing additional houseboat slip capacity would respond to 

existing and future, increased demand for houseboating and the existing 

users’ preference for slips rather than moorings.

Our Analysis

The demand for day use and group day use is predicted to increase, particularly for 

the recreation areas near Merced and surrounding communities. Merced ID’s proposal 

for additional group day use areas and improvements at day use areas responds to this 

identified recreational need. Merced ID does not propose additional overnight capacity, 

which appears appropriate because according to occupancy data, existing and future 

demand for overnight use can be met with the existing number of campsites at the 

project. 

Merced ID proposes to develop non-motorized trails near the lower elevation 

portions of the project; however, visitor responses to the unmet demand trail survey 

indicate a need for non-motorized trail opportunities near Bagby, specifically, the Merced 

River Trail. The current condition of the Merced River Trail and periodic reservoir 

inundation discourages visitors from using this trail. Additionally, the trail along the 

south side of Lake McClure near Bagby is in poor condition. As proposed, the project 

would continue to affect the Merced River Trail because reservoir inundation would 

prevent public access and erosion would continue to wash out portions of the trail. 

Merced ID’s proposal to maintain the existing segment of the Merced River Trail along 

the north shoreline and construct a pedestrian bridge over Merced River to connect the 

trail segments would allow visitors to use the trail year-round without experiencing 

access issues due to inundation. In addition, developing a conceptual plan, in 

consultation with BLM, as specified in BLM preliminary 4(e) condition 20, for the 

Merced River Trail from McSwain dam to the Bagby recreation area would provide 

additional access to the reservoir shoreline and meet non-motorized trail demand at the 

project.
320

Merced ID also proposes new facilities for general recreational enjoyment. 

Merced ID believes aerators placed in swimming areas would enhance visitor use through 

improved aeration and circulation, but visitor survey responses did not indicate this need 

and relicensing studies did not indicate any water quality problems at the swimming 

areas. Providing aerators in swimming areas does not appear to address a project effect, 

but visitors may enjoy having water spraying in the swimming areas. Adding sand to the 

swimming beaches would improve beach suitability and address visitor needs for 

improved conditions at the swimming areas. Because playgrounds and volleyball courts 

are provided at some recreation areas, constructing these facilities at other recreation 

areas would offer consistent amenities among the recreation areas. This approach could 

better distribute recreational use across the recreation areas and reduce any effects of 

crowding on holidays or if use increases in the future.

Providing a paved bicycle lane would help meet an identified recreational need at 

the project and visitor safety would be improved along about 5 of the 7.8 miles of the 

project road between County Road J16 and the proposed parking area for the McSwain 

shoreline trailhead. However, it is not clear why the proposed route does not extend the 

length of the project road because the road extends almost another 3 miles to existing 

project recreation facilities and bicyclists would likely use this portion to the road.

Evaluating increased number of houseboat slips on Lake McClure, as Merced ID

proposes, would be an appropriate and responsible approach to determining whether 

additional slips are necessary and, if so, determining the suitable locations. Existing 

boating densities indicate there is additional capacity for houseboating on Lake McClure. 

An evaluation that considers the number of additional houseboats that could be safely 

accommodated on the reservoir would provide a means to ensure that crowding on the 

reservoir does not become an issue. Providing these additional facilities, if feasible, 

would respond to a future increase in demand for houseboating.

Merced ID proposes to construct the new Mack Island recreation area with 

campsites accessible by boat or non-motorized trail and with recreation improvements 

along the shoreline. Although additional overnight capacity does not appear necessary, 

providing these campsites would provide an opportunity not currently available at this 

part of the project. Considering the trail access that would be developed to the island 

would encourage user-created sites, designating campsites would be a proactive approach 

to managing overnight use in order to minimize resource damage (e.g., sites too close to 

the water and sanitation). Designating the shoreline for non-motorized uses, such as 

swimming, water play, and non-motorized boating, would minimize user conflict and 

provide for public safety by providing a location for water contact recreation that is away 

from areas where boats are launched.

Implementation Schedule for Recreation Enhancements

The implementation schedule provided in Merced ID’s revised Recreation 

Facilities Plan shows when it would rehabilitate and construct recreation facilities 
321

(Merced ID, 2014g). Table 3-24 shows the general span of time when Merced ID would 

rehabilitate or construct new facilities at the recreation areas during the first 15 years of a 

new license. Modifications to existing facilities for accessibility would be completed 

when the facility is rehabilitated. Merced ID would make a good faith effort to complete 

construction and reconstruction activities at a facility within 1 year of commencement. 

Merced ID may complete major capital improvements sooner than scheduled. Based on 

annual consultation with BLM, Merced ID may also adjust the schedule, as needed, for 

facilities located on BLM-managed lands. 

Table 3-24. Schedule for rehabilitating existing and constructing new recreation 

facilities (Source: Merced ID, 2012e, as modified by staff).

Project Recreation 

Area Description

Implementation

(within years of license 

issuance)

McClure Point Boat launch (new) and marina 1 to 2

Boat launch parking area, fish 

cleaning station, and restroom 3

Swimming area improvements 1 to 4

Campground loops 2 to 6

Circulation roads 2 to 7

Park model cabins (new) 3 to 7

Group day use area (new) 4 to 5

Barrett Cove Boat launch parking lots and 

overflow parking area 3

Swimming area improvements 4 to 5

Campground loops 8 to 13

Circulation roads 6 to 10

Park model cabins (new) 1 to 3

Horseshoe Bend Boat launch parking lot and 

swimming area improvements 3 to 5

Boat launch 12 to 13

Campground loops 2 to 4

Circulation roads 2 to 5

Park model cabins (new) 6 to 7

Pedestrian trail (new) 6
322

Project Recreation 

Area Description

Implementation

(within years of license 

issuance)

Bagby Boat launch 5 to 6

Campground 7

Shepherd’s Point 8

Circulation roads 6 to 7

Interpretive displays (new) 4

Mack Island (new) Trail and parking area 13 to 15

Swim area amenities and 

campsites 13 to 15

Circulation roads 13 to 15

McSwain Boat launch parking lot, marina 

and swimming area improvements 2 to 4

Boat launch 8 to 10

Picnic and day use areas 3 to 6

Campground loops 4 to 7

Circulation roads 3 to 7

Shoreline trail (new) 5

Park model cabins (new) 1 to 6

Paved bicycle lane on Lake 

McClure Road 9

Our Analysis

The construction and rehabilitation schedule would span the first 15 years of a 

new license; however, a new license would likely be longer than 15 years. Because most 

of the improvements would be completed within the first 7 years of a new license term 

with no provision for subsequent rehabilitation, facility conditions could degrade over the 

license term (which could be 30 to 50 years in duration) and public safety issues could 

develop later in the license term. Although the plan states that water systems would 

typically be replaced once during the license term, the schedule does not include water 

systems. Including water system assessments in the schedule would ensure adequate 

water systems are provided at the recreation areas. Staggering rehabilitation of loops 

within each campground over several years would ensure sufficient overnight capacity 

during reconstruction periods; however, visitors would be exposed to construction traffic 
323

and noise over a period of years. This effect could be reduced by planning activities after 

Labor Day and before Memorial Day. 

The schedule indicates rehabilitating existing facilities, in general, before trails 

and new facilities are constructed. Although this approach properly prioritizes correcting 

existing problems, rehabilitation of some campground loops with poor and inaccessible 

facilities would not begin until 8 years after license issuance. Safety concerns for the 

public using these facilities would increase because they would continue deteriorating for 

8 years before rehabilitation. In addition, these facilities would continue being 

inaccessible to persons with disabilities until rehabilitated. These effects would be more 

prominent at Bagby recreation area because alternative facilities are not available and the 

only accessible facilities are the boat launch parking area and restrooms at Bagby 

campground and boat launch.

Merced ID proposes to construct new facilities within 1 to 15 years of license 

issuance. In general, the park model cabins would be the first new facilities provided and 

the non-motorized trails would be the last facilities provided. This approach does not 

appear to prioritize the provisions of new facilities consistent with identified needs for 

recreation facilities and opportunities. For example, Merced ID states that visitors did 

not identify a need for park model cabins, yet these cabins would be provided as soon as 

1 year after license issuance. Similarly, visitor responses, the Statewide Comprehensive 

Outdoor Recreation Plan or SCORP, and agency and stakeholder comments indicate an 

existing and increasing future demand for non-motorized trail opportunities, but trails are 

the last new facilities that would be constructed. Consequently, it does not appear that 

providing new facilities according to the schedule would meet identified needs in a 

timely manner.

Recreation Monitoring Program

Project recreation use over the license term will change in response to many 

factors such as population growth, new technologies and changes in activity participation. 

To ensure recreation needs are addressed through the license term Merced ID proposes to 

implement a recreation monitoring program to estimate recreation use levels, identify 

recreation use effects, assess visitor tolerances for effects (e.g., crowding, user conflicts, 

and facility conditions), and management actions that could be used to address identified 

issues. The program includes standards for quantifying recreation management 

objectives that would prompt review for determining a need for management action. The 

plan contains standards for monitoring facility occupancy, perceived crowding, and user 

conflicts. Every 6 years, Merced ID would collect and compile facility occupancy data 

and conduct direct counts of activity type, people, vehicles, and watercraft at the project 

recreation facilities during the peak recreation season; visitor surveys would be 

conducted every 12 years. Monitoring would be accomplished in the first year after 

license issuance and every 6 years to coincide with Form 80 reporting. Through its 

monitoring program, Merced ID would collect information for completing Form 80 as 

well as information about a much wider range of project recreation use and effects.
324

The Recreation Facility Plan explains Merced ID’s approach for reporting 

monitoring results, consulting with BLM, and reviewing the plan for possible revision. 

As needed during the term of the license, Merced ID would meet annually with BLM to 

discuss measures needed to ensure public safety and provide for adequate protection and 

use of facilities located on BLM-managed lands. This annual meeting would provide the 

opportunity to identify upcoming recreation projects and to review, and possibly adjust, 

the schedule for completing recreation projects relative to logistics, permits, and other 

items requiring coordination. Merced ID would designate a liaison to coordinate with 

BLM as a single point of contact whenever planning, constructing or reconstructing 

recreation facilities, making major improvements, or performing major maintenance on 

BLM-managed land. Merced ID would report the recreation monitoring results to BLM 

and other unspecified agencies for a 60-day review period. Merced ID would review, 

update, and revise the Recreation Facilities Plan in consultation with BLM and other 

unspecified agencies. Merced ID would prepare plan updates affecting federal land in 

consultation with BLM. For plan revisions affecting other land, Merced ID would revise 

the plan in consultation with unspecified agencies. Merced ID would provide plan 

revisions to BLM and other unspecified agencies for a 30-day comment period prior to 

filing the plan with the Commission for approval.

Our Analysis

Monitoring recreation use would document whether or not project visitor needs 

are being met and would identify recreation use-related effects. The schedule and 

monitoring elements proposed are consistent with the Commission’s regulations related 

to filing Form 80 recreation use reports at 6-year intervals (18 CFR §8.11) and would 

provide adequate information for reporting use, adjusting recreation management actions 

(e.g., implementation schedule for facility development), and determining whether a 

Recreation Facilities Plan revision is necessary. Consulting with BLM would ensure 

agency coordination to protect environmental and cultural resources on federal land when 

constructing, operating, and maintaining recreation facilities. Providing recreation 

monitoring results to the California Department of Parks and Recreation, California 

DFW, and FWS in addition to BLM, providing additional input opportunities regarding 

potential recreation needs, consulting with these agencies, and FWS regarding plan 

revisions affecting non-federal land would enable input from these agencies to be 

considered during the plan revision and approval process.

Reservoir Level, Flow Information, and River Access Signage at Crocker-Huffman 

Diversion Dam

Reservoir levels and quantity of flow influence access, visitor satisfaction, and 

recreational use (e.g., watersports). Enabling visitors to know current reservoir levels and 

flows would allow them to know whether conditions are suitable for their activities and, 

if necessary, make alternative plans. To address this need, Merced ID would continue to 

provide a link on its website to California DEC where the following real-time 

information is provided: (1) levels of Lake McClure and McSwain reservoir; (2) Merced 
325

River downstream of Merced Falls; (3) Dry Creek near Snelling; (4) Merced River near 

Snelling; (5) Merced River at Cressey; and (6) Merced River near Stevinson. In addition, 

Merced ID would coordinate with California DWR to provide real-time flow for Merced 

River at Shaffer Bridge (USGS gage no. 11271290). If it is not possible to show the realtime flow at Shaffer Bridge, Merced ID would show this information on its website.

Merced ID would construct a parking area with an unspecified capacity and install 

river access directional signage at the existing gravel-surfaced parking area at Merced 

Falls Road near Crocker-Huffman diversion dam.

Our Analysis

Providing real-time, reservoir-level information would allow visitors to the project 

to know whether conditions are suitable for their planned activities. If necessary, visitors 

could adjust their destination or schedule to have more enjoyable trips that meet their 

expectations. 

Providing flow information would allow visitors using the Merced River 

downstream of the project to determine whether flow conditions are suitable for their 

planned activities. Because Merced ID measures flow downstream of the project, it 

would likely be straightforward for Merced ID to provide this information to the public. 

However, because this reach of the Merced River is outside of the project, it would not 

enhance project recreation use. Similarly, providing a parking area near CrockerHuffman diversion dam would improve access for non-project recreational use 

downstream of the project.

Lake McClure Water Surface Elevation

Reservoir water-surface elevations are a key factor in the functionality of boat 

ramps. As the reservoir level falls below the end of the surfaced ramp, boating access to 

the project reservoir can be limited when launching requires using the exposed shoreline 

that has unsuitable slope, rocks, and mud. Merced ID proposes to minimize this effect of 

reservoir drawdown by committing to make a good faith effort to maintain the water 

surface elevation of Lake McClure as high as possible from April through October and to 

provide a minimum pool of no less than 115,000 acre-feet, which equates to a lake level 

elevation of about 640 feet, except when necessary to maintain minimum streamflows.

Our Analysis

The content of the proposed measure is the same as license article 44 of the 

existing license. If the project were operated the same as it is currently operated, the 

effects on the boat ramps would be the same as those which currently exist—three of the 

five ramps function year-round in all water year types, one ramp functions year-round in 

below normal, above normal, and wet water year types, and one ramp functions yearround in only above normal and wet water year types. However, it is likely the “high as 

possible” elevation would be lower because more water would need to be released to 

meet generally higher proposed instream flow requirements. Similarly, the reservoir may 
326

more frequently fall below the target minimum pool elevation. It is not possible to 

quantify the effect on boat ramp availability because the measure is not a compliance 

target. However, any decreased availability would be temporary and minor and would 

affect only some of the boat launches because several boat ramps are functional even at 

low reservoir elevations. Providing real-time reservoir elevation information, as Merced 

ID proposes, would let visitors know whether conditions are suitable for their trip, further 

minimizing any potential effect of reservoir drawdowns.

McSwain Reservoir Minimum Water Level

To address the effects of potential reservoir drawdown on boating access for 

McSwain reservoir, Merced ID proposes to make a good faith effort to operate the 

reservoir at an elevation no lower than 388 feet, except when necessary to maintain 

minimum streamflows or make repairs. 

Our Analysis

It is not possible to quantify the effect on boat ramp availability because the 

measure is not a compliance target. The minimum reservoir elevation specified in the 

proposed measure should allow the boat ramp to remain functional, except when 

additional water may be needed to meet increased minimum flow requirements or make 

repairs. However, if the reservoir level declines below elevation 388 feet, the public 

could not use the only boat ramp at this reservoir, although it still may be possible to 

launch car-top boats. The cyclic reservoir fluctuations combined with possibly drawing 

down the reservoir below elevation 388 feet has the potential to strand boaters on the 

reservoir. Although this circumstance may only occur infrequently, the effect could be 

minimized by closely monitoring project operation and posting information at the boat 

ramp when circumstances exist that could potentially cause the boat ramp to be 

unavailable. Providing real-time reservoir elevation information, as Merced ID proposes, 

would also let visitors know whether conditions exist, or potentially exist, that could 

affect boat ramp availability.

Fish Stocking

Merced ID proposes to annually stock both Lake McClure and McSwain reservoir 

at historic levels. Specifically, Merced ID proposes to stock the following in Lake 

McClure: 32,000 to 70,000 catchable-size rainbow trout with a 5-year running average 

target number of 48,000 fish; 4,000 to 20,000 fingerling kokanee with a 5-year running 

average target number of 15,000 fish; and 35,000 to 75,000 fingerling Chinook salmon 

with a 5-year running average target number of 45,000 fish. In McSwain reservoir, 

Merced ID proposes to stock 1,000 to 2,000 catchable-sized rainbow trout with a 5-year 

running average target of 1,500 fish. Merced ID states it would consult with California 

DFW and use angler data from recreation monitoring to make decisions on stocking 

throughout the term of the license.

California DFW recommends Merced ID provide 55,000 pounds of hatchery 

salmonids to be stocked at the project reservoirs in the first two years of license issuance. 
327

In addition, California DFW recommends Merced ID develop a fish stocking plan for 

Lake McClure and McSwain reservoir, in consultation with California DFW and BLM, to 

include the annual funding of stocking in project reservoirs and annual consultation on 

fish stocking targets, fish species, acquisition of fish, and verification of the previous 

year’s stocking commitment. 

The Water Board specifies in preliminary WQC condition 16 that Merced ID 

develop and submit a fish stocking plan in consultation with the anadromous fish 

committee that it specified in its preliminary WQC condition 1 within 3 months of license 

issuance. In addition, the Water Board specifies Merced ID stock 32,000 to 70,000 

catchable-sized fish and 39,000 to 95,000 fingerlings in Lake McClure and 1,000 to 

2,000 catchable-sized rainbow trout in McSwain reservoir starting the first year of the 

new license term. The fish used to stock should be only native cold water species and 

should come from facilities free of invasive species.

The Conservation Groups recommend Merced ID stock Lake McClure with 

444,600 to 973,000 Southern Sierra Nevada DPS watershed genetically-compatible 

fingerling rainbow trout with a 5-year running average target number of 667,200 fish and 

40,000 to 90,000 fingerling Central Valley spring-run Chinook salmon evolutionary 

significant unit with a 5-year running average target number of 60,000 fish. In addition, 

the Conservation Groups recommend Merced ID stock McSwain reservoir with 1,000 to 

2,000 genetically catchable-sized rainbow trout with a 5-year average target number of 

1,500 fish.

Our Analysis

Angling is one of the primary recreational activities associated with the project. 

Stocking fish in both Lake McClure and McSwain reservoir would ensure that the 

recreational fishery is maintained for the term of the new license. Although PG&E’s 

proposal to stock both project reservoirs at historic levels would ensure the recreational 

fishery is maintained, the demand for angling at the project is projected to increase over 

the term of the new license. Both California DFW and the Water Board’s proposals for 

stocking numbers in Lake McClure and McSwain reservoir are comparable to PG&E’s 

proposed stocking numbers; the Conservation Groups proposed stocking numbers for 

Lake McClure seems excessive in comparison. It is difficult to determine if any of these 

stocking numbers would be adequate for the duration of the license. Developing a fish 

stocking plan would address fish stocking in Lake McClure and McSwain reservoir based 

on changes in recreational use, angling demand, availability of hatchery fish, and future 

California DFW fish stocking management targets. The plan would include annual 

consultation with California DFW, the Water Board, and other appropriate stakeholders 

to determine fish species, stocking numbers, and sizes and it would provide the flexibility

to increase or decrease stocking numbers, change fish stocking sizes, and change the 

frequency of annual consultation. The plan would also include stipulations for the 

acquisition of fish (e.g., native, cold water species from facilities free of invasive 

species).
328

Although the responsibility of fish stocking is mandated to California DFW by 

California law, we note that Merced ID is ultimately response for the management of all 

project reservoirs and would be responsible for the stocking of fish if required under a 

new license. 

Operation, Maintenance, and Administration 

BLM preliminary 4(e) condition 21 specifies that within 90 days of license 

issuance, Merced ID enter into an operation and maintenance agreement to provide 

annual funding in a contributed funds account set up by BLM to be used to offset 

operation, maintenance, management, and administration costs incurred while managing 

public use of BLM-administered lands in and around the project.

Our Analysis

It is appropriate for Merced ID to be responsible for operating and maintaining the 

facilities that support project recreation to provide safe and adequate public recreation 

facilities. Although BLM specifies Merced ID enter into an operation and maintenance 

agreement to provide funding for the agency to operate and maintain BLM-administered 

lands in and around the project, this mechanism would not relieve Merced ID of its 

responsibility to maintain project facilities at the project. Further, it is unclear how these 

funds would accomplish a project purpose or improve a project effect. Although the 

proposed funding is meant to offset operation, maintenance, and management costs, the 

Commission has no way of ensuring these funds would be used for project operation or 

maintenance activities.

Off-road Vehicle Access at Piney Creek

BLM specifies in preliminary condition 23 that within 1 year of license issuance 

Merced ID identify and map where ORV roads are and where they enter public land, 

whether road closure is feasible, determine physical road closures and signage where 

closure is not feasible, and provide law enforcement assistance to enforce road closures.

Merced ID’s proposal is consistent with BLM preliminary 4(e) condition 23, but 

limits ORV road closures at Piney Creek to ORV roads located on lands administered by 

BLM within the project boundary.

Our Analysis

BLM specifies the implementation of ORV road closures and signage at Piney 

Creek to prevent ORV access. Implementing road closures and installing signage would 

benefit project resources by preventing ORV use in undesignated areas, which can affect 

vegetation, habitats, and potentially, cultural resources. Although Merced ID proposes 

limiting ORV road closures to roads within BLM-administered lands, implementing these 

measures on all project lands at Piney Creek would stop further erosion and would ensure 

continued protection of the affected resources at the project in the area of Piney Creek.
329

Merced Falls Project

PG&E proposes no changes to the operation and maintenance of the Merced Falls’

project recreation facilities, including River’s Edge Fishing Access area and the car-top 

boat launch at Merced Falls Fishing Access area. PG&E would continue to allow free 

access to project waters. Monitoring recreation use and facility capacity levels would 

continue through the FERC Form 80 process every 6 years. 

Our Analysis

A number of formal and informal recreation sites exist at the Merced Falls 

impoundment. PG&E maintains the River’s Edge Fishing Access area and its associated 

sites, but there is also an informal angler trail along the northern shoreline and two 

informal parking areas on either side of the Hornitos Bridge. Although Merced ID 

maintains the majority of facilities at the Merced Falls Fishing Access area (restroom and 

parking area), recreationists depend on the other facilities at Merced Falls Fishing Access 

area to access the car-top boat launch. 

The Recreation Resource Report (PG&E, 2011b) notes that the parking facilities at 

Merced Falls Fishing Access area need repair. Specifically, the parking area is gravel 

with some potholes and could be graded or resurfaced to provide an improved surface for 

physically challenged recreationists. PG&E proposes to continue to operate and maintain 

the car-top boat launch; however, there is no assurance that the rest of the facilities at the 

Merced River Fishing Access area, or any of the informal recreation sites at the Merced 

Falls impoundment, would be maintained or remain accessible to the public over the term 

of a new license. While overall use at the project is low compared to upstream projects, 

recreation use54 is robust enough that access to both formal and informal recreation 

facilities at the project should be maintained. All the facilities are located within the 

project boundary and PG&E ultimately would be responsible to operate and maintain

them for the term of a new license. Further, PG&E’s proposal to continue to monitor 

visitor use and facility capacity levels through the FERC Form 80 process would help 

assess changes in recreational use and capacity at these facilities and ensure adequate 

recreation opportunities are provided over the term of a new license. 

Canoe Portage Trail

PG&E proposes to work with stakeholders to develop signage at the canoe portage 

trail to enhance safety for boaters using the site. 

The Conservation Groups propose that PG&E maintain the canoe portage trail 

around the south end of Merced Falls dam, including developing signage at the trail. 

 

54 Recreation use estimates from the Recreation Resource Report (PG&E, 2011b)

visitor count suggest that with a recreation season lasting from May 1 to September 30

(152 days), the project supported approximately 3,040 days in 2010. 
330

Our Analysis

The canoe portage trail around the south side of Merced Falls dam receives low to 

moderate use. PG&E maintains the relatively low quality of the boating experience at the 

project and the availability of other similar reaches in central California do not justify the 

cost to improve access below Merced Falls dam. PG&E believes that providing formal 

access to the downstream area below Merced Falls dam would likely require an easement 

across private property, which could entail a significant cost. 

Currently, boaters are forced to portage around the south side of the dam on 

private property to access the stream reach below Merced Falls dam. PG&E notes that

obtaining an easement would be a significant cost, however, it provides no evidence or 

cost estimates to formalize this undeveloped area (approximately 1,000 square feet) 

adjacent to the project. Formalizing the canoe portage trail and adding directional 

signage would ensure boaters have a clear and safe passageway around the dam and 

would decrease the chance of boaters unintentionally trespassing on private lands. 

McSwain Tailrace 

Merced ID’s application for the McSwain Project notes that there is an existing 

recreational facility at the McSwain tailrace for the Merced Falls Project. Although it 

cannot find supporting documentation, Merced ID states that PG&E constructed a small 

car-top boat launch that provides access to the Merced Falls impoundment. To ensure 

this facility continues to be available for public use, Merced ID proposes to assume 

operation and maintenance responsibility under the terms of an off-license agreement 

(Merced ID, 2013b). 

Our Analysis

Little is known about this recreation site’s current use, facilities, and condition 

because it was not included in the Recreation Resource Report (PG&E, 2011b) nor was it 

included in PG&E’s license application. An existing road, owned and maintained by 

Merced ID, located on the north side of the Merced Falls impoundment provides access 

to the tailrace water of McSwain powerhouse. However, Merced ID states that it does 

not currently use, and has not used, the road for project operation or project-related 

recreation for the McSwain Project. 

The need for this area as a specific recreation site is also questionable. 

Considering current use levels and the location of this recreation site near the Merced 

Falls Fishing Access area, this area may best serve the project as an informal public 

access. However, more information is needed to determine if a car-top boat launch does 

exists and if it is located within the Merced Falls Project boundary.

Fish Stocking

California DFW recommends that PG&E provide 11,000 adult-sized rainbow trout 

to be stocked at the Merced Falls impoundment for the first 2 years after license issuance. 
331

California DFW further recommends a fish stocking plan be developed for the Merced 

Falls impoundment for the rest of the license term. PG&E supports this recommendation.

Our Analysis

Angling is one of the most popular activities at the Merced Falls Project. 

According to the Recreation Resource Report (PG&E, 2011b), 92 percent of respondents 

reported fishing as their primary activity at the project. Stocking 11,000 adult-sized 

rainbow trout in the Merced Falls impoundment for the first 2 years after license issuance 

would allow PG&E to continue to provide angling opportunities at the project without 

disruption while PG&E develops a fish stocking plan with California DFW for the rest of 

the license term.

3.3.5 Land Use 

3.3.5.1 Affected Environment

Merced River Project

Overview

Land ownership within the project boundary is composed of federal land 

administered by BLM and land owned by Merced ID, and other private entities (table 

3-25). 

Table 3-25. Land ownership in the project boundary (Source: Merced ID, 2012b).

Development

Merced ID

(acres)

BLM

(acres)

Private

(acres)

Total

(acres)

New Exchequer 7,577.5 3,134.7 13.2 10,725.4

McSwain 907.5 20.2 0 927.7

Total 8,450.0 3,154.9 13.2 11,653.1

BLM administers public land at two of the project recreation areas—McClure 

Point and Horseshoe Bend. The marina access road and parking area for McClure Point 

recreation area are located on public land, and nearly all of the land, including the land 

underlying the developed recreation facilities at the Horseshoe Bend recreation area, is 

administered by BLM.

Mariposa County

All land within the existing project boundary is located within Mariposa County. 

The project includes a few small facilities located in Merced County, such as conduits for 

delivering water to the Merced NWR, but these are not located within the project 

boundary.
332

Land use within Mariposa County is varied and classified for either public or 

private use. Three broad areas of land use characterize the existing land use pattern in 

Mariposa County. In the eastern part of the county, federal land associated with 

Yosemite National Park dominates the land use pattern. In the western part of the 

county, where the project is located, land is primarily used for agricultural purposes. The 

remainder of the county is home to rural residential areas and small communities with 

commercial and industrial uses and high-density housing. Of the county’s approximate 

931,200 acres of land, 57 percent of this land is public land that encompasses Yosemite 

National Park, the Sierra and Stanislaus National Forests, and BLM-managed lands. 

Private land use accounts for about 43 percent of the land within the county.

Public land in Mariposa County is not subject to county jurisdiction. Mariposa 

County manages private land use to comply with the Mariposa County General Plan and 

county zoning ordinances. The Mariposa County General Plan has five land use 

categories, four of which are applicable to the project (table 3-26). 

Table 3-26. Mariposa County land use categories applicable to land located in the 

vicinity of the Project (Source: Merced ID, 2012a).

Land Use Category Description

Agriculture/Working 

Landscape

Lands for production, extraction, or harvesting of food, fiber, 

timber, and minerals on large parcels of 160 acres or larger.

Natural Resources Lands for open space, recreation, ecosystem conservation, 

watershed protection, environmental protection, conservation of 

natural resources and protection of health and safety.

Planning Area Special planning areas for which area plans are adopted by the 

board of supervisors. These are mini-general plans adopted to 

meet the needs of each town, community, or uniquely identified 

special area of the county. The nearest such area to the project is 

the Lake Don Pedro Town Planning Area.a

Residential Lands for single family dwellings outside the Planning Area land 

use classification.

a A Lake Don Pedro Town Plan has been proposed for the Lake Don Pedro subdivision 

located south of the project. There is no current information pertaining to when the 

Lake Don Pedro Town Plan may be approved and implemented. All lands that would 

be included in this Town Plan are currently categorized as Planning Study Area.

To the southwest of Lake McClure and around McSwain reservoir, land is 

designated as agriculture/working landscape. On the north, east, and west of Lake 

McClure and upstream along the Merced River, land is designated as Natural Resources 

land. Land along the northern half of the west shore of Lake McClure is designated as a 

planning study area; the area includes part of the Lake Don Pedro Town Planning Area, a 
333

planned residential area. The town of Coulterville just northeast of Lake McClure is also 

designated as a Town Planning Area, with residential land use and rural-scale 

development of “urban” center amenities to serve community needs. West of the project 

in the San Joaquin Valley lies an extensive network of irrigation canals, predominantly 

for agricultural and rural residential uses.

Public Land

A portion of the project is located on BLM-administered land and is managed as 

part of the Sierra Resource Management Area, which encompasses approximately 

230,000 acres in 16 counties, primarily in the foothills of the Sierra Nevada mountain 

range between Yuba and Mariposa Counties. BLM manages the Sierra Resource 

Management Area in accordance with the Sierra Resource Management Plan (BLM, 

2008). The Sierra Resource Management Plan identifies ACECs—areas of federal land 

where special management attention is required to protect relevant and important natural 

or cultural resource values. As shown in figure 3-42, three separate ACECs are located 

near the project: (1) Merced River, (2) Bagby Serpentine, and (3) Limestone 

Salamander, and were designated for the following purposes:

 Merced River ACEC—maintain consistency with Merced River’s 

designation as a Wild and Scenic River;

 Bagby Serpentine ACEC—protect the Henneke soil series and serpentine 

endemic species; and 

 Limestone Salamander ACEC—promote the recovery of listed species and 

improve the status of candidate and special-status species to eliminate the 

need to officially list these species. 

No special land use restrictions apply, at this time, to the Bagby Serpentine ACEC. 

BLM’s conservation strategy for the limestone salamander specifies the following 

guidance regarding activities in the Limestone Salamander ACEC: (1) prevent all 

surface‐disturbing activities that would alter or degrade confirmed or potential limestone 

salamander habitat on BLM-managed lands; (2) maintain vegetative cover in the ACEC 

within specification outlined in the Management Plan for the Limestone Salamander Area 

of Critical Environmental Concern; and (3) identify additional limestone salamander 

occurrences and consolidate BLM holdings within the species’ range and adjust ACEC 

boundaries as necessary.
334

Figure 3-42. Areas of critical environmental concern identified in Sierra Resource 

Management Plan (Source: BLM, 2008).

Specially Designated Areas at and near the Project

The main stem of the Merced River is a designated Wild and Scenic River from its 

sources—Red Peak Fork, Merced Peak Fork, Triple Peak Fork, and Lyell Fork on the 

south side of Mount Lyell in Yosemite National Park—downstream to the NMWSE of 

Lake McClure (elevation 867 feet). The South Fork Merced River is a designated Wild 

and Scenic River from its source near Triple Divide Peak in Yosemite National Park to 

the confluence with the main stem. Section 3 of Public Law 102-432 provides that 

Merced River’s Wild and Scenic River designation shall not affect the continued 

operation and maintenance of the project, including flood control operation, or the 

Commission’s authority to issue a new license for the project within the existing project 

boundary. Individual segments of the main stem and South Fork Merced River are 

managed by the Park Service, the Forest Service, or BLM. BLM manages the segment 

immediately upstream of the project extending to about 4 miles upstream of Briceburg 

under its Merced Wild and Scenic River Management Plan (BLM, 1991). By agreement 

with the Park Service and the Forest Service, BLM manages all commercial whitewater 

use of the Merced River between El Portal and Bagby.

No wilderness areas or National Scenic trails are located in the vicinity of the 

project.
335

Shoreline and Water Surface Management

Merced ID does not have a formal shoreline buffer zone policy for project 

reservoirs. Merced ID-owned and privately owned lands on project reservoir shorelines 

are managed in accordance with the Mariposa County General Plan. Federally owned 

lands along project reservoir shorelines are managed in accordance with BLM policies. 

Similarly, Merced ID does not have a formal written shoreline policy for permitting 

shoreline facilities (e.g., docks, piers, and bulkheads) on the project reservoirs, except to 

allow such development when it is consistent with Merced ID’s operational requirements, 

public safety, project recreation and other resource management plans, and compliance 

with all federal, state, and local regulations. 

Merced ID regulates houseboating on Lake McClure using a permit system and 

guidance provided in its Lake McClure houseboat policies (Merced ID, 2010b). The 

houseboat policy requires that houseboat permit holders conduct self-inspections. In 

2008, Merced ID reported 241 permits had been issued for houseboats on Lake McClure.

Wildland Fire Prevention and Suppression

Merced ID is unaware of any project-caused fires in the past 15 years, and it does 

not have a formal policy regarding fire prevention and suppression. If a fire were to 

occur at the project, Merced ID would notify appropriate emergency response agencies. 

Merced ID implements fire prevention measures (e.g., keeping available onsite shovels, 

water, and radios) when completing project work on BLM-administered land at the 

project. When burning project-related debris, Merced ID acquires permits and approvals 

from appropriate agencies and complies with any project-specific measures (e.g., burning 

during a certain time of day or year) that may be specified as part of a required permit.

Law Enforcement

Law enforcement at the project reservoirs and recreation facilities is shared 

between Mariposa County Sheriff’s Department and Merced ID. Funding for the 

Mariposa County sheriff's deputies to patrol and enforce the laws and regulations on the 

water at Lake McClure and McSwain reservoir is provided by California Department of 

Boating and Waterways. Mariposa County Sheriff’s Department deputized the Merced 

ID’s Parks Department rangers to provide law enforcement at the project’s land-based 

recreational facilities. However, rangers are not permitted to carry fire arms, and they 

rely on the Mariposa County Sheriff’s Department to respond to more serious incidents 

and violations.

The response time of the Mariposa County Sheriff’s Department to the project 

ranges from 30 to 60 minutes, depending on the location of the incident. Travel time 

from the lower elevation area of the project (McSwain reservoir) to the highest elevation 

area (Bagby recreation area on Lake McClure) is approximately 22 miles or 30 minutes 

by road. Law enforcement issues at the project reservoirs are frequently related to 
336

alcohol use (e.g., fights or loud noise from parties during quiet hours) graffiti, and 

occasionally weapons.

Project Access

Merced ID uses federal, state, county, and private roads to access the project. 

Vehicular access to McSwain dam and powerhouse and New Exchequer dam and 

powerhouse is by way of several Merced ID-owned roads that intersect Lake McClure 

Road. Lake McClure Road is within the project boundary from its intersection with 

County Road J16 to its terminus inside McClure Point recreation area. Project access 

roads that intersect Lake McClure Road include McSwain powerhouse access road, 

Village Drive, and Exchequer dam road.

Merced Falls Project

The Merced Falls Project is located on the border of Merced and Mariposa 

Counties. The county line bisects the project about midway through the Merced Falls 

impoundment nearly adjacent to the Hornitos Bridge. The total area within the existing 

project boundary is 75.6 acres, including 1.0 acre of federal land (table 3-27). 

Table 3-27. Land ownership in the project boundary (Source: PG&E, 2012).

Land Ownership Acres

Federal (BLM)a 1.0

Patented privately owned lands 54.1

Licensee-owned lands 20.5

Total 75.6

a Ownership of this land is uncertain due to an unresolved determination of navigability 

on the Merced River. See 45 FR 75214 (November 14, 1980). PG&E has been and 

intends to continue to assume these are federal lands, and to pay annual federal land 

charges thereon.

Within Mariposa County, the project is located on agricultural/working landscape 

designated lands. The goal of this land use designation is to maintain the economic use 

of the land, as well as the scenic and open space functions. 

Within Merced County, the project is located on agricultural designated lands. 

The agricultural designation serves to support productive agricultural lands and promote 

the agricultural industry. 

The nearest community to the project is Snelling, which is a small, unincorporated 

community in Merced County approximately 6 miles west of the project. The nearest 

incorporated community is the city of Merced, located approximately 24 miles southwest 

of the project. 
337

3.3.5.2 Environmental Effects

Merced River Project 

Project Boundary Adjustments

Merced ID proposes to adjust the project boundary to: (1) include land where the 

proposed Mack Island non-motorized recreation area would be located; (2) include the 

main access road to McSwain powerhouse; and (3) exclude land in the vicinity of 

McSwain dam. 

Our Analysis

In accordance with regulation, the project boundary must enclose all principal 

project works and lands necessary for operation and maintenance of the project and other 

project purposes, such as recreation, shoreline control, or protection of environmental 

resources (18 CFR §4.51). Including land in the project boundary where the nonmotorized recreation area would be located would ensure that the Commission would 

have the oversight necessary to require Merced ID to provide adequate public 

recreational access and use of these lands. Because the access road leading to McSwain 

powerhouse serves this sole purpose, it is, by definition, a project road and should be 

located within the project boundary to comply with Commission regulations. Merced 

ID’s proposal would add 215.59 acres for the recreation area and 1.06 acre for the road to 

McSwain powerhouse.

Removing lands from the project boundary is appropriate in situations where the 

land is not necessary for project operation and maintenance, including recreational 

purposes. Merced ID’s proposal would remove land in the vicinity of McSwain dam 

from the project boundary as shown in figure 3-43.
338

Figure 3-43. Land proposed for exclusion from the project boundary (Source: Merced ID, 2012a, Exhibit G)
339

Adjusting the boundary in the vicinity of McSwain powerhouse access road would 

remove about 30 acres of land that is also included in the Merced Falls Project boundary. 

An Merced ID-owned and maintained road, which is located on the north side of Merced 

Falls reservoir, provides access to the tailwater of McSwain powerhouse and one of 

several non-project related river access sites operated and maintained by Merced ID. 

Merced ID states that it does not currently use, and has not used, the road for project 

operation or project-related recreation, so Merced ID does not consider it to be a project 

road. Although it cannot find supporting documentation, Merced ID states that PG&E 

constructed a small car-top boat launch that provides access to Merced Falls reservoir. 

To ensure this facility continues to be available for public use if the land is removed from 

the Merced River Project boundary, Merced ID proposes to assume operation and 

maintenance responsibility under the terms of an off-license agreement (Merced ID, 

2013b). Removing the road from the project boundary would remove the Commission’s 

oversight of this area regarding recreational access to the project tailwater. However, 

because the road primarily provides access to Merced Falls reservoir (FERC Project No. 

2467), public access to the project tailwater would continue to be the responsibility of the 

Merced Falls licensee.

Merced ID proposes to remove some of its land along the Merced Falls reservoir 

shoreline from the project boundary. Merced ID leases this land for grazing and there are 

no project uses or project access on this parcel of land. This land lies within the Merced 

Falls Project boundary. If this land were removed from the Merced River Project 

boundary, Merced ID would still have sufficient access to operate and maintain the 

project. Public access for recreational use at the project would not be diminished because 

it is not adjacent to the project reservoir or any project recreation facility.

Management of Project-related Roads

Merced ID proposes to implement its proposed Transportation Management Plan

filed on September 22, 2014, to provide guidance for rehabilitating and maintaining 

project roads.55 The plan identifies and includes a map of six asphalt-surfaced project 

roads for a total of 12.9 miles, all of which are located on Merced ID-owned land. The 

plan does not address roads within project recreation areas because these roads are 

addressed in the Recreation Facilities Plan. The plan provides a programmatic approach 

for inspecting and maintaining the six roads and states that unspecified BMPs for road 

maintenance would be used to guide treatments and protect environmental resources. 

The Water Board specifies in preliminary WQC condition 21 that Merced ID 

develop a Transportation Management Plan within 1 year of license issuance to include: 

 

55 Roads within the project boundary that MID primarily uses to operate and 

maintain the project.
340

 a map identifying all roads associated with the project, appurtenant 

facilities, and locations of drainage structures, streams, surface water 

bodies, ephemeral and intermittent waters, wetlands, and equipment storage 

and service areas;

 a road inventory to address project use and non-project use of the roads, 

condition surveys, associated facilities, improvement needs, road closures, 

and safety, jurisdiction, and maintenance responsibilities; and

 an annual road monitoring and maintenance report to include conditions of 

roads, conditions of drainage structures and runoff patters after major storm 

events, measures to improve performance in comparison to the Forest 

Service’s National BMPs Road Management Activities, and a schedule for 

repair.

Our Analysis

In its letter to Merced ID dated June 13, 2012, Commission staff identified several 

inadequacies in the Transportation Management Plan filed with the final license 

application. Specifically, staff requested Merced ID to:

 revise table 2.2-1 in the plan to include all roads that provide access to 

project recreation facilities and identify each project facility accessed by 

all project road;

 revise table 2.2-1 to provide the number of lanes, road width, and buffer 

widths that extends to the project boundary, as appropriate, and indicate 

whether each road is open for public use and if there is any shared use;

 for any roads not open to the public, show gate locations on figure 2.2-1 of 

the plan; and

 revise the plan to include whether or not Merced ID proposes to add or 

remove any project roads from the existing project boundary and if 

Merced ID proposed to upgrade or change the level of public access for 

any existing project road.

Commission staff requested that Merced ID revise and refile the plan. In its 

response to the Commission dated October 10, 2012, Merced ID (2012e) stated it would 

revise and refile the plan to include the requested information and include an additional 

road segment. While Merced ID revised and refiled the plan on September 22, 2014, to 

include a list of roads within project recreation areas, the plan continues to lack adequate 

content for Commission approval. 

The transportation plan adequately identifies the six project roads that provide 

primary routes of access for operating and maintaining the project, including access to the 

existing and proposed recreation areas. In addition to lacking sufficient content for 

Commission approval, it does not include any details regarding the road condition survey
341

frequency, describe any approach for monitoring use over the term of the license, or 

identify BMPs that would be implemented, also specified by the Water Board in 

preliminary WQC condition 21. Because the plan does not include sufficient 

information, it is uncertain whether project roads would continue to meet needs for public 

recreational access. Although the Water Board specifies that the plan should use the 

Forest Service BMPs for guidance, no project roads are located on Forest Service land. 

In its response to comments, Merced ID stated it would use Merced County, Mariposa 

County, and/or BLM’s BMPs to identify road treatments to improve road performance. 

Including an inventory of current road conditions, measures to improve conditions 

according to relevant local, county and BLM BMPs, and an approach to monitor use over 

the term of the license would address the level of access that would be maintained 

through proper annual and long-term maintenance of project roads.

Fire Prevention and Response

Merced ID proposes to implement its Fire Prevention and Response Plan, as filed 

with the final license application and revised on September 22, 2014, to provide fire 

prevention measures, reporting, and safe fire practices for Merced ID and its contractors 

to follow when operating and maintaining the project. The plan identifies the various 

agency plans and regulations that Merced ID referenced to prepare the plan, provides the 

fire history on lands in the vicinity of the project, and identifies the state and federal laws 

and regulations with which it would comply when operating and maintaining the project. 

Elements of the plan include descriptions of Merced ID’s actions, responsibilities, and 

access related to wildland fire preparedness and reporting, including:

 equipment and tools for Merced ID staff and job sites;

 fire index monitoring and activity curtailment, as appropriate;

 debris burning;

 vegetation clearance;

 communication systems;

 access routes to recreation areas and helicopter landing areas;

 fire investigation; and 

 emergency contact information.

Based on Merced ID’s ignition analysis, the plan also includes fire prevention 

education and signage at recreation facilities. The plan would be reviewed and 

potentially revised in consultation with BLM and the California Department of Forestry 

and Fire Protection during the license term on an unspecified schedule. Merced ID

would provide the revised plan to the agencies for a minimum 60-day review period 

before filing it with the Commission for approval.
342

Merced ID’s proposed Fire Prevention and Response Plan is consistent with BLM

preliminary 4(e) condition 25; however, BLM specifies that Merced ID obtain BLM 

approval of the plan before filing it for Commission approval.

Our Analysis

By implementing its Fire Prevention and Response Management Plan, Merced ID

would improve planning for and management of wildfires and improve the coordination 

of wildfire protection and prevention measures that could reduce wildfire occurrence in 

the vicinity of the project. Provisions in the plan and consultation with BLM and the 

California Department of Forestry and Fire Protection could also improve suppression 

efforts, thereby minimizing damage caused by wildfires that may occur in the project 

vicinity. Because fire-related circumstances would likely change over the term of a new 

license, it would be appropriate to periodically review the plan, as Merced ID proposes, 

to determine if the plan should be revised. 

Merced Falls Project

There are no construction or land use changes proposed in the new license 

application. However PG&E does propose to modify the project boundary. The 

proposed modifications would change the current project boundary area from 75.6 acres 

to 70.8 acres (see figure 3-44). The changes would remove 4.8 acres of land from the 

project boundary on the northeastern shoreline of the Merced Falls impoundment. PG&E 

states these lands are not needed for project purposes. 

Our Analysis

The project boundary must enclose all principal project works and lands necessary 

for operation and maintenance of the project and other project purposes, such as 

recreation. PG&E states that these lands are not needed for project purposes; however, in 

section 3.3.4, Recreation Resources, we note that recreation features that serve the 

Merced Falls Project are located on the lands proposed for removal. More specifically, 

portions of the Merced Falls Fishing Access area and the informal angler trail may be 

within the lands proposed for removal. If these lands are deemed necessary for project 

recreation, then the proposed project boundary changes would need to be modified to 

ensure adequate public access to these lands over the term of a new license. 
343

Figure 3-44. Map of proposed project boundary changes (Source: PG&E, 2012).
344

3.3.6 Cultural Resources

3.3.6.1 Affected Environment

Section 106 of the NHPA, as amended, requires the Commission to take into 

account the effects of licensing a hydropower project on properties listed or eligible for 

listing in the National Register and allow the Advisory Council on Historic Preservation 

(Advisory Council) a reasonable opportunity to comment if any adverse effects on 

historic properties are identified within the project’s APE. 

Historic properties are defined as any district, site, building, structure, or object 

that is included in or eligible for inclusion in the National Register. In this document, we 

also use the term “cultural resources” to include properties that have not been evaluated 

for eligibility for listing in the National Register. In most cases, cultural resources less 

than 50 years old are not considered eligible for the National Register. Cultural resources 

need enough internal contextual integrity to be considered historic properties. For 

example, dilapidated structures or heavily disturbed archaeological sites may not have 

enough contextual integrity to be considered eligible. TCPs are a type of historic 

property eligible for listing in the National Register because of their association with 

cultural practices or beliefs of a living community that: (1) are rooted in that 

community’s history or (2) are important in maintaining the continuing cultural identity 

of the community (Parker and King, 1998). Section 106 also requires that the 

Commission seek concurrence with the California SHPO on any finding involving effects 

or no effects on historic properties. If TCPs have been identified, section 106 also 

requires that the Commission consult with interested Native American tribes that might 

attach religious or cultural significance to such properties.

If existing or potential adverse effects have been identified on historic properties, 

license applicants need to develop an HPMP to seek to avoid, reduce, or mitigate the 

effects. Potential effects that may be associated with a hydroelectric project include any 

project-related effects associated with the day-to-day operation and maintenance of the 

project after issuance of a new license. During development of an HPMP, the applicants

should consult with the Commission, Advisory Council, California SHPO, Native 

American tribes, and BLM. In most cases, the HPMP would be implemented by 

execution of a PA that would be signed by the Commission, Advisory Council (if it 

chooses to participate), the California SHPO, and other consulting parties. 

Cultural History Overview

Researchers have attempted to identify prehistoric temporal sequences for the 

vicinity of the Merced River and Merced Falls Projects based on differing artifact 

assemblages that indicate adaptations to environmental and other changes. Two primary 

sequences have been defined: the Yosemite Archaeological Sequence and the 

Chowchilla River Archaeological Sequence. These sequences are both associated with 

the Sierra Miwok, Central Miwok, and Foothill Yokuts people.
345

The Yosemite Archaeological Sequence has been divided into three primary 

complexes. During the period associated with the Crane Flat Complex (1,000 Before 

Christ [BC] to 500 Anno Domini [AD]), resident populations had not yet taken up bow 

and arrow technology and used the atlatl (i.e., a spear thrower) for hunting purposes. The 

atlatl used Elko-like projectile points typically manufactured from obsidian obtained from 

local sources. Groundstone tools included metates and handstones, but the use of mortars 

and pestles was not widespread. During the period associated with the Tamarack 

Complex (500–1200 AD), projectile point size decreased, indicating a possible change in 

technology from the atlatl to use of the bow and arrow. During this time, an increase in 

acorn processing is evidenced by the presence of more bedrock mortar features and 

cobble pestles. The trend toward smaller projectile points continued into the period 

identified as the Mariposa Complex (1,200–1800 AD). At this time, Cottonwood and 

Desert side-notched points are prevalent. Also at this time, the presence of large bedrock 

mortar sites containing hundreds of cupules indicates and even greater reliance on acorn 

processing. This change may indicate an increase in population.

The Chowchilla Archaeological Sequence also contains three temporal sequences 

during which populations were relatively high but with an intermittent period of decline. 

The earliest of these, the Chowchilla Phase (800 BC–550 AD) is characterized by 

projectile points that were similar to those found at Crane Flat Complex sites but include 

points with concave bases and contracting stems. However, unlike the Crane Flat 

Complex, pestles and cobble mortars have been recovered from sites dating to the 

Chowchilla Phase. Additionally, there is evidence of elaborate funerary practices with 

grave goods at this time as well as trade with populations in the adjacent Great Basin and 

southwestern California. Small projectile points with contracting stems are typically 

found in archaeological sites dating to the Raymond Phase (550–1500 AD). Pestles and 

cobble mortars continued to be used, but unlike the previous phase, fewer bedrock 

mortars are found and burials generally lack grave goods. This indicates a period of 

population decline. During the subsequent Madera Phase (1500–1859 AD), populations 

again increased. Smaller projectile points were more prevalent, and new technologies 

appeared. These included arrow shaft straighteners, pendants, and items manufactured 

from steatite. Burial practices varied to include cremation, and villages often contained 

sweathouses, housepit residential structures, and other features. 

Ethnographically, the Merced River and Merced Falls Projects are located within 

the traditional territory of the Southern Sierra Miwok people. Subsistence activities 

focused on hunting large game, such as deer, antelope, and elk. Fishing and the 

collection of local plant resources supplemented the diet. Acorns, collected in the cooler 

months, were a particularly important staple. Acorns were processed using ground stone 

tools such as mortars and pestles. Other implements that the Sierra Miwok people used 

included flaked stone tools such as scrapers, choppers, projectile points, and knives. 

Willows and other plant materials were woven into baskets for storage purposes.

Spanish explorers were the first Europeans to contact the indigenous California 

populations in the late 1700s. Spanish missions and pueblos were established, and native 
346

peoples who had not succumbed to introduced disease were often brought to these 

settlements against their will to serve as workers. In 1882, Spanish rule over California 

was replaced with Mexican governance. Mexican ranchos of thousands of acres were 

granted to individuals primarily for cattle ranching purposes. One such grant of greater 

than 44,000 acres was issued to General John C. Fremont. This property was located on 

Mariposa Creek between the mountains of the Sierra Nevada and the San Joaquin, 

Chowchilla, and Merced Rivers.

The gold rush of 1848 resulted in mining of many of the gravel deposits and 

streams of the Sierra Nevada. While gold was the main mining focus in the vicinity of 

the project, other materials such as silver, lead, zinc, copper, and tungsten were also 

found in the area. Several mining camps were located near the project area including 

Bagby, Barret City, Exchequer, and Horseshoe Bend. One of these camps, the Exchequer 

Camp, is inundated by the Merced River Project’s Lake McClure. 

Agriculture, cattle ranching, and tourism were also important to the growing 

economy of the area. While large operations, such as Miller & Lux established in 1881, 

ran thousands of head of cattle and sheep on open range, farmers also purchased land to 

grow crops such as wheat, barley, and cotton. In 1870, construction of the Central 

Pacific Railroad from Lathrop through the Central Valley began, and in 1871, the line 

reached Merced County. The line replaced unreliable river boats as a means of 

transporting good and also led to increased tourism in the area, including to Yosemite 

Valley. 

Hydroelectric power essentially developed out of the use and conveyance of water 

from the Merced River during the California gold rush era, especially involving hydraulic

mining. Dams such as the Merced Falls, Fremont, and Benton Mills dams were built on 

the river as early as the 1850s. Many of these dams were also used for hydro mechanical 

power associated with mills involved with hard rock mining and the grinding of grain. 

By the 1890s, hydroelectric power was implemented in higher elevations of California, 

first for mining operations, and then to power local towns and municipalities associated 

with the mines. By the turn of the 19th century, hydroelectric facilities were constructed 

on the Merced River, such as the Kittridge dam, flume, and powerhouse, that was used to 

power the Nameless Mine and associated rock crusher at Jasper Point. Out of an original

grist mill dam built on the Merced Falls in 1854, a hydropower facility was built at the 

site in the 1890s, and Merced Falls and Utility Company (sold, reorganized, and later 

incorporated into PG&E) purchased the facility in 1900 for hydroelectricity, and in the 

following year, built a concrete dam in place of the older timber dam. Irrigation dams 

and conveyance systems were also developed as far back as the 1860s to provide a 

reliable source of water for agriculture in the often arid Merced River Valley and were 

later augmented with harnessing electricity from hydropower. As an irrigation district, 

Merced ID was developed between 1917 and 1919, and began construction on the 

original Exchequer concrete dam in 1922. 
347

Merced River Project

Area of Potential Effects 

Pursuant to section 106, the Commission must take into account whether any 

historic property could be affected by issuance of a new license within a project’s APE. 

The APE is defined as the geographic area or areas that an undertaking may directly or 

indirectly cause alterations in the character or use of historic properties, if any such 

properties exist. Merced ID defined the APE as consisting of all lands, project facilities, 

and features located within the project boundary and any lands outside of the project 

boundary where cultural resources may be affected by project-related activities. There 

are 11,653.3 acres in the existing project boundary. By letter dated April 19, 2011, the 

California SHPO concurred with Merced ID’s definition of the APE (letter from M.W. 

Donaldson, California SHPO, California Department of Parks and Recreation, Office of 

Historic Preservation, Sacramento, CA, to B. Kelly, Merced ID, Merced, CA, filed 

February 27, 2012). However, on February 14, 2013, Merced ID requested California 

SHPO concurrence with an expanded APE that includes two additional areas located 

outside of the project boundary where project activities could affect cultural resources

(letter from B. Kelly, Merced ID, Merced, CA, to M.W. Donaldson, California SHPO, 

California Department of Parks and Recreation, Office of Historic Preservation, 

Sacramento, CA, filed April 8, 2013). These areas consist of approximately 221 acres 

located at the Horseshoe Bend recreation area and 29.5 acres located near New 

Exchequer dam. 

Project-specific Cultural Resources

As summarized above, early mining endeavors resulted in the construction of 

water control systems in the Sierra Nevada. Some of these structures, including ditches 

and reservoirs, were later used to generate hydroelectric power. Irrigation canals were 

also constructed to provide water to ranches and farms. Several irrigation companies 

formed to convey mountain water to lower elevation lands. One such company was the 

Crocker Huffman Land and Water Company. Merced ID was established on December 

8, 1919, and in 1922, it purchased the Crocker Huffman Land and Water Company 

irrigation system and selected the Exchequer Mining Company on the Merced River for 

the location of its first dam. By 1926, the Exchequer dam—Lake McClure—and 

associated canals and power system had been constructed. At the time, the dam was 

considered to be the largest dam of its kind.

In 1964, Merced ID sought to expand its storage and generation capabilities. The 

old powerhouse was removed, and the New Exchequer and McSwain dams were 

completed in 1967. The Old Exchequer dam became a footing of the New Exchequer 

dam.

Archaeological and Historic-Era Sites—Merced ID conducted a review of records 

and files housed at the Central California Information Center and BLM to determine the 

location and adequacy of any previous surveys and to identify previously recorded 
348

archaeological sites, historic structures, and other resources within the proposed project 

boundary. The records search found that 14 previous cultural resource investigations had 

been undertaken within, or partially within, the project APE. These studies resulted in 

the identification of 15 sites within the APE—seven prehistoric sites (a village site, four

milling stations, a milling station with a midden and lithic scatter, and a milling station 

with petroglyphs), seven historic-era sites (two mining sites, Yosemite Valley railroad, 

Bagby Benton mills, Bruschi Mine, Horseshoe Bend mining town, and Highway 49), and 

one site that contained both prehistoric and historic components (a milling station and 

lithic scatter in association with the Bondville mining camp). Another existing cultural 

resource within the APE was a historic stone building. 

Merced ID conducted archaeological survey of all accessible lands within the 

project APE between 2008 and 2010, and again in 2013. Approximately 6,759 acres 

were surveyed, and a total of 186 archaeological sites and 90 isolated artifacts were 

documented. Of the 186 archaeological sites documented within the APE, 131 are 

historic-era sites, 29 are prehistoric, and 26 contain both prehistoric and historic-era

components. Details pertaining to the 186 cultural resource sites identified in the project 

APE were provided in Merced ID’s December 2013 amended HPMP (Merced ID, 

2013c). 

Of the 29 prehistoric sites, the majority (21) are milling station sites with no other 

archaeological materials or features. These sites contain at least one bedrock mortar 

cupule, milling slick, or milling basin. One site contains six separate features within the 

site boundary that contained a combined total of 63 milling surfaces. Of the remaining 

eight prehistoric sites, two sites were identified as lithic scatters. Two additional

temporary camp sites that reflect limited seasonal occupation were also identified. These 

sites may or may not contain milling features, but they typically contain lithic scatters 

and midden or possible midden deposits. Three sites were identified as larger base camps 

that may contain evidence of house structures. These sites also typically contain bedrock 

milling features. Finally, one site was identified as a base camp or village site with more 

than 159 milling features, but the site also contains numerous zoomorphic and abstract 

petroglyph features. The site is also unique in that the bedrock mortars also contain 

numerous small cupules of the type frequently found in “pitted boulders” (Payen, 1966, 

as cited by Merced ID, 2013c).

Multi-component sites primarily consist of historic-era features or refuse deposits 

located with prehistoric milling stations. Several of the sites, however, also contain other 

prehistoric features or materials such as midden development, housepit depressions, lithic 

scatters, and/or groundstone artifacts.

Of the 131 historic period sites, 53 sites are mining or mining related. These sites 

include placer mining debris and features such as adits, tailings, walls, foundations, waste 

rock locations, and other features. Other sites include historic railroad features associated 

with the Yosemite Valley Railroad, roads and trails, retaining walls and fences, 

transmission lines, structural foundations, water control features, features and structures 
349

associated with historic habitation sites, retaining walls, refuse deposits, land survey 

markers, and the historic town site of Bagby.

All but 2 of the 186 archaeological sites recorded in the APE remain unevaluated 

for their National Register eligibility. Of the two sites that have been evaluated, one has 

been determined eligible for the National Register. This particular site (P-22-0739) is an 

aboriginal village site with a possible place name associated with it. The other site is the 

Yosemite Valley railroad grade, and it has been determined ineligible for the National 

Register. 

Historic Buildings, Structures, and Districts—The current Merced Hydroelectric 

System was constructed in the mid- to late 1960s and does not currently meet the 50-year 

age requirement for listing on the National Register eligibility. While most of the Old 

Exchequer dam (site MID-215), now a footing of the current dam, was inundated during 

relicensing surveys, the portion of the old dam that was visible appears to be intact. 

However, the remains of the old dam were evaluated as ineligible for listing on the 

National Register because dams of this type are not uncommon and the setting of the dam 

has been greatly compromised by construction of the new system and other modern 

developments. A gaging station (MID-111) located downstream from the dam was also 

documented. This station pre-dates the current system and may be associated with the 

original project. However, the gaging station was also evaluated as ineligible for listing 

on the National Register. 

Other structures associated with the project include residential and maintenance 

buildings. These buildings, which were recorded as a single site (MID-12), include 15 

historic-era structures. A total of eight of these structures are residential and date from 

the late 1920s to the early 1940s. Two garages date to 1947 and a third to 1950. The site 

includes a pool of unknown age, but a pool maintenance building dates to 1939. Finally,

a water tower of unknown age is also present at the site. These 15 structures have been 

modified and maintained using modern materials, and Merced ID recommends that they 

no longer retain historic integrity. For this reason, Merced ID recommends that they are 

not eligible for listing in the National Register.

Traditional Cultural Properties—In October 2008, the Commission consulted 

with the Washoe Tribe of Nevada and California, the Tuolumne Band of Me-Wuk 

Indians, the Chicken Ranch Rancheria Tribal Council, and the California Valley Miwok 

Tribe. The intent of this consultation was to determine whether any of the tribes had 

interest in the proposed project and whether they would like to participate in the 

relicensing effort. The California Miwok Tribe and the Chicken Ranch Rancheria both 

responded with requests for including the Southern Sierra Miwuk Nation (also known as 

the American Indian Council of Mariposa County/Southern Sierra Miwuk Nation) in the 

tribal consultation process. The Southern Sierra Miwuk Nation are considered to be the 

most likely descendants who lived along the Merced River prior to European contact. On 

November 16, 2008, the Southern Sierra Miwuk Nation provided the Commission with a 

copy of a completed Pre-Application Document questionnaire issued by Merced ID. The 
350

questionnaire identified the Southern Sierra Miwuk Nation’s interest in the project, 

contact information, and other important information. In the questionnaire, the Southern

Sierra Miwuk Nation requested formal consultation with Merced ID and the Commission 

regarding the project.

Merced ID consulted with the Southern Sierra Miwuk Nation between 2008 and 

2012 to discuss the tribe’s concerns regarding cultural resources and the potential need 

for a TCP study. A Memorandum of Agreement for a TCP study was executed between

Merced ID and Southern Sierra Miwuk Nation on May 19, 2011. It provides protocols 

for completion of the TCP study. A TCP report was completed by Merced ID in

November 2013. Archival research has been done on the TCP study, but no interviews

with tribal members have been completed so far with MID’s contracted ethnographer. 

Nevertheless, the TCP study shows that there is the potential to connect some of the 

recorded archaeological sites within the APE with ethnographic villages of the Miwok. 

Merced ID states that to date, no potential TCPs of importance to the Southern Sierra 

Miwuk Nation have been identified within the project APE. However, Merced ID is

continuing consultation with the tribe to identify and document National Register-eligible 

TCPs within the APE and assess the project’s effects (if any) on these resources.

Merced Falls Project

Area of Potential Effects

PG&E defines the APE as encompassing all lands within the FERC project 

boundary, in addition to a 20-foot buffer above the Merced Falls impoundment high 

water line. The APE consists of a total of 74.4 acres; however, approximately 68 acres 

are inaccessible due to the impoundment, in addition to some private lands that cannot be 

accessed. As a result, 5.8 acres were inventoried for cultural resources. For TCPs, the 

buffer zone above the Merced Falls impoundment is expanded to 100 feet above the high 

water line. 

Project-specific Cultural Resources

As summarized above, the project and associated APE were the result of 

hydroelectric development during and after 1916, resulting in the existing dam and 

impoundment, and other associated structures. Companies associated with hydroelectric 

development at Merced Falls began with the San Joaquin Light and Power Corporation, 

incorporated in the 1910, and where they acquired a deed for the Merced Falls and Gas 

Electric Company and put into service the Merced Falls substation (PG&E, 2014). As 

mentioned before, an earlier power house had been constructed at the falls in the 1890s, 

but was put out of service by floods in 1911. The powerhouse was then replaced and put 

back into operation in 1916. In 1930, the San Joaquin Light and Power Company 

purchased additional property around the falls and expanded the hydropower facility. 

The project facilities at Merced Falls were improved, resulting in a new concrete 

diversion dam, substation building, and additional structures. In 1938, San Joaquin Light 
351

and Power Company was officially merged with PG&E. At that time, PG&E filed an

application with Federal Power Commission for a license to operate the Merced Falls 

Power Plant. In 1969, PG&E was issued a major license to operate the project overall in 

place of its preceding minor license. Improvements, reconstructions, and modifications 

of the project continued into the 1980s and 1990s. 

Archaeological and Historic-Era Sites—PG&E conducted a review of the existing 

records at the California Historical Resources Information System at the University of 

California, Stanislaus, along with records kept at the California State Library, Water 

Resources Collection Center, University of California Berkeley, Bancroft Library, 

University of California Berkeley, Merced County Library, Merced County Museum, and 

at the consultant’s research library. A previously recorded historic period archaeological 

site was located within the project’s APE consisting of the remains of the Merced Falls 

Yosemite Sugar Pine Lumber Mill that was built in 1912. 

PG&E, through its cultural resource contractor, conducted an intensive survey of 

the accessible 5.8 acres of land within the APE. Remains of the Merced Falls Yosemite 

Sugar Pine Lumber Mill were located within the APE, consisting of a railroad spur grade, 

various historic concrete foundation features, and a crane foundation for transferring logs 

from the impoundment/pond area to a milling processing station, along with a scatter of 

various iron and glass artifacts. The majority of the Yosemite Sugar Pine Lumber Mill 

lies outside the APE, and could not be fully recorded since most of the site lies on private 

property and where access was denied by the landowner to do additional archaeological 

survey. As a result, this particular archaeological site could not be evaluated for National 

Register eligibility, however, for management purposes, PG&E considers to treat this 

particular resource as if it was eligible for the National Register, and the SHPO agreed 

with this particular approach (PG&E, 2014). Linear remnants of the Yosemite Valley 

Railroad (circa 1905) were also located along the north shore of the impoundment within 

the APE. Based on documentation dating to 2011, this particular portion of the railroad 

had been considered ineligible for the National Register by the SHPO involving a 

previous undertaking of another federal agency (PG&E, 2014). 

No other historic or prehistoric archaeological sites were found within the APE. 

Historic Buildings, Structures, and Districts—The Merced Falls Hydroelectric 

Project began in 1915 and work continued through 1916. The 1915–1916 project 

essentially consisted of the Merced Falls dam and powerhouse facility. Overall, the 

project includes the dam, powerhouse, generator, garage, control room and gauge house 

buildings, switch yard, fish ladder, flow-pipe for the Kesley and Snelling ditches, and 

related power generation structures. Among the various project features, the project dam 

consists of a concrete diversion dam 573-feet long, 34-feet high, and was reconstructed in 

1930. Associated with the dam is a concrete fish ladder consisting of ten 7-foot square 

boxes. The garage, control room, and gauge house buildings were built in 1915. When 

the project was put into operation in 1916, the control house served as the original 

powerhouse. The existing powerhouse consists of a 1930 one-story metal outdoor 
352

structure containing a single turbine and generator. Overall, the project facilities have 

been extensively modified over the years on up to the 1980s and 1990s, and as a result, 

PG&E considers them all ineligible for inclusion in the National Register (PG&E, 2014). 

Traditional Cultural Properties—PG&E initially contacted Southern Sierra 

Miwuk Nation, Amash Musun Tribal Band, North Valley Yokuts Tribe, Choinumni 

Tribe, Chukchansi Tribe, and North Fork Mono Rancheria. The American Indian 

Council of Mariposa County/Southern Sierra Miwuk Nation (Southern Sierra Miwuk 

Nation56) was the only Native American group who requested to be kept abreast of the 

Merced Falls relicensing process and participated with PG&E in ascertaining whether 

there were TCPs in or near the project’s APE. Consultation with the Southern Sierra 

Miwuk Nation and PG&E began in January 9, 2009, and again in August and October of

2010. A Memorandum of Understanding was executed between PG&E and the Southern 

Sierra Miwuk Nation on July 23, 2010. It provides protocols for completion of the TCP 

study. PG&E finished a draft of the TCP study in January 2012. Background research 

for the possible presence of TCPs in and near the project area were gathered from a 

number of sources, from the Merced County Library, Merced County Museum and 

Archives, Mariposa County Museum, Yosemite National Park, and other research 

institutions. Earlier ethnographic interviews with Miwuk informants were also compiled 

and reviewed. Correlations with archaeological sites and ethnographic/historic villages 

were also made, and a particular Native American village and associated archaeological 

site was located on the north bank of the Merced River west of the Merced Falls APE. 

Discussion with contemporary tribal members involved with the TCP study did not yield

any known village sites associated with distant Miwok ancestors or descendants. The 

TCP study itself involved work and data gathered by a contracted ethnographer, 

commissioned by PG&E. 

The TCP investigations and study demonstrated that the overall project area along 

the Merced River was of considerable importance to Miwok peoples for ceremonial,

traditional fishing and collecting activities, spanning thousands of years. A good case

can be made, supported by ethnographic accounts and modern-day tribal informants, that 

long stretches of the Merced River corridor had direct generational ties with living 

peoples going back to at least 150 years and could be considered as a more extensive 

TCP. Within the project’s APE, research and tribal interviews with members of the 

Southern Sierra Miwuk Nation demonstrated that there are locations where traditional 

collection of fish, aquatic resources, and botanical resources took place. As a result, a 

TCP, called the Merced Falls TCP, was established within the APE, and consists of the 

Merced Falls impoundment, shores, and adjacent lands up to 100 feet away. The TCP 

was considered eligible for the National Register, and to which the SHPO concurred with 

its eligibly on February 29, 2012 (PG&E, 2014). 

 

56 This group is the same group that MID consulted during its TCP study. 
353

3.3.6.2 Environmental Effects

Merced River Project

Project-Related Effects on Cultural Resources 

Project-related effects on cultural resources within the APE are likely to occur 

from project operation and maintenance, use and maintenance of project roads, 

recreation, vandalism, and modifications or repairs to project facilities. Project effects 

are considered to be adverse when an activity may alter, directly or indirectly, the 

characteristics of a historic property that qualify the property for inclusion in the National 

Register. If adverse effects are found, such effects would need to be resolved in 

consultation with the California SHPO, and with other parties. Merced ID has identified 

a number of different types of project-related effects on historic properties such as project 

maintenance, operation, reservoir fluctuations, recreation, artifact collection and

vandalism (Merced ID, 2013c). 

Routine maintenance and operation of the project system, vegetation management, 

road construction and use, and emergency repairs to system components can result in 

impacts to archaeological sites and historic structures in the project APE. In particular, 

both inundation and reservoir fluctuation, which can cause erosion, deflation, and/or 

artifact transport and deterioration, can adversely affect resources. When reservoir levels 

are low, sites that are typically inundated are also frequently susceptible to artifact 

collection and impacts from ORV traffic. 

The project vicinity is also popular for recreational activities, including fishing, 

boating, camping, hiking, and picnicking. These activities can result in inadvertent 

damage to cultural resources. Erosion along footpaths can expose cultural materials and 

increase vandalism and looting. Furthermore, use of project recreation facilities in the 

vicinity of historic properties may increase their susceptibility to vandalism and looting. 

Finally, cattle grazing in the project area may disturb cultural sites, particularly in areas 

where soils are damp.

Historic Properties Management Plan 

On December 31, 2013, Merced ID filed an amended HPMP to address project 

effects on historic properties with its final license application. The amended HPMP 

includes, but is not limited to, measures for: 

 avoiding National Register-eligible sites;

 stabilizing and protecting sites from erosion, recreation, and other impacts;

 implementing anti-looting approaches that may include education, signage, 

and law enforcement;

 site testing and data recovery where impacts are unavoidable;

 monitoring procedures and site condition assessment protocols;
354

 dealing with inadvertent discoveries and emergency situations;

 unanticipated discoveries of human remains on both private and public 

lands;

 training personnel for better understanding of cultural resources and

responsible management for them;

 continued consultation with agencies, including the California SHPO, and 

Native American tribes; 

 completion of archaeological surveys, National Register evaluations, and 

TCP studies; and

 periodic reporting and review/revision of the HPMP.

The amended HPMP also includes a more detailed and site-specific National 

Register Evaluation Plan. Among other things, the National Register Evaluation Plan 

identifies and prioritizes unevaluated sites for National Register evaluation and treatment 

that are experiencing on-going project-related effects. Such sites also require additional 

in-depth cultural investigations to determine National Register eligibility. On other 

unevaluated sites that are not being affected by the project, these particular sites will be 

avoided and continued to be treated as if such sites were eligible for the National 

Register. The HPMP also provides a detailed schedule on when various aspects of the 

plan will be carried out during the term of the new license. 

Agency Comments on Historic Properties Management Plan

In its comments on the initial draft HPMP filed with the Commission on January 

26, 2012, BLM questioned the adequacy of Merced ID’s cultural resources identification 

efforts and the measures to protect historic properties provided in Merced ID’s draft 

HPMP. BLM stated that it would appreciate the opportunity to review the inventory 

report and HPMP once Merced ID has revised these documents to address BLM 

comments and concerns. On April 2, 2012, Merced ID requested that the Commission 

grant it an additional 15 months, until May 30, 2013, to complete any additional 

fieldwork and to file a revised HPMP. Merced ID continued to consult with BLM, and 

on May 29, 2013, Merced ID requested an additional extension, until December 30, 2013, 

to file the revised HPMP. The Commission granted this request on June 13, 2013, and 

Merced ID filed an amended HPMP with the Commission on December 31, 2013. The 

amended HPMP was revised again based on subsequent changes to the cultural resources 

inventory report, and was submitted to BLM and involved Indian tribes on March 20, 

2014 (Merced ID, 2014). The amended HPMP was also submitted to the SHPO. Both 

the SHPO (filed August 5, 2014) and BLM have made additional comments on the 

amended HPMP, and Merced ID is in the process of addressing these comments and 

anticipates that a final revised HPMP will be filed with the Commission by the end of 

2014 (see Merced ID response to BLM preliminary 4(e) conditions, August 21, 2014). 
355

BLM specifies in preliminary condition 24 that Merced ID obtain BLM approval 

of its HPMP before submitting it to the Commission. Upon Commission approval, 

Merced ID would implement its HPMP. On August 21, 2014, in its alternative 

conditions, Merced ID indicated that the amended HPMP (filed with the Commission on 

December 31, 2013) would be revised again to (1) include the recent discovery of three 

new cultural resources; (2) assign state resource numbers to all sites; (3) incorporate 

SHPO and BLM comments on the Cultural Resources Inventory Report; and 

(4) incorporate SHPO, BLM, and comments from the involved tribes on the revised 

amended HPMP. After addressing these comments, Merced ID plans to file the revised 

amended HPMP with the Commission at the end of 2014. 

Our Analysis

After Merced ID makes adequate revisions to the amended HPMP, we expect to 

see a final revised HPMP at the end of this year that would meet all of the Commission’s 

requirements under section 106. Once we receive the final revised HPMP, we would 

attach it to a PA and execute it with the California SHPO (in anticipation that upon 

notification, the Advisory Council would choose not to participate in the PA). Once a 

decision to issue a new license for this project is made, Merced ID would implement its

HPMP under the stipulations of the PA for the term of the new license. Merced ID, 

BLM, and the Southern Sierra Miwuk Nation would be invited to sign the PA as 

concurring parties. Execution of the PA would ensure that Merced ID adequately

addresses any existing and potential adverse effects on historic properties identified 

within the project’s APE through the implementation of the final HPMP.

Merced Falls Project

Project-related Effects on Cultural Resources

Similar to the Merced River Project, project-related effects on cultural resources 

within the Merced Falls APE would likely occur from project operation and maintenance, 

including vegetation management and recreation activities. Nevertheless, the APE 

around the Merced Falls Project is small (approximately 6 acres), and is restricted to the 

impoundment area of the project. Although there are no above-ground project facilities 

considered to be eligible for the National Register within the project’s APE, there is one 

historic archaeological site (the Yosemite Sugar Pine Merced Falls Lumber Mill) that 

would be treated as National Register-eligible. Furthermore, the identified National 

Register-eligible Merced Falls TCP is also within the project’s APE, and has sustained 

importance to the Southern Sierra Miwuk Nation over many generations as a location for 

gathering aquatic and botanical resources. 

Historic Properties Management Plan

To resolve any potential project-related adverse effects on the Merced Falls TCP 

within the APE, PG&E crafted an HPMP that would preserve and protect this TCP for 
356

the term of a new license. Among other things, the HPMP includes measures to preserve 

and protect the important aspects of this TCP and to monitor the TCP area within the 

APE at regular intervals over the term of a new license. Furthermore, the HPMP also 

recommends that the Yosemite Sugar Pine Merced Falls Lumber Mill be treated as if it is 

National Register-eligible, and details steps that would be taken in the event of projectrelated adverse. The HPMP includes, but is not limited to, the following measures: 

 a plan and procedure for consultation with the SHPO and Southern Sierra 

Miwuk Nation when project activities might affect properties considered 

to be eligible for the National Register; 

 a plan to deal with inadvertent discoveries and emergency situations if and 

when they arise; 

 a plan to deal with unanticipated discoveries of human remains; 

 monitoring and evaluating cultural resources below the present 

impoundment area when opportunities exist to survey these areas at low 

water levels; 

 training of project personnel regarding the sensitivity of the Merced Falls 

TCP and for the day-to-day management and avoidance of this site; 

 a process for the continued consultation with Southern Sierra Miwuk 

Nation and the SHPO; and 

 periodic reporting and review/revision of the HPMP. 

Agency Comments on the Historic Properties Management Plan

PG&E sent a draft HPMP to the SHPO on March 4, 2013, and the SHPO 

responded on September 9, 2013, that it did not concur with the draft document. Based 

on the SHPO’s comments, PG&E resubmitted a revised HPMP on August 8, 2014, and 

on September 15, 2014, the SHPO responded that it concurred with PG&E’s HPMP, 

dated June 2014, and that the HPMP would adequately address project-related effects on

historic properties for the undertaking involving a new license for the project (PG&E, 

2014, Appendix B). 

Our Analysis

Commission staff concurs with PG&E’s June 2014 HPMP and the associated steps 

to resolve project-related adverse effects on historic properties for the term of any new 

license. As a result, Commission staff intends to execute a PA with the SHPO (in 

anticipation that upon notification, the Advisory Council would decline to participate in 

the PA). The stipulations in the PA would, in turn, implement PG&E’s HPMP upon 

issuance of a new license for the project. PG&E and the Southern Sierra Miwuk Nation 

would be concurring parties to the PA. Execution of the PA and implementation of the 

HPMP would ensure that PG&E appropriately protects and preserves the Merced Falls 

TCP, and that future encounters with other possible historic properties would be handled 
357

in accordance with the HPMP and include consultation with the parties associated with 

the PA. 

3.3.7 Aesthetic Resources

3.3.7.1 Affected Environment

Merced River Project

The Merced River Project is located in the Sierra Nevada foothills west of 

Yosemite National Park in oak woodland vegetation type (see section 3.3.2.1, Terrestrial 

Resources). The viewsheds at and near the project have few structures, so the natural 

vegetation and canyons dominate the views. The eastern extent of the project has steep, 

dramatic hills and the landscape in the western portion of the project consists of gently 

rolling hills. The project is located in Mariposa County on land owned by Merced ID and 

private entities, as well as on federal land administered by BLM (see section 3.3.5.1, 

Land Use).

The project reservoirs are visible from the reservoirs and adjacent land. New 

Exchequer dam, powerhouse, spillway, dike, and other buildings have light colors, 

uniform textures, and geometric shapes that, as seen in the foreground and near middle 

ground from Lake McClure Road, contrast with the surrounding landscape. McSwain 

dam and powerhouse have low to moderate visual contrast as viewed from locations near 

Lake McClure Road and Merced Falls Project. The foreground view of McSwain dam 

from the McSwain recreation area contrasts with the surrounding landscape. Contrasting 

elements include the industrial shapes and lines of the trash rack and intake facilities and 

linear appearance of the guardrail on the top of the dam. Brightly colored, orange 

floating safety booms on both reservoirs located near the dams contrast with views of the 

reservoir surface and surrounding landscape.

Merced ID characterized visual resources using BLM’s visual assessment 

protocols and guidance in BLM’s Sierra Resource Management Plan and the Mariposa 

County General Plan, as applicable. Objectives for visual resources in the Sierra 

Resource Management Plan include maintaining the existing visual quality of the: 

(1) Lake McClure/State Route 49 viewshed; and (2) Merced Wild and Scenic River. The 

appearance of project dams, powerhouses, appurtenant buildings and five recreation areas 

located on or near federal land is compliant with BLM land management guidance for all 

background views and for most middle ground views. New Exchequer dam begins to 

contrast with its surroundings at views less than 2 miles and highly contrasts when 

viewed from the foreground along Lake McClure Road and the reservoir when the water 

surface is low. 

Three of the five project recreation areas (Bagby, Horseshoe Bend, and McClure 

Point) are located on federal land administered by BLM or have adjacent federal land. 

The housing unit and water tank at Horseshoe Bend are not consistent with BLM visual 

resource management objectives. The contrasting view of the unvegetated swath of soil 
358

that appears as the level of McClure Lake recedes is also inconsistent with BLM visual 

resource management objectives; adjacent Merced ID-owned lands have a similar 

contrasting appearance.

Facilities on Merced ID-owned land were also evaluated for visual contrast. Near 

New Exchequer dam, the foreground and immediate middle ground views of geometric 

shapes and light colors of appurtenant buildings, spillway, and dike strongly contrast with 

the natural landscape. The gray colored, rough textured rock facing of New Exchequer 

dike moderately contrasts with the surrounding landscape. Viewed from downstream of 

McSwain dam, the dam has a moderately contrasting appearance. The powerhouses at 

each dam have muted colors and moderately contrasting appearances. Barrett Cove and 

McClure Point recreation areas foreground views of maintenance buildings and storage 

yards highly contrast with surrounding landscape, but the recreation area site design and 

road locations allow these facilities to blend well into the landscape. McSwain reservoir 

only fluctuates a few feet, so there is little, if any, change to the view of the shoreline 

caused by changes in water surface elevation.

Merced Falls Project

The Merced Falls Project is located in Merced and Mariposa Counties near the 

base of the western slope of the central Sierra Nevada Mountain Range. To the east and 

north, foothill terrain dominates the landscape, while to the south and west, flat 

agricultural land is prevalent. The land is mostly undeveloped with the exception of a 

few rural residences. The scenery along the southern shoreline includes rolling pastoral

hills with scattered oaks, while Lake McClure Road runs along the northern shoreline. 

The banks are lined in some places with trees and other vegetation.

Project facilities include a 575-foot-long and 34-foot-high concrete gravity dam, 

and a powerhouse consisting of steel building housing the turbine generator unit adjacent 

to a single-story concrete control room structure. There is no transmission line associated 

with the project. The impoundment level is maintained at the same elevation year round, 

which avoids fluctuating water levels. 

3.3.7.2 Environmental Effects

Merced River Project

Visual Resource Plan

Merced ID proposes to implement a Visual Resource Plan, filed on September 22, 

2014, to provide guidance for the management of visual resources on lands administered 

by BLM within the project boundary. The plan includes identifying project facilities in 

need of visual resource mitigation, addressing project facility building materials (e.g.,

paint colors, landscaping, spoil piles), and implementing visual resource measures to 

bring existing and new project facilities into compliance with visual resource objectives 
359

in BLM’s Sierra Resource Management Plan. Merced ID included the following specific 

measures for Barrett Cove and Horseshoe Bend recreation areas:

 painting the Barrett Cove recreation area maintenance yard 

warehouse/storage building a gray-green color to blend the facilities with 

the surrounding landscape; 

 planting vegetation to screen the warehouse area from the parking lot;

 painting the Horseshoe Bend recreation area maintenance yard warehouse 

and water tank a gray-green color to blend the facilities with the 

surrounding landscape;

 removing the existing ranger station house located below the water tank 

and constructing a new house near the maintenance yard; and

 planting shrubs to screen the maintenance yard warehouse from the main 

entry road.

Merced ID would secure BLM approval of the color used to paint any facilities 

located on BLM-managed land.

Merced ID’s proposed Visual Resource Plan is consistent with BLM preliminary

4(e) condition 26; however, BLM specifies before implementing the plan, Merced ID 

obtain BLM approval of the plan and file it for Commission approval.

Our Analysis

The visual resource assessment did not identify many concerns or inconsistencies 

of project feature appearances relative to guidance contained in applicable plans. Merced 

ID’s proposal to implement a Visual Resource Plan would identify project facilities in 

need of mitigation from visual resource impacts, improve the visual appearance at Barrett 

Cove and Horseshoe Bend recreation areas, and provide a mechanism to manage and 

monitor visual resources over the term of a new license. Over the license term,

management actions and recreation use patterns could affect visual resources at the 

project. Monitoring visual resources and consulting with BLM on an annual basis, at a 

minimum, would provide necessary information to determine whether additional 

treatments would be necessary to achieve visual quality objectives. Because future 

project activities could affect views of not only BLM-managed lands but all project lands, 

it would be appropriate to include all project lands in the Visual Resource Plan. 

Merced Falls Project

PG&E does not propose any new construction or changes to project operation that 

would affect aesthetic resources.
360

Our Analysis

Project operation targets stable impoundment levels and manage downstream 

flows in concert with Merced ID’s upstream facilities. This results in negligible reservoir 

fluctuations, which reduces negative impacts on aesthetic resources at the project. 

Future development of lands adjacent to the project could affect visual resources; 

however, PG&E owns only a small amount of property outside the project boundary and 

has little control over the development of lands outside the project boundary.

3.4 NO-ACTION ALTERNATIVE

Under the no-action alternative the Merced River project and the Merced Falls 

project would continue to operate as they have in the past. None of the licensee’s 

proposed measures or the resource agencies’ recommendations and mandatory conditions 

would be required. 

Merced River Project

Under the no-action alternative: (1) anadromous fish habitat would not be 

enhanced as a result of a minimum instream flow and pulse flows, (2) spawning habitat 

for fish species would not be enhanced, (3) there would be no means to monitor the status 

of anadromous fish, (4) there would be no plan to protect federally listed species or

survey for federally listed species not previously surveyed, and (5) recreation facilities 

would not be improved and new facilities would not be constructed. 

Merced Falls Project

Under the no-action alternative: (1) there would be no formalized plan or setting 

for the coordination of project operation or environmental measures with the upstream 

Merced River Project, (2) there would be no plan to enhance LWD habitat in the Merced 

Falls reach, (3) there would be no protection plans for federally listed species, and 

(4) recreation facilities, including a canoe trail, would not be maintained.
361

4.0 DEVELOPMENTAL ANALYSIS

In this section, we look at the Merced River and Merced Falls Projects’ use of the 

Merced River for hydropower purposes to see what effect various environmental 

measures would have on the projects’ costs and power generation. Under the 

Commission’s approach to evaluating the economics of hydropower projects, as 

articulated in Mead Corp.,

57 the Commission compares the current project cost to an 

estimate of the cost of obtaining the same amount of energy and capacity using the likely 

alternative source of power for the region (cost of alternative power). In keeping with 

Commission policy as described in Mead Corp., our economic analysis is based on 

current electric power cost conditions and does not consider future escalation of fuel 

prices in valuing the hydropower project’s power benefits.

For each of the licensing alternatives, our analysis includes an estimate of: (1) the 

cost of individual measures considered in the EIS for the protection, mitigation, and 

enhancement of environmental resources affected by the projects; (2) the cost of 

alternative power; (3) total project costs (including the operation and maintenance cost, 

and the cost of environmental measures); and (4) the difference between the cost of 

alternative power and total project costs. If the difference between the cost of alternative 

power and total project cost is positive, the projects produce power for less than the cost 

of alternative power. If the difference between the cost of alternative power and total 

project cost is negative, the projects produce power for more than the cost of alternative 

power. 

4.1 POWER AND DEVELOPMENTAL BENEFITS OF THE PROJECT

As currently operated, the Merced River Project has an authorized installed 

capacity of 103.5 MW and generates an average of 387 GWh annually (based on 

operation model results); the Merced Falls Project has an authorized installed capacity of 

3.4 MW and generates an average of 14.4 GWh annually.

Tables 4-1 and 4-2 summarize the assumptions and economic information we use 

in our analysis. This information was provided by Merced ID and PG&E in their 

respective license applications for the Merced River Project and the Merced Falls Project. 

We find that the values provided by Merced ID and PG&E are reasonable for the 

purposes of our analysis. Cost items common to all alternatives include: taxes and 

insurance costs; net investment (the total investment in power plant facilities remaining to 

be depreciated); estimated future capital investment required to maintain and extend the 

 

57 See Mead Corporation, Publishing Paper Division, 72 FERC ¶ 61,027 (July 13, 

1995). In most cases, electricity from hydropower would displace some form of fossilfueled generation, in which fuel cost is the largest component of the cost of electricity 

production.
362

life of plant equipment and facilities; relicensing costs; normal operation and 

maintenance cost; and Commission fees.

Table 4-1. Parameters for the economic analysis of the Merced River Hydroelectric 

Project (Source: Merced ID, 2012a). 

Parameter Value

Period of analysis (years) 30

Net investment, $a $26,991,500

Relicensing cost, $b $17,000,000

Operation and maintenance, $/yearc $14,784,530

Commission fees, $/yeard $163,180

Energy value – New Exchequer 

($/MWh)e

35.84 (peak) 24.56 (off-peak)

Energy value – McSwain ($/MWh)f 60.84 (peak) 49.56 (off-peak)

Capacity value ($/kW-year)g 162

Short-term interest rate (percent)h 3.875

Long-term interest rate(percent)i

Discount rate (percent)j

6.375

6.375

a Net investment is the depreciated project investment allocated to power purposes.

b Relicensing costs include the administrative, legal/study, and other expenses to date.

c Existing plant operation and maintenance includes operation and maintenance related 

to environmental measures associated with the current license.

d Commission fees are based on statements of annual charges received from the 

Commission for federal lands and administrative charges based on authorized 

capacity.

e Source: Application for New License, exhibit D, table D-6.2.2. 

f Energy values for McSwain powerhouse are based on New Exchequer plus a 

$25/MWh renewable energy credit added per California Renewable Portfolio 

Standards (Senate Bill X1-2, signed by Governor Brown in April 2011).

g The capacity value is based on the amortization and fixed operation and maintenance 

cost for a combined-cycle combustion turbine.

h Short-term interest rate provided in license application, Exhibit D, section 5.1.

i Long-term bond rate provided in license application, Exhibit D, section 5.1.

j Assumed by staff to be same as long-term interest rate.
363

Table 4-2. Parameters for the economic analysis of the Merced Falls Hydroelectric 

Project (Source: PG&E, 2012). 

Parameter Value

Period of analysis (years) 30

Taxes State 8.84%

Federal income tax rate 31.91%

Net investment, $a $3,800,000

Future major capital cost, $b $201,000 per year

Relicensing cost, $c $4,400,000

Operation and maintenance, $/yeard $387,000

Commission fees, $/yeare $8,000

Energy value ($/MWh) 9.1

Capacity value ($/MW-year) 162

Interest rate 8.79%

Discount rate 8.79%

a Net investment is the depreciated project investment allocated to power purposes.

b Future major capital costs include major plant rehabilitation to maintain present-day 

capability.

c Relicensing costs include the administrative, legal/study, and other expenses to date.

d Existing plant operation and maintenance includes operation and maintenance related 

to environmental measures associated with the current license.

e Commission fees are based on statements of annual charges received from the 

Commission for federal lands and administrative charges based on authorized 

capacity.

4.2 COMPARISON OF ALTERNATIVES

4.2.1 Merced River Project

Table 4-3 compares the installed capacity, annual generation, cost of alternative 

power, estimated total project cost, and difference between the cost of alternative power 

and total project cost for each of the alternatives considered in this draft EIS: no action, 

Merced ID’s proposal, the staff alternative, and staff alternative with mandatory 

conditions.
364

Table 4-3. Summary of the annual cost of alternative power and annual project cost for 

the alternatives for the Merced River Hydroelectric Project (Source: staff).

No Action

Merced ID’s

Proposal

Staff 

Alternative

Staff 

Alternative 

with 

Mandatory 

Conditions

Authorized 

installed capacity 

(MW)

103.5 103.5 103.5 103.5

Annual generation 

(GWh)

387 389 368 368

Dependable 

capacity (MW)

57.5 57.5 57.5 57.5

Annual cost of 

alternative power

($/MWh)

77.6 77.4 78.8 78.8

Annual project cost

($/MWh)

45.2 72.8 81.7 89.3

Difference between 

the cost of 

alternative power 

and project cost

($/MWh)

32.4 4.6 (2.9)a(10.5)

a A number in parentheses denotes that the difference between the cost of alternative 

power and project cost is negative, thus the total project cost is greater than the cost of 

alternative power.

4.2.1.1 No-action Alternative

Under the no-action alternative, the project would continue to operate as it does 

now. The project has an authorized installed capacity of 103.5 MW, a dependable 

capacity of 57.5 MW, and generates an average of 387,000 MWh of electricity annually. 

The average annual project cost is about $17,492,000, or $45.2/MWh. When we multiply 

the on-peak and off-peak energy components by the corresponding alternative energy 

cost and add a value to account for the project’s 57.5 MW of dependable capacity, we 

calculate a total value of the project’s power of $30,020,000, or $77.6/MWh in 2014 

dollars. To determine whether the proposed project is currently economically beneficial, 

we subtract the project’s cost from the value of the project’s power. Therefore, the 
365

project costs $12,527,000, or $32.4/MWh, less to produce power than the likely 

alternative.

4.2.1.2 Merced ID’s Proposal

Merced ID’s proposed project environmental/recreational resources measures are 

listed in table 4-5.

As proposed by Merced ID, the annual cost of operating the project is $28,331,000 

or $72.8/MWh. As proposed, the project would have an authorized installed capacity of 

103.5 MW, a dependable capacity of 57.5 MW, and would generate an average of 

389,000 MWh of energy annually. When we multiply the on-peak and off-peak energy 

components by corresponding alternative energy cost and add a value to account for the 

project’s dependable capacity, the result is the total value of the project’s power of 

$30,127,000, or $77.4/MWh. To determine whether the proposed project is economically 

beneficial, we subtract the project’s cost from the total value of the project’s power. The 

result is that in the first year of continued operation, the project would cost $1,795,000 or 

$4.6/MWh less than the likely alternative.

4.2.1.3 Staff Alternative

Table 4-5 also shows the staff-recommended measures, including additions, 

deletions, and modifications to Merced ID’s proposed environmental protection and 

enhancement measures, and the estimated cost of each. 

As proposed by staff, the annual cost of operating the project is $30,090,000 or 

$81.7/MWh. With staff’s recommended measures, the project would have an authorized 

installed capacity of 103.5 MW, a dependable capacity of 57.5 MW, and would generate 

an average of 368,000 MWh of energy annually. When we multiply the on-peak and offpeak energy components by corresponding alternative energy cost and add a value to 

account for the project’s dependable capacity, the result is the total value of the project’s 

power of $29,003,000, or $78.8/MWh. To determine whether the proposed project is 

economically beneficial, we subtract the project’s cost from the total value of the 

project’s power. The result is that in the first year of continued operation, the project 

would cost $1,077,000 or $2.9/MWh more than the likely alternative.

4.2.1.4 Staff Alternative with Mandatory Conditions

The cost of the mandatory and other measures not recommended by staff are 

included in table 4-5. Staff’s alternative with mandatory measures adds fish passage and 

requires the filing of annual operation plans. Any operation and maintenance cost BLM 

would require Merced ID to pay would also add to the costs for this alternative. With 

mandatory conditions added, the cost of operating the project is $32,866,000 or 

$89.3/MWh. This alternative would have an average annual generation of 368 GWh, and 

an average annual power value of 29,003,000, or about $78.8/MWh. Overall, the project 
366

would produce power at a cost that is $3,863,000 or $10.5/MWh more than the cost of 

alternative power. 

4.2.2 Merced Falls Project

Table 4-4 compares the installed capacity, annual generation, cost of alternative 

power, estimated total project cost, and difference between the cost of alternative power 

and total project cost for each of the alternatives considered in this draft EIS: no action, 

Merced ID’s proposal, the staff alternative, and staff alternative with mandatory 

conditions.

Table 4-4. Summary of the annual cost of alternative power and annual project cost for 

the alternatives for the Merced Falls Hydroelectric Project (Source: staff).

No Action

Merced ID’s

Proposal Staff Alternative

Installed capacity (MW) 3.4 3.4 3.4

Annual generation 

(GWh)

14.4 14.4 14.4

Dependable capacity 

(MW

1.9 1.9 1.9

Annual cost of 

alternative power

($/MWh)

112.4 112.4 112.4

Annual project cost

($/MWh)

153.8 155.5 157.8

Difference between the 

cost of alternative 

power and project cost

($/MWh)

(41.4) (43.1) (45.4)

a A number in parentheses denotes that the difference between the cost of alternative 

power and project cost is negative, thus the total project cost is greater than the cost of 

alternative power.

4.2.2.1 No-action Alternative

Under the no-action alternative, the project would continue to operate as it does 

now. The project has an authorized installed capacity of 3.4 MW, a dependable capacity 

of 1.9 MW, and generates an average of 14,400 MWh of electricity annually. The 

average annual project cost is about $2,215,000, or $153.79/MWh. When we multiply 

the average annual energy by the alternative energy cost and add a value to account for 

the project’s 1.9 MW of dependable capacity, we calculate a total value of the project’s 
367

power of $1,618,000, or $112.38/MWh in 2014 dollars. To determine whether the 

proposed project is currently economically beneficial, we subtract the project’s cost from 

the value of the project’s power. Therefore, the project costs $596,000 or $41.41/MWh 

more to produce power than the likely alternative.

4.2.2.2 Applicant’s Proposal

PG&E’s proposed project resource measures are listed in table 4-6. 

As proposed by PG&E, the annual cost of operating the project is $2,239,000 or 

$155.5/MWh. As proposed, the project would have an authorized installed capacity of 

3.4 MW, a dependable capacity of 1.9 MW, and would generate an average of 14,400 

MWh of energy annually. When we multiply the average annual energy by the 

alternative energy cost and add a value to account for the project’s dependable capacity, 

the result is the total value of the project’s power of $1,618,000 or $112.4/MWh. To 

determine whether the proposed project is economically beneficial, we subtract the 

project’s cost from the total value of the project's power. The result is that in the first 

year of continued operation, the project would cost $621,000 or $43.1/MWh more than 

the likely alternative.

4.2.2.3 Staff Alternative

The staff alternative would have the same capacity and energy attributes as

PG&E’s proposal. Table 4-6 shows the estimated cost of the additional staffrecommended environmental protection and enhancement measures, including the 

estimated cost of any changes to PG&E’s proposed measures. 

With staff’s recommended measures, the annual cost of operating the project is 

$2,273,000 or $157.8/MWh. Staff’s alternative would have an authorized installed 

capacity of 3.4 MW, a dependable capacity of 1.9 MW, and would generate an average of 

14,400 MWh of energy annually. When we multiply the average annual energy by the 

alternative energy cost and add a value to account for the project’s dependable capacity, 

the result is the total value of the project’s power of $1,618,000, or $112.4/MWh. To 

determine whether the proposed project is economically beneficial, we subtract the 

project’s cost from the total value of the project's power. The result is that in the first 

year of continued operation, the project would cost $655,000 or $45.4/MWh more than 

the likely alternative.

4.3 COST OF ENVIRONMENTAL MEASURES

Tables 4-5 and 4-6 give the cost of each of the environmental enhancement 

measures considered in our analysis. We convert all costs to equal annual (levelized) 

values over a 30-year period of analysis to give a uniform basis for comparing the 

benefits of a measure to its cost.
368

4.3.1 Merced River Project

Table 4-5. Cost of proposed and recommended measures for the Merced River Hydroelectric Project (Source: staff).

Enhancement/Mitigation 

Measures Entity

Staff 

Recommende

d?

Capital Cost

(2014$)

Annual 

Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

General

1. Annual consultation with BLM. Merced ID (GEN1); 

BLM (recommendation 1)

Do not adopt $0 $10,580 $10,580

2. Annual employee training. Merced ID (GEN2) Adopt $0 $12,000 $12,000 

3. Annual review of special-status 

species.

Merced ID (GEN3) Do not adopt $0 $8,000 $8,000 

4. Consultation regarding new 

ground-disturbing activities on 

federal lands.

Merced ID (GEN4) Adopt $0 $0 $0

5. Consultation regarding new 

facilities on federal lands.

Merced ID (GEN5) Adopt $0 $0 $0 

6. Develop and implement a 

coordinated operation plan for 

the Merced River Project and 

the Merced Falls Project.

Merced ID (GEN6) Adopt $0 $5,880 $5,880

7. Pay BLM annual operation and 

maintenance costs.

BLM Do not adopt Cost not 

specified
369

Enhancement/Mitigation 

Measures Entity

Staff 

Recommende

d?

Capital Cost

(2014$)

Annual 

Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

Geology and Soil Resources

1. Develop and implement a 

recreation facilities construction 

erosion control and 

reforestation plan.

Merced ID (G&S1) Adopt $0 $0 $0 

2. Develop and implement a 

LWM management plan. 

Merced ID (G&S2) Adopt $0 $12,460 $12,460 

Aquatic Resources

1. Develop and implement a 

recreation facilities construction 

hazardous material spill 

prevention.

Merced ID (WR1) Adopt $0 $0 $0 

2. Deliver water to Merced NWR. Merced ID (WR2) Adopt $0 $873,020 $873,020 

3. Streamflows and ramping rates. Merced ID (AQR1) Adopt $0 $187,000 $187,000 

4. Maintain Lake McClure 

minimum pool.

Merced ID (AQR2) Adopt $0 $0 $0 

5. Develop a general erosion 

control plan.

Water Board (condition 23) Adopt $10,000 $1,000 $4,000

6. Develop a hazardous spill 

prevention plan.

Merced ID (WR1); 

Water Board (condition 25–

29)

Adopt as 

modified by 

Water Board 

$10,000 $760
370

Enhancement/Mitigation 

Measures Entity

Staff 

Recommende

d?

Capital Cost

(2014$)

Annual 

Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

7. Continue 25 cfs release at New 

Exchequer dam.

California DFW 

(recommendation 3B[a])

Adopt Included in 

baseline 

operation cost

8. Develop water temperature 

monitoring plan.

Merced ID (T&E1); 

Water Board (condition 9); 

NMFS (recommendation 8); 

FWS (recommendation 5[j]); 

California DFW 

(recommendation 9[7])

Adopt 

(expanded 

Merced ID’s 

plan)

$35,000 $35,000

9. Develop a drought management 

plan.

Merced ID (AQR1); 

Water Board (condition 9);

Adopt 

(expanded 

Merced ID’s 

plan)

$10,000 $760

10. Develop a Merced NWR 

delivery plan.

Staff Adopt $60,000 $4,300

11. Develop an anadromous fish 

monitoring plan.

Merced ID (T&E2); 

Water Board (condition 20); 

California DFW 

(recommendation 3F)

Adopt

(expanded 

Merced ID’s 

plan)

$20,000 $1,520

12. Establish Merced river 

anadromous fish committee.

Merced ID (T&E3) Adopt $24,000 $24,000

13. Develop a gravel augmentation 

plan.

Conservation Groups, NMFS, 

California DFW, FWS

Adopt $30,000 $125,000 $127,280

14. Minimum instream flows. Staff Adopt $1,075,000 $1,075,000
371

Enhancement/Mitigation 

Measures Entity

Staff 

Recommende

d?

Capital Cost

(2014$)

Annual 

Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

15. Spring and fall pulse flows. Staff Adopt Included with 

minimum 

flows 

16. Minimum and pulse flows FWS Do not adopt $525,000 $525,000

17. Minimum and pulse flows California DFW Do not adopt $2,100,000 $2,100,000

18. Minimum and pulse flows NMFS Do not adopt $2,393,000 $2,393,000

19. Minimum and pulse flows Conservation Groups Do not adopt $1,667,000 $1,667,000

20. New minimum instream flow 

compliance gage.

NMFS; FWS; 

California DFW 

(recommendations 4, 5[A–F], 

and 9[1–6])

Do not adopt $150,000 $11,400

21. Develop fish passage upstream 

of Crocker-Huffman diversion 

dam.

Water Board, FWS, NMFS, 

Conservation Groups

Do not adopt $3,500,000 $2,500,000 2,766,000

22. Lower Merced River habitat 

restoration.

FWS, NMFS Do not adopt $100,000,000 

or more

$7,600,000

23. BMI monitoring. FWS (recommendation 8) Do not adopt $10,000 $50,000 $50,760

24. Monitor adult anadromous fish. Merced ID (T&E2) Adopt $300,000 $25,000 $47,800

25. Monitor juvenile anadromous 

fish.

Merced ID (T&E2) Adopt $100,000 $25,000 $32,600

26. Implement amended Aquatic 

Invasive Species Management 

Plan.

Merced ID (AQR4) Adopt $30,000 $2,280
372

Enhancement/Mitigation 

Measures Entity

Staff 

Recommende

d?

Capital Cost

(2014$)

Annual 

Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

Terrestrial Resources

1. Monitor western pond turtles, as 

part of TR6 protection plan.

Adopt $2,000 $2,000

2. Implement the Invasive Weeds 

Management Plan on federal 

lands integrated with a 

component on pest management 

and pesticide use.

Merced ID (TR1) Adopt as 

amended 

$0 $55,030 $55,030 

3. Implement the Vegetation 

Management Plan on federal 

lands.

Merced ID (TR2) Adopt as 

amended 

$0 $15,870 $15,870 

4. Implement the pesticide and 

herbicide use restrictions on 

federal lands.

Merced ID (TR3) Adopt as 

amended 

$0 $0 $0 

5. Implement bat management 

measures as part of a bat 

protection plan.

Merced ID (TR4) Adopt as 

amended

$0 $3,610 $3,610 

6. Implement the Bald Eagle 

Management Plan.

Merced ID (TR5) Adopt as 

amended

$0 $3,220 $3,220 

7. Implement the Limestone 

Salamander Habitat 

Management Plan.

Merced ID (TR6) Adopt as 

amended

$0 $2,260 $2,260 
373

Enhancement/Mitigation 

Measures Entity

Staff 

Recommende

d?

Capital Cost

(2014$)

Annual 

Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

Threatened and Endangered 

Species

1. Develop a protection plan for 

federally listed plants.

Water Board (condition 12 

and 13); 

FWS (recommendation 6[b]); 

BLM (recommendations 1

and 3)

Adopt $0 $2,500 $2,500 

2. Develop a protection plan for 

vernal pool fairy shrimp and its 

habitat.

Water Board (condition 6) Adopt $0 $2,500 $2,500 

3. Develop a protection plan for 

the San Joaquin kit fox.

Staff Adopt $0 $2,500 $2,500 

Recreational Resources

1. Implement the Recreation 

Facilities Plan for McClure 

Point recreation area on Lake 

McClure.

Merced ID (RR1a) Adopt $12,649,000 $453,500 $1,415,000 

2. Implement the Recreation 

Facilities Plan for Barrett Cove 

recreation area on Lake 

McClure.

Merced ID (RR1b) Adopt $16,270,000 $1,254,200 $2,491,000 

3. Implement the Recreation 

Facilities Plan for Horseshoe 

Bend recreation area on Lake 

McClure.

Merced ID (RR1c) Adopt $7,529,000 $477,100 $1,049,000 
374

Enhancement/Mitigation 

Measures Entity

Staff 

Recommende

d?

Capital Cost

(2014$)

Annual 

Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

4. Implement the Recreation 

Facilities Plan for the Bagby 

recreation area on Lake 

McClure.

Merced ID (RR1d) Adopt $4,547,000 $2,2670,000 $2,612,000 

5. Implement the Recreation 

Facilities Plan for the proposed 

Mack Island non-motorized 

recreation area on Lake 

McClure.

Merced ID (RR1e) Adopt $3,479,000 $170,800 $435,200

6. Implement the Recreation 

Facilities Plan for McSwain 

recreation area on McSwain 

reservoir.

Merced ID (RR1f) Adopt $9,094,000 $500,000 $1,191,000 

7. Provide recreation flow 

information and river access 

signage.

Merced ID (RR2) Adopt $2,000 $2,000

8. Develop a plan for stocking fish 

in Lake McClure and McSwain 

reservoir.

Merced ID (AQR3) Adopt as 

amended

$5,000 $35,000 $35,000 

Land Use and Aesthetics

1. Implement the Transportation 

Management Plan.

Merced ID (LU1) Adopt $0 $97,000 $97,000 

2. Implement the Fire Prevention 

and Response Plan on federal 

lands.

Merced ID (LU2) Adopt $0 $1,060 $1,060 
375

Enhancement/Mitigation 

Measures Entity

Staff 

Recommende

d?

Capital Cost

(2014$)

Annual 

Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

3. Implement the Visual Resource 

Plan on federal lands.

Merced ID (AER1) Adopt as 

amended 

$1,166 $1,166

4. Expand transportation plan to 

consult with agencies.

Adopt $0 $1,200 $1,200

Cultural Resources

1. Implement the HPMP. Merced ID (CR1) Adopt $0 $170,000 $170,000

4.3.2 Merced Falls Project

Table 4-6. Cost of proposed and recommended environmental mitigation and enhancement measures for the Merced 

Falls Hydroelectric Project (Source: staff).

Enhancement/Mitigation 

Measures Entity

Staff 

Recommended

?

Capital 

Cost

(2014$)

Annual Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

Aquatic Resources

1. Develop and implement a water 

quality plan.

PG&E Adopt $19,600 $6,000 every 

10 years

$6,300 

2. Develop an annual fish 

sampling plan.

PG&E Adopt $0 $16,000 $16,000

3. Continue LWD cleaning of 

intake.

PG&E Adopt $0 

(included)

$0 $0 
376

Enhancement/Mitigation 

Measures Entity

Staff 

Recommended

?

Capital 

Cost

(2014$)

Annual Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

4. Develop coordinated operation 

plan with Merced ID.

Staff Adopt $1,000 $1,000

5. Consult with technical advisory 

committee.

California DFW 

(recommendation 1); 

NMFS (recommendation 7)

Adopt $2,200 $2,200

6. Expand current LWD 

management plan.

Staff Adopt $13,800 $13,800

7. Expand PG&E’s proposed 

annual fish sampling plan in the 

Merced Falls reach.

California DFW 

(recommendation 1)

Adopt $20,000 $20,000

8. Develop fish passage. Conservation Groups; FWS 

(recommendation 1)

Do not adopt $65,000 $13,000

9. Water temperature monitoring 

and mitigation.

California DFW 

(recommendation 1)

FWS (recommendation 4); 

NMFS (recommendation 8)

Do not adopt $45,000 $45,000

10. Expand fish monitoring. NMFS (recommendation 4) Do not adopt $35,000 $35,000

11. Gravel augmentation. Water Board (condition 2); 

NMFS (recommendation 2); 

Conservation Groups

Do not adopt $80,000 $80,000

Terrestrial Resources

1. Develop a bald eagle 

management plan.

FWS (recommendation 5); 

Water Board (condition 5)

Adopt $0 $2,000 $2,000
377

Enhancement/Mitigation 

Measures Entity

Staff 

Recommended

?

Capital 

Cost

(2014$)

Annual Cost 

(2014$)

Levelized 

Annual 

Cost 

(2014$)

2. Develop a noxious weed and 

invasive plants control plan 

integrated with a component for 

pest management and pesticide 

use notification.

California DFW 

(recommendation 7); 

Water Board (condition 2)

Adopt $0 $15,000 $15,000

Threatened and Endangered 

Species

1. Develop a protection plan for 

the valley elderberry longhorn 

beetle.

FWS (recommendation 3); 

Water Board (condition 6)

Adopt $0 $2,000 $2,000

2. Develop a protection plan for 

the San Joaquin kit fox.

California DFW

(recommendation 7); 

Water Board (condition 2)

Adopt $0 $2,000 $2,000

Recreational Resources

1. Continue to operate and 

maintain recreation facilities at 

the project. 

PG&E Adopt Included in 

existing 

operation 

cost

$0 $0 

2. Develop a fish stocking plan. PG&E Adopt $2,000 $1,000 $1,400

Cultural Resources

1. Implement the HPMP. Adopt $6,000 $1,200
378

This page intentionally left blank.
379

5.0 CONCLUSIONS AND RECOMMENDATIONS

5.1 COMPREHENSIVE DEVELOPMENT AND RECOMMENDED 

ALTERNATIVE 

Sections 4(e) and 10(a)(1) of the FPA require the Commission to give equal 

consideration to the power development purposes and to the purposes of energy 

conservation; the protection of, mitigation of damage to, and enhancement of fish and 

wildlife; the protection of recreational opportunities; and the preservation of other 

aspects of environmental quality. Any license issued shall be such as in the 

Commission’s judgment will be best adapted to a comprehensive plan for improving or 

developing a waterway or waterways for all beneficial public uses. 

5.1.1 Merced River Project

This section contains the basis for, and a summary of, our recommendations for 

relicensing the Merced River Project. We weigh the costs and benefits of our 

recommended alternative against other proposed measures.

Based on our independent review of agency and public comments filed on this 

project and our review of the environmental and economic effects of the proposed 

project and its alternatives, we select the staff alternative as the preferred alternative. 

This alternative includes elements of the applicant’s proposal, section 4(e) conditions, 

section 401 water quality certification conditions, resource agency recommendations, 

alternative conditions under the Energy Policy Act of 2005, and some additional 

measures. We recommend this alternative because: (1) issuance of a new hydropower 

license by the Commission would allow Merced ID to operate the project as an 

economically beneficial and dependable source of electrical energy for its customers; 

(2) the 101.25 MW of electric energy generated capacity comes from a renewable 

resource that does not contribute to atmospheric pollution; (3) the public benefits of this 

alternative would exceed those of the no-action alternative; and (4) the recommended 

measures would protect and enhance fish and wildlife resources and would provide 

improved recreation opportunities at the project.

Finally, for the reasons outlined below, we recommend that certain conditions 

specified by the BLM and the Water Board not be included in the staff alternative. The 

conditions we are not recommending include: (1) funding to offset operation, 

maintenance, management, and administration costs incurred by BLM; (2) annual 

consultation to review project status and plans, results of studies, necessary 

modifications to plans, and protection measures for newly listed species; (3) a review of 

the lists of federally listed and special-status species and evaluation of potential project 

effects on newly listed species; and (4) a fish passage plan. We recognize, however, 

that the Commission must include these conditions in any license due to their 

mandatory nature.
380

In the following section, we make recommendations as to which environmental 

measures proposed by Merced ID or recommended by agencies and other entities 

should be included in any license issued for the project. In addition to Merced ID’s

proposed environmental measures, we recommend additional staff-recommended 

environmental measures to be included in any license issued for the project. We also 

discuss which measures we do not recommend including in the license.

5.1.1.1 Measures Proposed by Merced ID

Based on our environmental analysis of Merced ID’s proposal discussed in 

section 3.0 and the costs discussed in section 4.0, we recommend including the 

following environmental measures proposed by Merced ID in any license issued for the 

project. Our recommended modifications to Merced ID’s proposed measures are shown 

in italic.

Aquatic Resources

 Establish a Merced River technical advisory committee (T&E2) that 

expands the scope beyond measures that pertain only to anadromous fish 

downstream of the Crocker-Huffman diversion dam (such as topics that 

pertain to resident fish, aquatic and terrestrial monitoring results, and 

actions that could affect BLM-managed land, including Lake McClure 

water level management); establish guidelines for conducting meetings

that provide ground rules for decision making; and add BLM and the 

Park Service to the entities invited to participate on the committee 

because Lake McClure water management affects resources within the 

jurisdiction of these two agencies.

 Develop a coordinated operation plan for the Merced River and Merced 

Falls Projects (GEN6) in consultation with the Water Board, BLM, FWS, 

California DFW, NMFS, and the Park Service.

 Develop a site-specific erosion control and restoration plan in consultation 

with the Water Board, California DFW, FWS, and BLM and file the plan 

with the Commission at least 90-days in advance of initiating construction 

of recreation or other project facilities (G&S1); the plan would apply to 

construction on all land within the project boundary, not just on or 

affecting BLM-managed land.

 Develop a site-specific construction and non-routine maintenance

hazardous materials spill prevention, control, and countermeasure plan in 

consultation with the Water Board, California DFW, FWS, and, if 

construction is proposed on BLM-managed land, BLM, and file the plan 

with the Commission at least 90-days in advance of initiating construction 
381

or non-routine maintenance; the plan would apply to all construction and 

non-routine maintenance within the project boundaries, not just 

recreation facilities.

 For all controllable flows above 200 cfs, restrict the rate of change of 

releases from McSwain dam during any 1-hour period to not more than 

double or less than one-half the amount of controlled release from the 

reservoir at the start of the change; to measure compliance, flows would 

be measured at 1-hour intervals at the ramping rate compliance gage 

(AQR1 Part 2) at McSwain powerhouse; flows and stage at 1-hour 

intervals would also be monitored at the existing gage immediately 

downstream of Crocker-Huffman diversion dam and data from both gages 

annually reported to the Commission after review by the technical 

advisory committee.

 Measure and document compliance with minimum instream flow at the 

existing USGS gage 11271290 at Shaffer Bridge. Make the monitoring 

data available to the public in readily accessible formats and provide the 

data to USGS for inclusion in its annual hydrology summary reports 

(AQR1 Part 4).

 Monitor water temperature at four to eight sites selected by the technical 

advisory committee (T&E1).

 Maintain a minimum pool of not less than 115,000 acre-feet in Lake 

McClure except for drawdowns necessary to maintain minimum 

streamflows. Measure compliance at the existing USGS gage 11269500 

daily and convert the stage reading to acre-feet of storage (AQR2); 

annually report these data to the Commission to document compliance 

with water management measures and, when applicable, drought 

management plans.

 Notify the Water Board, BLM, FWS, NMFS, and California DFW by 

March 10 of the second or subsequent dry/critically dry water year if 

Merced ID has drought concerns. By May 1 of these same years, consult 

with these same agencies to discuss the project’s operational plans to 

manage drought conditions and file a drought plan with the Commission 

with a request for expedited approval (AQR1 Part 5). Implement the 

drought plan upon Commission approval.

 Operate the project for flood control as prescribed by the Corps and 

approved by the Commission (WR3).
382

 Provide 15,000 acre-feet of water to the Merced NWR annually unless 

otherwise agreed in advance by FWS and as approved by the Commission

(WR2).

 Develop, in consultation with the technical advisory committee, the Corps, 

and the California Department of Transportation, a LWM and debris

management plan that describes existing locations of LWM collection in 

Lake McClure and McSwain reservoir, potential options for moving the 

LWM collected to the Merced River downstream of Crocker-Huffman 

diversion dam, and suitable locations where LWM and debris can be 

placed in the active channel and possibly mobilized by 2- to 5-year high 

flow events. No LWM or debris would be stockpiled on BLM-managed 

land. 

 Annually monitor Chinook salmon and O. mykiss58 abundance in the 

Merced River downstream of Crocker-Huffman diversion dam using one 

RST (from January 1 through May 31) and one adult counting weir (from 

October 1 through December 31). The location of the monitoring stations 

would be determined by the technical advisory committee and approved 

by the Commission. Monitoring results would be posted on a publicly 

available website on the Monday following the week of data collection. 

An annual report would be developed in consultation with the technical 

advisory committee and filed with the Commission (T&E2).

 Implement the Amended Aquatic Invasive Species Management Plan filed 

on April 23, 2014, and supplemented on September 5, 2014 (AQR4), after 

revising it to include provisions to document incidental observations by 

Merced ID staff and consultants of quagga and zebra mussels, New 

Zealand mudsnails, Asian clams, American bullfrog, Eurasian milfoil, 

Brazilian elodea, and hydrilla and reporting of any incidental 

observations that rise to the level of needing follow-up management 

actions to the Commission. Consult with BLM, California DFW, and the 

Water Board on the staff-recommended plan revision and should the need 

to update the plan be identified in the future.

 

58 In this draft EIS, O. mykiss refers to both the anadromous (steelhead) and 

resident (rainbow trout) form of this species.
383

Terrestrial Resources

 Implement the Invasive Species Management Plan on federal land (as 

filed with the final license application) (TR1, as amended) with the 

following modifications to:

– stipulate that the measures in the plan apply to all land within the 

project boundary, including treatment measures for the existing 

population of perennial pepperweed on Merced ID land; 

– provide details about the specific BMPs; 

– integrate a component on pest management and pesticide use,

requiring agencies to be notified each year, for the upcoming year, of 

pesticide use on Merced ID’s land and on land administered by BLM

such that Merced ID would not use pesticides and herbicides on land 

administered by BLM without the prior written approval of BLM (TR3, 

as amended); and

– include descriptions and examples of the unexpected outbreaks that 

would not require notification of pesticide use to agencies.

 Implement the Vegetation Management Plan on federal land (as filed 

with the final license application) (TR2, as amended) with the following

modifications: 

– provide details about the specific BMPs that would be implemented as 

part of the plan;

– include maps in section 3.0 to show locations of elderberry plants and 

identify which plants show signs of occupancy by the valley elderberry 

longhorn beetle.

– require consultation with BLM, California DFW, and FWS during the 

planning phases for any new disturbance to identify the need for predisturbance surveys and develop protection measures for Commission 

approval for any sensitive species in the disturbance area; and

 Implement the Bald Eagle Management Plan (as filed with the final 

license application) (TR4, as amended) with modifications to:

– include information about roost sites on public information boards; 

– describe activities that would be considered emergencies, and why 

these activities would supersede bald eagle protection; 

– protect winter roost trees from vegetation management and future 

construction activities to reduce potential for degrading these areas;

and
384

– revise protocols and methodologies to be consistent with those 

recommended by FWS.

 Develop a bat protection plan for Commission approval including

measures to document all known bat roosts at project facilities, and if 

bats could be subject to human disturbance, install humane exclusion 

devices (TR5).

 Implement the Limestone Salamanders Sensitive Areas Management 

Plan (as filed with the final license application) (TR6, as amended) with 

modifications to:

– provide details about the specific BMPs that would be implemented as 

part of the plan; and

– site new hiking trails or modifications to existing hiking trails outside 

limestone salamander sensitive habitat. 

 Develop a protection plan for western pond turtles for Commission 

approval including measures to record the incidental observations of 

western pond turtles.

Threatened and Endangered Species

 Provide annual employee training regarding the identification of the 

special-status, non-native species, and sensitive areas that are known to 

occur in the project area and their locations in the project boundary 

(GEN2).

 Review special-status species lists annually, assess new species, and if 

necessary, consult with agencies to develop and implement special-status 

species protection measures, after Commission approval (GEN3).

 To minimize project-related and cumulative effects on the California 

tiger salamander, develop a protection plan for California tiger 

salamanders for Commission approval that includes the measure to

avoid use of pesticides in California tiger salamander habitat.

 Develop a protection plan for the San Joaquin kit fox for Commission 

approval, including provisions for surveys and protection and mitigation 

measures to minimize project-related and cumulative effects on the San 

Joaquin kit fox.
385

Recreation Resources

 Implement the Recreation Facilities Plan, filed on September 22, 2014,

with the following modifications to:

– extend the proposed paved bicycle lane along the entire length of Lake 

McClure Road (7.8 miles) between County Road J16 and the proposed 

parking area from the McSwain shoreline trailhead;

– remove the provision for a host site at the project’s Horseshoe Bend 

recreation area campground;

– identify the location of the project’s three floating restrooms provided 

on Lake McClure, and include an operation and maintenance schedule 

and construction and rehabilitation measures (if needed) for each 

restroom; and

– revise the implementation schedule to: to begin construction no earlier 

than Labor Day and no later than Memorial Day to avoid the primary 

recreation season; begin construction at the project’s Bagby 

recreation area within 2 years of license issuance; begin construction 

of the project’s non-motorized trails at the project’s Horseshoe Bend 

recreation area, McSwain reservoir shoreline, and the new Mack 

Island recreation area within 3 years of license issuance; begin 

rehabilitation planning at each project campground within 3 years of 

license issuance (to be completed within 6 years of license issuance);

and include a mid-license term rehabilitation assessment in the 

implementation schedule that would identify any project facilities and 

or water systems in need of rehabilitation. 

 Provide real-time recreation information on the California DEC (RR2), 

including:

– flow information for the Merced River below Merced Falls, Dry Creek 

near the city of Snelling, the Merced River near the cities of Snelling, 

Cressey, and Stevinson (existing measure);

– elevations for Lake McClure and McSwain reservoir (existing 

measure); and

– flow information for the Merced River at Shaffer Bridge (USGS gage 

no. 11271290). 

 Construct a parking area and install river access directional signage at the 

project’s existing gravel-surfaced parking area at Merced Falls Road near 

the Crocker-Huffman diversion dam (RR2).
386

 Develop a conceptual plan to align the project’s existing Merced River 

Trail to a new trail segment that would follow along the shoreline of 

Lake McClure and McSwain reservoir, filed on September 22, 2014.

 Annually stock rainbow trout, fingerling kokanee, and Chinook salmon 

in Lake McClure and McSwain reservoir for recreational fishing 

(AQR3).

Land Use

 Implement the Transportation Management Plan, filed on September 22, 

2014, to ensure project roads are adequately maintained, with the 

following modification:

– include an inventory of all project roads and current road conditions, 

a detailed schedule of maintenance based on that inventory, relevant 

BMPs that would be implemented, a schedule for monitoring project 

road use over the term of the license, and a schedule for consultation 

with BLM and the California Department of Forestry and Fire 

Protection.

 Implement the Fire Prevention and Response Plan, filed on September 

22, 2014, to provide for management, reporting, and the prevention of 

wildfires at the project.

Cultural Resources

 Implement the final HPMP upon license issuance. 

Aesthetics

 Implement the Visual Resources Plan, filed on September 22, 2014, to 

ensure visual quality objectives are met at the project through monitoring 

and consultation for all project lands.

5.1.1.2 Additional Measures Recommended by Staff

In addition to Merced ID’s proposed measures listed above, we recommend 

including the following staff-recommended measures in any license issued for the 

Merced River Project.

Aquatic Resources 

 Details of elements to be included in site-specific erosion control and 

restoration plans to protect project waters from erosion and sedimentation. 
387

 Details of elements to be included in hazardous material spill prevention, 

control, and countermeasure plans to protect project waters from 

contaminants.

 Use of the Hughes method to determine water year type.

 A staff minimum instream flow regime downstream of Crocker-Huffman 

diversion dam for the purpose of enhancing physical habitat, densitydependent conditions, and water temperature for Chinook salmon and 

O. mykiss.

 A 25-cfs minimum flow release from New Exchequer dam to ensure the 

channel is not dewatered.

 A water temperature monitoring plan in the Merced River between 

Crocker-Huffman diversion dam and Shaffer Bridge.

 A fall pulse flow to attract adult anadromous salmonids to the mouth of 

the Merced River and stimulate upstream migration.

 Spring pulse flows to stimulate outmigration of rearing anadromous 

salmonids and inundate riparian floodplains.

 A drought management plan.

 A Merced NWR water delivery plan.

 An anadromous fish monitoring plan.

 A gravel augmentation plan to enhance spawning habitat for anadromous 

salmonids.

Threatened and Endangered Species

 Develop a protection plan for vernal pool fairy shrimp and its habitat to 

reduce project effects on fairy shrimp and associated habitat.

 Develop a protection plan for federally listed plants potentially occurring 

at or near the project to minimize project effects on these plant species.

 Develop a protection plan for the California red-legged frog, foothills 

yellow-legged frog, and western spadefoot to reduce project effects on 

these species.

Recreation Resources

 Develop and implement a fish stocking plan that includes the species, 

size, and amount of fish to be stocked in Lake McClure and McSwain 

reservoir based on recreational use, angling demand, and state fish 
388

stocking management targets, and an implementation schedule to ensure 

appropriate recreational fish stocking at the project for the license term. 

Below, we discuss our rationale for our additional staff-recommended measures.

Erosion Control and Restoration Plans

Under the proposed project and staff alternative, the following activities would 

cause ground-disturbance at the project: construction of new recreation facilities, 

rehabilitation of existing recreation facilities, and non-routine maintenance such as 

replacement of existing project facilities. As discussed in section 3.3.1.2, Merced ID 

provides no details on what measures it would implement under its proposed erosion 

control and restoration plans to control erosion resulting from the ground-disturbing 

activities. Consequently, we have no basis to conclude whether or not erosion related to 

the ground-disturbing activities would be controlled by Merced ID. The Water Board 

[preliminary WQC condition 23] specifies that Merced ID should have measures in 

place to control excessive erosion, excessive sedimentation, and turbidity at the 

beginning of and throughout any ground-clearing activities, excavation, or any other 

project activities that could result in erosion or sediment discharges to surface waters. 

In addition, the Water Board specifies that erosion control blankets, liners with berms, 

and/or other erosion control measures should be used for any stockpile of excavated 

material to control runoff resulting from precipitation, and prevent material from 

contacting or entering surface waters. We find that the inclusion of a provision that 

Merced ID implement the protective elements specified by the Water Board under the 

proposed site-specific erosion control and restoration plans would protect environmental 

resources at and near the project from the effects of erosion. Therefore, we recommend 

that Merced ID develop, in consultation with the Water Board, California DFW, FWS, 

and BLM, specific elements of its proposed erosion control and restoration plans. The 

plans should include, at a minimum, the following: (1) a description of BMPs for 

erosion control that would be applied in specific circumstances; (2) provisions for 

inspecting erosion control measures while they are in place; (3) emergency protocols for 

erosion and sedimentation control (e.g., steps that would be taken if control measures 

fail during a storm event); (4) techniques that would be used to stabilize sites once 

construction is completed; and (5) a description of when and what type of water quality 

monitoring of surface waters would occur during and after ground-disturbing activities. 

Identifying such measures and protocols in the erosion control and restoration plans 

would assure that erosion does not unacceptably degrade water quality adjacent to 

construction and other ground-disturbance sites. For these reasons, we conclude that 

development of erosion control and restoration plans with our recommended 

components would be worth the estimated levelized annual cost of $4,000.

Hazardous Material Spill Prevention, Control, and Countermeasure Plans

Under the proposed project and staff alternative, the following activities would or 

could entail the use of hazardous materials (e.g., fuels, coolants, lubricants, herbicides, 
389

and pesticides) at the project: construction of new recreation facilities, rehabilitation of 

existing recreation facilities, and non-routine maintenance such as replacement of 

existing project facilities. Merced ID provides no details regarding the contents that 

would be included in its proposed construction hazardous materials spill prevention, 

control, and countermeasure plans for each activity that may involve use of 

contaminants. Consequently, as discussed in section 3.3.1.2, we have no basis to 

conclude whether or not the release of contaminants would be controlled by Merced ID. 

The Water Board specifies various measures to minimize the chances of contaminants 

reaching project waters (preliminary WQC conditions 25 [three measures], 26 [three 

measures], 27 [six measures], 28 [five measures], and 29 [one measure]; see section 

3.3.1.2 for details of these measures). We find that including in the site-specific 

hazardous materials spill prevention, control, and countermeasure plans a provision that 

Merced ID implement the protective principles specified by the Water Board would 

protect surface water and groundwater at and near the project from contaminants. 

Therefore, we recommend that Merced ID develop, in consultation with the Water 

Board, California DFW, BLM, and FWS, specific elements of its proposed hazardous 

material spill prevention, control, and countermeasure plans. The plans should include, 

at a minimum, the following: (1) a description of the BMPs for contaminant control 

that could be applied in specific circumstances; (2) emergency protocols for spill 

containment and remediation; (3) the location of emergency cleanup equipment in the 

event of contaminant release; (4) identification of the entities to be contacted in the 

event of a spill; (5) designated equipment refueling and maintenance areas; 

(6) provisions requiring equipment to be cleaned and inspected prior to entering a 

construction site to ensure it is in proper functioning condition; (7) post-spill water 

quality monitoring protocols to ensure remediation measures are effective; and (8) a 

listing of applicable local, state, and federal regulations that pertain to prevention of

spills and protection of water quality. Identifying such measures and protocols in the 

hazardous materials spill prevention, control, and countermeasure plans would assure 

that surface water and groundwater are protected from contaminants. Therefore, we

conclude that development of hazardous material spill prevention, control, and 

countermeasure plans with our recommended components would be worth the estimated 

levelized annual cost of $760. 

Determination of Water Year Type

Precipitation and runoff patterns vary considerably in the San Joaquin River 

Basin, and aquatic communities have adapted to these variances. Water management in 

this region accounts for this variability by establishing water year types that guide water 

allocation decisions. A water year type determination at the Merced River Project 

would govern how instream flow releases are adjusted based on meteorological 

conditions. Several different approaches to establishing water year types have been 

developed.
390

Merced ID’s proposed measure AQR1, Part 3, would calculate a water supply 

index for the Merced River based on unregulated (unimpaired) runoff below Merced 

Falls (i.e., inflow to Lake McClure) using the same methods currently used for the San 

Joaquin Valley Water Year Hydrologic Classification (San Joaquin Valley 60-20-20 

Index), which was developed by the Water Board for the San Joaquin River Basin as 

part of its Bay-Delta regulatory activities (Water Board 2006b). Five water year types 

would be established within this index: wet, above normal, below normal, dry, and 

critically dry. The water year types would be calculated as 60 percent of the current 

year’s April through July inflow plus 20 percent of the current year’s October through 

March inflow plus 20 percent of the previous year’s index. The numerical breakpoints 

(in thousands of acre-feet) for the five water year classifications for the San Joaquin 

Valley 60-20-20 Index and the Merced 60-20-20 Index methods are presented in 

table 5-1. 

Table 5-1. Comparison of alternative water-year type classifications. 

Water year type

San Joaquin Valley 

60-20-20 Index 

Classificationa

Merced ID’s 

Proposed Merced 

60-20-20 Index 

Classification

California DFW’s 

Recommended 

Classification 

(Hughes Method)

(in thousands acre-feet)

Wet >3,800 >650 >1,307

Above Normal >3,100 and <3,800 >530 and <650 >919 and <1,307

Below Normal >2,500 and <3,100 >420 and <530 >546 and <919

Dry >2,100 and <2,500 >360 and <420 >339 and <546

Critical <2,100 <360 <339

a Source: Water Board 2006b

Merced ID would begin using its proposed approach to determining water year 

type within 90 days of license issuance. For each year, water year type would initially 

be established in February and updated in March, April, and May. From May 15 to 

February 14 of the following year, Merced ID would base water year type on California 

DWR’s forecast published in May. Merced ID states that the water-supply indices for 

February and March would be calculated using the 90 percent exceedance forecast for 

unregulated runoff and the April and May indices would be calculated using the 75

percent exceedance forecast for unregulated runoff. FWS amended 10(j) 

recommendation 3(A1) and the Conservation Groups also recommend Merced ID’s 

proposed approach to determining water year types. Additional details on the Merced 

60-20-20 Index are presented in sections 3.3.1.1 and 3.3.1.2.
391

NMFS [10(j) recommendation 1.1A(7)] and California DFW [10(j) 

recommendation 3A] recommend that Merced ID use the “Hughes method” to 

determine water year type for instream flow releases. NMFS and California DFW state 

that Merced ID’s approach to water year determination using a 90 percent exceedance 

forecast for February and March and 75 percent exceedance forecast for April and May 

creates overly conservative predictions of inflows. California DFW estimates that this 

would result in drier than actual water year operations being implemented for February 

and March 40 percent of the time and for April and May, 25 percent of the time. The 

Hughes method is based on the water year forecast of unregulated runoff of the Merced 

River below Merced Falls published near the beginning of each month from February 

through May in California DWR’s Bulletin 120. Unlike the Merced 60-20-20 Index

that factors current and past-year conditions, the Hughes method does not rely on carry 

over storage within Lake McClure. NMFS and California DFW note that the Merced 

60-20-20 Index provides a disincentive for water conservation by reducing 

environmental flows when carry-over storage is low. California DFW recommends that 

the water year types be defined as having numerical breakpoints (in thousands of acrefeet) based on unregulated inflow to Lake McClure reported for water years 1901 to 

2012 (see table 5-1). California DFW also recommends that Merced ID perform an 

update to the water year type determination at the end of the water year using California 

DWR’s “October update,” which, if published, uses observed monthly unregulated 

runoff for the river rather than forecasted runoff.

Merced ID’s proposal and NMFS and California DFW’s recommendation to base 

water year type on California DWR’s forecast of unregulated runoff of the Merced 

River would both follow an accepted approach implemented in similar watersheds 

contributing to the San Joaquin and Sacramento Valleys. The agencies and the 

Conservation Groups agree that the Merced 60-20-20 Index as proposed by Merced ID 

would result in more conservative water-year type estimates than would the Hughes 

method. Specifically, calculation of the February and March indices and the April and 

May indices using California DWR’s 90 and 75 percent exceedance forecasts, 

respectively, instead of the median (50 percent exceedance; i.e., distinction between 

below and above normal conditions) forecast would produce lower runoff estimates that 

are biased towards ascribing below normal conditions. Additionally, incorporating 

updated, observed unregulated runoff volumes published by California DWR in 

October, when available, would improve water year type determination under either 

method throughout the water year and into the subsequent one compared with the 

forecast-based, Merced 60-20-20 Index determination. 

Based on our analysis in section 3.3.1.2, adoption of the Hughes method 

recommended by NMFS and California DFW would accomplish the following: 

(1) continued adherence to the California DWR’s forecasts for annual unregulated 

runoff in the Merced River during February, March, April, and May, (2) incorporation 

of updated observed runoff (full natural flows), when available, rather than complete 

reliance on forecast-based water year type, and (3) use of type classifications (numerical 
392

breakpoints) based on a quartile-based distribution of the full hydrologic record for the 

watershed. Therefore, we recommend that Merced ID use the Hughes method to 

determine water year type because it is more hydrologically comprehensive and does 

not discount for previous year storage in Lake McClure. The cost of establishing the 

water year type using the Hughes method would be similar to the cost associated with 

Merced ID’s proposed method. 

Minimum Instream Flows Downstream of Crocker-Huffman Diversion Dam

Merced ID’s, the agencies’, and the Conservation Groups’ proposed and 

recommended minimum flow regimes are all substantially different (tables 3-9 and 

3-10). Merced ID modeling results show variable habitat availability by flow regime 

and modeled life stage for Central Valley steelhead and fall run Chinook salmon. 

Balancing the different resource values associated with each flow regime represents a 

complex series of tradeoffs (e.g., enhancing temperature conditions for specific fish 

species and life stages with the limited amount of cold pool water in Lake McClure, 

enhancing physical habitat for specific life stages of anadromous fish, providing flows 

that encourage juvenile outmigration because the temperature regime is unlikely to be 

favorable, and conserving water for irrigation purposes) to derive a reasonable flow 

regime. 

As discussed in section 3.3.1.2, we consider the approach to establishing an 

appropriate minimum flow regime presented in the California DFW rationale document 

for its 10(j) recommendations to be a reasonable framework upon which to build a 

minimum flow regime compared to the approaches provided by FWS, NMFS, and the 

Conservation Groups. California DFW provides significant details (12 pages) on its 

recommended flows for the entire year. FWS and NMFS’ rationale does not cover the 

entire year, and the Conservation Groups embed irrigation restrictions into most of its 

flow recommendations. The California DFW flow regime seeks to: (1) enhance 

physical Chinook salmon spawning and incubation habit during late fall and early 

winter when water temperatures are not overly constraining; (2) consider densitydependent variables as fry emerge from spawning gravel in late January through 

February; (3) enhance water temperatures for smoltification during the spring; and (4) 

provide reasonable physical habitat for O. mykiss juveniles and adults during the 

summer. 

The California DFW recommended flow regime from October 16 through 

January 15 is intended to enhance Chinook salmon spawning and incubation habitat. 

The California DFW recommended minimum flows during this time for wet, above 

normal, and below normal water years (225 to 275 cfs) would provide about 80 to 100 

percent of the maximum WUA, depending on water year type and the specific reach 

between Crocker-Huffman diversion dam and Shaffer Bridge (Merced ID, 2013a). 

However, providing a minimum flow of 175 cfs during wet and above normal water 

years (which is the same as the FWS recommended target flow from October 16 

through February 28 and comparable to Merced ID’s proposed 180 and 160 cfs during 
393

wet and above normal water years from October 16 through January 31) would provide 

about 73 to 96 percent of maximum WUA and conserve Lake McClure water for use 

later in the year compared to the higher minimum flows during comparable water years 

recommended by NMFS, California DFW, and the Conservation Groups. The 

California DFW recommended minimum flows of 150 and 140 cfs during dry and 

critically dry water years would provide about 67 to 85 percent and 65 to 80 percent of 

the maximum WUA, respectively. We consider this to be a reasonable enhancement 

when water is scarce. However, flows of 150 cfs in October of dry years and 140 cfs 

during critically dry years and 140 cfs in November of critically dry years are more than 

would occur in the Merced River if the project did not exist (i.e., unregulated flows). 

We therefore recommend minimum flows during October and November that 

correspond to the unregulated flows for dry and critically dry water years shown in table 

3-12 to conserve Lake McClure storage (i.e., 100 and 120 cfs during dry and critically 

dry Octobers, respectively, and 130 cfs during critically dry Novembers). These flows 

are comparable to FWS’ target flows of 100 cfs non-pulse flow releases during October 

and November. Applying the 150 cfs minimum flow to below normal water years, 

which we also consider to be representative of relatively scarce available water, would 

also represent a reasonable enhancement compared to existing conditions. Merced ID’s 

proposed minimum flow from October 16 through January of 100 and 80 cfs during dry 

and critically dry water years would only provide about 48 to 55 percent and less than 

37 percent of the maximum WUA, respectively. Although this would represent an 

enhancement compared to the existing 60 cfs minimum flow, it would be unlikely for 

such a minor increase in potential Chinook salmon spawning and incubation habitat to 

result in tangible biological benefits to the community in the Merced River. Table 5-2

shows our recommended minimum flows for the entire year.

California DFW presents data that indicates that upon emergence, Chinook 

salmon fry survival is density dependent, with lower survival rates associated with 

higher densities. Increasing flows reduce density and enhance survival. Predicted 

survival of newly emerged fry between January 16 and the end of February would be 

between 60 and 100 percent for initial fry densities of 1,000,000 to 100,000, 

respectively, with flows of 400 cfs. This is the basis for the California DFW 

recommended minimum flow of 400 cfs during this period, regardless of water year 

type. Considering that minimum flows that would support spawning and incubation 

would be scaled back by most proposed and recommended flow regimes during less 

than wet water year types, we consider it appropriate to scale back the initial 

recommended flow of 400 cfs accordingly to conserve Lake McClure water for later 

use. Flows of 350 and 300 cfs during above normal and below normal water years, 

respectively, would still provide from about 98 to 100 percent fry survival assuming a 

starting density of 100,000 fry (which we consider a reasonable assumption because of 

the low escapement of Chinook salmon of natural origin during recent years; see figure 

3-22). These minimum flows are consistent with the recommended NMFS minimum 

flows for the first half of February in above normal and wet water years and exceed the 
394

Merced ID proposed and FWS recommended minimum flows for January and February. 

Continuing the California DFW recommended late fall-early winter minimum flow of 

150 and 140 cfs during dry and critically dry water years from mid-January to the end of 

February would provide about 92 and 91 percent fry survival, respectively, assuming a 

starting density of 100,000 fry. We consider this to represent a reasonable enhancement 

that would conserve water for later use when water is scarce.

During March and April, the California DFW minimum flow regime focuses on 

attempting to achieve the EPA temperature guideline of 16°C (60.8°F) for Chinook 

salmon and steelhead rearing and emigration. During wet and above normal water 

years, the California DFW minimum flow modeling results show the goal would be 

achieved down to RM 32.5 (Shaffer Bridge); in below normal water years to RM 38.0; 

in dry water years to RM 45.0; and critically dry water years to RM 46.5 (about 3.5 

miles downstream of the diversion dam). The reach from Crocker-Huffman diversion 

dam to RM 45.0 currently includes some of the best salmonid spawning and rearing 

habitat in the lower Merced River. However, we find two flows recommended by 

California DFW to be unnecessary. During the April 1 through 15 time frame, a higher 

minimum flow of 620 cfs would not be necessary during below normal water years to 

achieve the EPA guideline of 16°C (60.8°F) at RM 38.0 considering that a minimum 

flow of 590 cfs would achieve the guideline downstream to Shaffer Bridge (RM 32.5). 

For other 2-week periods during March and April, California DFW modeling shows that 

decreasing minimum flows as water years become drier would achieve the temperature 

goal at the designated river locations. Similarly, during April 1 through 15, the 

California DFW recommended flow of 560 cfs during critically dry water years is not 

necessary to achieve the temperature goal at RM 46.5 considering that a minimum flow 

of 510 cfs would achieve the goal down to RM 45.0. We find that minimum flows of 

560, 560, and 510 cfs during below normal, dry, and critically dry water years, 

respectively, from April 1 through April 15, would likely achieve appropriate water 

temperature enhancements comparable to the California DFW analogous flows of 620, 

510, and 560 cfs, while conserving water during below normal and critically dry water 

years. Monitoring water temperature would confirm our findings. NMFS and the 

Conservation Groups’ minimum flow regimes during March and April are generally 

higher than those recommended by California DFW, and although higher flows could 

further enhance the lower Merced River temperature regime, it would come at the cost 

of reduced water storage in Lake McClure, which means that there would be less water 

available during the irrigation season and reduced cold pool water for late spring 

temperature enhancement.

During May, most stakeholders recommend a pulse flow (in addition to 

recommended minimum flows) or high minimum flows that would inundate riparian 

floodplains and serve to stimulate young anadromous salmonid outmigration. The FWS 

target flow recommendation would inundate floodplains for 69 days from late March 

through early June in wet water years, 27 days in late March through mid-April in above 

normal water years, 12 days in late March through early April in below normal water 
395

years, and 5 days in late March during dry water years. These high spring flows are 

discussed under Spring Pulse Flows; however, during any such pulse or high flow 

releases, there would likely be water temperature enhancements in the lower Merced 

River unless the cold pool storage in Lake McClure had been expended during previous 

flow releases. Extending the California DFW recommended minimum flows for the 

April 16 through April 30 time frame into May until the beginning of a spring pulse 

flow would maintain any enhanced temperature condition if there is sufficient cold pool 

storage available.

With the relatively high staff recommended spring minimum flows as described 

previously, we expect there to be little if any Lake McClure cold pool water available to 

provide temperature enhancements to the lower Merced River during the summer. 

Assuming most Chinook salmon juveniles and smolt emigrate from the lower Merced 

River with a spring pulse flow, we focus on flows that provide suitable physical habitat 

for O. mykiss juveniles and adults, some of which are likely to remain in the lower 

Merced River throughout the summer. A minimum flow of 200 cfs that begins at the 

conclusion of a spring pulse flow (which we assume would be on June 1) and continues 

until October 15 or the start of a fall adult Chinook salmon attraction pulse flow would 

provide 90 to 98 percent of the maximum WUA for juvenile and adult O. mykiss 

(Merced ID, 2013a). This summer minimum flow is recommended by California DFW 

and comparable to the minimum flows recommended by the Conservation Groups. 

However it is lower than most of the minimum flows recommended by NMFS and 

FWS. It is unclear to us what additional habitat value higher summer minimum or 

target flows would provide, and higher flows would further deplete water storage in 

Lake McClure. However, flows of 200 cfs in August and September of dry years are 

more than would occur in the Merced River if the project did not exist (i.e., unregulated 

flows). We therefore recommend minimum flows during August (70 cfs during dry and 

60 cfs during critically dry) and September (60 cfs) that correspond to the unregulated 

flows for dry and critically dry water years shown in table 3-12 to conserve Lake 

McClure storage.

For the reasons discussed above, we recommend that Merced release the 

instantaneous minimum flows shown in table 5-2. Our recommended minimum flow 

regime includes elements of all agency-recommended flows and attempts to strike a 

balance between aquatic habitat enhancement and maintaining Lake McClure water 

storage for irrigation and water temperature enhancements. We recognize that our 

recommended minimum flow would reduce the average amount of water available for 

irrigators by an additional 20,000 acre-feet annually compared to existing conditions 

and would reduce the average annual generation by about 21 GWh at an estimated 

annual cost of $1,075,000. We conclude that the habitat enhancements for anadromous 

salmonids, potentially including federally listed Central Valley steelhead, would be 

worth any such costs.
396

Table 5-2. Staff-recommended minimum flows (cfs) by water year type (Source: staff).

Wet Above Normal Below Normal Dry Critically Dry

Jan 1-Jan 15 175 175 150 150 140

Jan 16-Feb 400 350 300 150 140

Mar 1-15 270 270 270 240 200

Mar 16-31 410 410 370 370 310

Apr 1-15 590 590 560 560 510

Apr 16-30 790 790 780 570 570

May 1-15 790a 790a 780a 570 a 570 a

May 16-31 790 a 790a 780a 570a 570a

June-July 200 b 200 b 200 b 200 b 200b

Aug 200 200 200 270 260

Sept 200 200 200 60 60

Oct 200c 200c 200c 100c 120c

Nov 175d 175d 150d 150d 130d

Dec 175 175 150 150 140

a Minimum flow up to the onset of the spring pulse flow.

b Minimum flow at the conclusion of the spring pulse flow.

c Minimum flow up to the onset of the fall pulse flow.

d Minimum flow at the conclusion of the fall pulse flow.
397

We summarize the expected effects and costs of proposed and recommended 

flow regimes based on Merced ID’s and staff’s modeling in table 5-3. The staffrecommended minimum flow regime would enhance salmonid spawning and incubation 

habitat; however, the degree of enhancement would be reduced during drier water years 

to conserve water for irrigation. The staff-recommended minimum flow would enhance 

temperature for salmonid fry rearing during the spring, but temperature objectives 

would only be achieved in 5.0 and 3.5 miles of river downstream of Crocker-Huffman 

diversion dam in an attempt to balance water for irrigation and generation with water for 

habitat enhancements. We recognize that the relatively high spring minimum flows that 

we recommend would still come at substantial costs to irrigators and power generation, 

but protecting the lower Merced River populations of Chinook salmon and O. mykiss by 

enhancing fry growth to the point where the probability of successful outmigration is 

increased prior to the summer would be worth the cost.

Minimum Instream Flow Downstream of New Exchequer Dam

California DFW [10(j) recommendation 3B(a)] recommends that Merced ID 

provide a minimum flow of 25 cfs below New Exchequer dam at all times. This is 

identical to what is required by article 40 of the current license. Merced ID contends 

that McSwain reservoir backs up to New Exchequer dam and there is no need for an 

instream flow requirement. However, although McSwain reservoir may back up to the 

base of New Exchequer dam when McSwain reservoir is at full pool, this is likely not 

the case when McSwain reservoir is drawn down. During drawdowns, a short riverine 

section exists and releasing a minimum flow of 25 cfs would ensure that this channel is 

not dewatered. We therefore recommend that Merced ID continue to release a 

minimum flow of 25 cfs from New Exchequer dam and document compliance with this 

measure as it does currently. Because this is a continuation of an existing measure, the 

cost of this measure is included in the existing operation and maintenance costs of the 

project.
398

Table 5-3. Comparison of estimated effects and costs of flow regimes associated with proposed and recommended flow 

regimes compared to existing conditions (Source: Merced ID, 2014c,d; staff)

Potential Effects Cost

Proponent Fall-Run Chinook 

Salmon

CV Steelhead EPA Water 

Temperature 

Guidelines

Water Deliveries Energy 

Generation

Value of 

Project 

Power

Merced ID -Reduces effective 

spawning habitat by 

4%

-Increases effective 

habitat for fry and 

juvenile rearing by 1%

-Nearly optimal 

physical spawning 

habitat in late 

October-January of 

wet and above normal 

water years, slight 

enhancement in other 

water years 

-Nearly optimizes inchannel fry and 

juvenile rearing 

physical habitat

-Reduces effective 

spawning habitat by 

5%

-No change in effective 

fry or juvenile rearing 

habitat 

-Increases effective 

adult rearing habitat by 

1%

-Physical juvenile oversummer in-channel 

rearing habitat 

optimized or nearly so 

in wet and above 

normal water year 

-Moderate enhancement 

in other water years

-Criteria for 

Chinook salmon 

juvenile rearing 

and emigration at 

RM 42.0a

exceeded 25% of 

the time

-Criteria for 

steelhead 

smoltification at 

RM 42.0 exceeded 

46% of the time

Significant shortages 

in 6 of 36 years and 

average annual 

shortage of 1,000 

acre-feet more than 

under existing 

conditions

Average 

annual 

increase of 1 

GWh

Average 

annual 

increase of 

$66,000
399

Potential Effects Cost

Proponent Fall-Run Chinook 

Salmon

CV Steelhead EPA Water 

Temperature 

Guidelines

Water Deliveries Energy 

Generation

Value of 

Project 

Power

NMFS -Reduces effective 

spawning habitat by 

4% 

-Increases effective 

habitat for fry by 1% 

and juveniles by 4% 

-October-January 

physical spawning 

habitat nearly optimal

-In-channel fry and 

juvenile physical 

habitat reduced 

-Increases effective 

spawning habitat by 

1%

-Increases effective fry 

habitat by 2% and 

juvenile over-summer 

effective rearing 

habitat by 2%

-Increases effective 

adult rearing habitat by 

4% 

-Physical juvenile oversummer in-channel 

rearing habitat 

moderately enhanced 

in all water years

-Criteria for 

Chinook salmon 

juvenile rearing 

and emigration at 

RM 42.0a 

exceeded 11% of 

the time

-Criteria for 

steelhead 

smoltification at 

RM 42.0 exceeded 

42% of the time

Significant shortages

in 19 of 36 years and

average annual 

shortage of 101,000 

acre-feet

Average

annual 

reduction of

41 GWh 

Average

annual 

reduction of

$2.393

million
400

Potential Effects Cost

Proponent Fall-Run Chinook 

Salmon

CV Steelhead EPA Water 

Temperature 

Guidelines

Water Deliveries Energy 

Generation

Value of 

Project 

Power

FWS (amended) -Reduces effective 

spawning habitat by 

5%

-Increases effective 

habitat for fry by 3% 

and juveniles by 4% 

-November-February 

physical spawning 

habitat nearly optimal 

in wet and above 

normal water year 

types, slight 

enhancement in other 

water years

-In-channel fry and 

juvenile physical 

habitat reduced

-Reduces effective 

spawning habitat by 

5%

-Increases effective fry 

habitat by 3%

-No change in effective 

juvenile rearing habitat

-1% increase in 

effective adult rearing 

habitat 

-Physical juvenile oversummer in-channel 

rearing habitat 

optimized or nearly so 

in wet and above 

normal water year 

-Moderate enhancement 

in other water years

-Criteria for 

Chinook salmon 

juvenile rearing 

and emigration at 

RM 42.0a

exceeded 21% of 

the time

-Criteria for 

steelhead 

smoltification at 

RM 42.0 exceeded 

43% of the time

-Physical juvenile 

over-summer inchannel rearing 

habitat nearly 

optimized or 

nearly so in all 

water years

Significant shortages

in 12 of 36 years and

average annual 

shortage of 24,000 

acre-feet more than 

under existing 

conditions.

Average

annual 

reduction of

10 GWh

Average

annual 

reduction

of

$525,000
401

Potential Effects Cost

Proponent Fall-Run Chinook 

Salmon

CV Steelhead EPA Water 

Temperature 

Guidelines

Water Deliveries Energy 

Generation

Value of 

Project 

Power

California DFW -Reduces effective 

spawning habitat by 

2% 

-Increases effective 

habitat for fry and 

juveniles by 6% 

-Physical spawning 

habitat optimized or 

nearly so from midOctober to midJanuary in all but 

critically dry water 

years

-In-channel fry and 

juvenile physical 

habitat reduced

-Increases effective 

spawning habitat by 

4%

-Increases effective fry 

rearing habitat by 16%

-No change in juvenile 

over-summering 

effective habitat 

-4% increase in 

effective adult rearing 

habitat 

-Criteria for 

Chinook salmon 

juvenile rearing 

and emigration at 

RM 42.0a

exceeded 1% of 

the time 

-Criteria for 

steelhead 

smoltification at 

RM 42.0 exceeded 

39% of the time 

-Physical juvenile 

over-summer inchannel rearing 

habitat optimized 

or nearly so in all 

water year types

Significant shortages

in 22 of 36 years and

average annual

shortage of 138,000 

acre-feet more than 

under existing 

conditions

Average

annual 

reduction of

35 GWh

Average

annual 

reduction of

$2.1 million
402

Potential Effects Cost

Proponent Fall-Run Chinook 

Salmon

CV Steelhead EPA Water 

Temperature 

Guidelines

Water Deliveries Energy 

Generation

Value of 

Project 

Power

Conservation

Groups

-Decreases effective 

spawning habitat by 

2% 

-Increases effective 

habitat for fry by 5% 

and juveniles by 6% 

-Physical spawning 

habitat optimized or 

nearly so in all water 

year types 

-Physical spawning 

habitat optimized or 

nearly so from midOctober to midJanuary in all but 

critically dry water 

years 

-In-channel fry and 

juvenile physical 

habitat reduced

-No change in effective 

spawning habitat 

-Increases effective fry 

rearing habitat by 12%

-Increases juvenile oversummering effective 

habitat by 3%

-Increases effective 

adult rearing habitat by 

1% 

-Criteria for 

Chinook salmon 

juvenile rearing 

and emigration at 

RM 42.0a 

exceeded 14% of 

the time 

-Criteria for 

steelhead 

smoltification at 

RM 42.0 exceeded 

40% of the time 

-Physical juvenile 

over-summer inchannel rearing 

habitat decreased 

in June of wet 

water years, 

slightly enhanced 

in June of above 

normal water 

years, and 

optimized or 

nearly so in JulySeptember of other 

water year types

Significant shortages

in 36 of 36 years and

average annual 

shortage of 144,000 

acre-feet more than 

under existing 

conditions

Average

annual 

reduction of

29 GWh

Average

annual 

reduction of

$1.6 million
403

Potential Effects Cost

Proponent Fall-Run Chinook 

Salmon

CV Steelhead EPA Water 

Temperature 

Guidelines

Water Deliveries Energy 

Generation

Value of 

Project 

Power

Commission Staff -Estimated to reduce 

effective spawning 

habitat by about 2%

-Estimated to increase 

effective habitat for 

fry and juveniles by 

about 6%,

b physical 

spawning habitat 

optimized or nearly so 

from mid-October to 

mid-January in all but 

critically dry water 

years

-In-channel fry and 

juvenile physical 

habitat reduced

-Estimated to increase 

effective spawning 

habitat by about 4% 

-Estimated to increase 

effective fry rearing 

habitat by 16% 

-No change in juvenile 

over-summering 

effective habitat 

-4% increase in 

effective adult rearing 

habitatb

-Criteria for 

Chinook salmon 

juvenile rearing 

and emigration at 

RM 42.0a

estimated to be 

exceeded 1% of 

the time 

-Criteria for 

steelhead 

smoltification at 

RM 42.0 estimated 

to be exceeded 

39% of the timeb

-Physical juvenile 

over-summer inchannel rearing 

habitat optimized 

or nearly so in all 

water year types

Increase in water 

supply shortage of 

20,000 acre-feet

Average

annual 

reduction of

21 GWh 

Average

annual 

reduction of

$1.075

million 

a This reach includes the primary salmonid spawning and rearing habitat downstream of Crocker-Huffman diversion dam.

b Staff did not model this scenario, but uses the modeled flow regime of California DFW, which is similar to the staff alternative.
404

Water Temperature Monitoring Plan

Although Merced ID proposes to monitor water temperature, it does not propose 

to develop a plan that would document the rationale for monitoring locations or other 

details of how this monitoring would be implemented. 

The Water Board [preliminary WQC condition 19] specifies that Merced ID 

develop a water temperature monitoring plan in consultation with a technical advisory 

committee that includes provisions for the installation of four to eight water temperature 

monitoring devices. The plan would include: (1) a statement of goals and objectives; 

(2) a description of monitoring protocols; (3) a description of factors that may affect 

water temperature and identification of the ones that are project-related; (4) monitoring 

and reporting schedules; and (5) a plan for corrective actions if data indicate that project 

operation is increasing water temperature. 

Agency recommendations regarding monitoring water temperatures vary. NMFS 

[10(j) recommendation 8] recommends that water temperature and flows be measured at 

10 locations ranging from RM 62.0 to a location between Shaffer Bridge and the 

confluence with the San Joaquin River. NMFS states that measuring flow at temperature 

monitoring stations is important because temperature is related to flow and having both 

would better enable interpretation of the monitoring results given the many diversions 

that occur in the lower Merced River. FWS [10(j) recommendation 5(j)] recommends 

that Merced ID continuously monitor water temperature at about 5-mile intervals 

between New Exchequer dam (RM 62.0) and Shaffer Bridge (RM 32.8), which would 

include six locations. California DFW [10(j) recommendation 9(7)] recommends that 

Merced ID include in an overall monitoring plan (other parameters would also be 

included in this plan) provisions for continuously monitoring water temperature at RMs 

62.0, 56.0, 52.0 (below Crocker-Huffman diversion dam), 46.5, 45.0, 42.0, 38.0, and 32.8 

(Shaffer Bridge).

We conclude that water temperature monitoring would be appropriate to document 

conditions in the project-affected reach downstream of Crocker-Huffman diversion dam 

to Shaffer Bridge and its relationship to anadromous fish habitat. As discussed in section 

3.3.1.2, monitoring water temperature immediately downstream of Crocker-Huffman 

diversion dam at the existing flow gage would document conditions at the upstream limit 

of anadromous fish habitat. Monitoring water temperature at the existing gage at Shaffer 

Bridge would document conditions at the downstream end of the project-affected reach. 

Placement of gages at the upstream and downstream end of the project-affected reach 

would enable temperature to be correlated with associated flows. The diversions that 

occur within this reach are not project-related, but monitoring water temperature at 

intermediate locations would help to interpret whether temperature measurements at 

Shaffer Bridge are related to non-project factors such as irrigation returns. Overall, 

monitoring water temperature at several locations would provide data on whether projectrelated flow releases from Lake McClure are achieving expected water temperature 
405

enhancements within the limitations of the available cold water pool and enable such 

effects to be separated from non-project effects. Ultimately, when combined with flow 

and anadromous fish monitoring, this monitoring would provide a basis for evaluating the 

need for future adjustments to the project flow regime. However, monitoring flows at 

interim locations or downstream of Shaffer Bridge, as recommended by NMFS, would 

not have a relationship to hydroelectric project operation. Although monitoring water 

temperature upstream of Crocker-Huffman diversion dam would have some value for 

interpreting downstream results, releases from New Exchequer dam have a relatively 

short residence time in McSwain reservoir, Merced Falls reservoir, and the CrockerHuffman impoundment. 

Developing the water temperature monitoring plan specified in preliminary WQC 

condition 19 would allow temperature monitoring gages to be placed at locations agreed 

upon by a technical advisory committee. We therefore recommend that such a plan be 

developed. However, we conclude that the plan should also include the justification for 

the placement of each monitoring station as well as the coordinates of the selected 

stations. As we note in the previous paragraph, we find clear justification for placement 

of temperature monitors in the reach from Crocker-Huffman diversion dam to Shaffer 

Bridge, but we are not convinced that there would be need for more than eight stations. 

We find that the benefits of establishing a water temperature monitoring plan that relates 

to hydroelectric project operation in consultation with the technical advisory committee 

would be worth the estimated annualized cost of $35,000. 

Fall Pulse Flow

The primary purpose of fall pulse flows is to attract anadromous fish to upstream 

spawning areas of the Merced River. Merced ID does not propose to release a fall pulse 

flow. Pulse flows recommended by FWS, NMFS, California DFW, and the Conservation 

Groups are variable in terms of both volume and how they are defined. We converted all 

recommended pulse flows to acre-feet to enable an equal comparison of the 

recommendations. The recommendations for fall pulse flows range from 7,932 to 13,881 

acre-feet in dry years and from 12,500 to 19,830 acre-feet in wet years. The 

recommendations of NMFS and the Conservation Groups represent a continuation of 

existing conditions under the Memorandum of Understanding with California DFW, with 

a constant fall attraction flow release of 12,500 acre-feet regardless of water year type. 

California DFW and FWS recommend providing 1,000 or 1,200 cfs, respectively, for 

varying numbers of days depending on water year types, which equates to 11,880 to 

23,760 acre-feet, for California DFW’s recommendation and 7,932 to 19,830 acre-feet 

for FWS’ recommendation. California DFW notes its reason for its recommended 

maximum pulse flow of 1,000 cfs is to (1) avoid floodplain inundation, which would not 

be desirable during the spawning season, and (2) keep spawning Chinook salmon in the 

channel proper. Fall floodplain inundation is atypical during the Chinook salmon 

spawning period and if redds should be constructed in the inundated floodplain during a 

short-term attraction flow release, they would be dewatered when the flows recede. The 
406

reduction in the fall pulse flow duration during dry and critically dry water years to 

11,880 and 7,932 acre-feet in the California DFW and FWS recommendations, 

respectively, would preserve water and associated cold pool storage in Lake McClure 

while simultaneously provide the benefits of fall pulse flows to attract adult Chinook 

salmon to the mouth of the Merced River. 

A fall pulse flow release would continue to attract adult Chinook salmon to the 

Merced River for spawning. Pulse flows should not be such that over bank flows occur 

to ensure that spawning occurs in the channel proper and therefore should be restricted to 

no more than 1,000 cfs. Releases of 1,000 cfs would need to occur for between 

approximately 6 and 7 days to reach the current, NMFS, and Conservation Groups’ 

recommended fall block pulse flow of 12,500 acre-feet. Increasing the number of days 

that fall pulse flows are released to 10 or 12 days, as FWS and California DFW 

recommend during wet, above normal, and below normal water years, could result in 

enhanced salmon attraction. However, it would also result in an additional depletion in 

the volume of water in Lake McClure. We consider the value of carrying over as much 

water as possible for use for habitat enhancement in the lower Merced River and 

irrigation during a following year to outweigh the potential increased attraction of 

Chinook salmon that could be achieved with an additional 3 to 6 days of fall releases. 

We therefore recommend a fall pulse flow release of 1,000 cfs during October or 

November until a total volume of 12,500 acre-feet is released, including the volume of 

water associated with the staff-recommended minimum flow during this period. Not 

including the volume of required minimum flows in the fall pulse flow could enable pulse 

flow releases to occur for a longer period of time, but as we note above, it would further 

deplete Lake McClure storage. Monitoring salmonid upstream migration in the lower 

Merced River, as we recommend, would provide data to assess the effectiveness of any 

fall pulse flow that may be included in a new license and provide a basis for adjustments, 

if necessary. The exact timing of the release would be determined by the technical 

advisory committee. This would essentially be a continuation of an existing measure 

with the exception that the current pulse flow release does not include the minimum 

flows included in the existing license (which range from 15 to 100 cfs under the current 

license). Therefore, the cost of pulse flow release is included in the cost of the minimum 

flow proposals. 

Spring Pulse Flows

Spring pulse flows from precipitation and melting snow pack in unregulated rivers 

can facilitate downstream migration of juvenile/smolt salmonids, transport bedload, 

remove fine sediments from spawning gravels and, when the floodplain is inundated, 

promote recruitment of riparian tree species such as cottonwoods. Lake McClure is 

operated for flood control and irrigation storage so that the high spring pulse flows are 

dampened (see figures 3-2 through 3-7). Releasing discrete Merced River pulse flows in 

the spring that to some degree mimic the pulse flows in unregulated rivers can provide 

some of these environmental benefits.
407

Merced ID does not propose to release a spring pulse flow. Discrete spring pulse 

flow volumes recommended by the agencies and Conservation Groups range from 7,920 

to 10,000 acre-feet in dry years and from 15,840 to 60,000 acre-feet in wet years. In 

general, NMFS and California DFW recommend higher pulse flows during wetter water 

years with the objective of providing at least some floodplain inundation to enhance 

riparian floodplain vegetation development and increase food availability for rearing 

native salmonids. In contrast, FWS and the Conservation Groups only recommend 

discrete spring pulse flows during the driest water years, although an extended spring 

pulse flow is embedded in the FWS and California DFW minimum flow 

recommendations. The basis for the approach given by the Conservation Groups and 

California DFW is that a late spring pulse flow would facilitate successful outmigration 

of those salmonids that are able to survive through the spring, prior to encountering low 

flow and high temperature conditions during the summer. Similarly, FWS states that by 

providing relatively cold water (i.e., cooler than 15oC) to the lower Merced River during 

the spring, smoltification of juvenile salmon and steelhead would be expedited, and 

outmigration would occur prior to low flow, high temperature conditions that promote 

disease and predation by warmwater predators. We conclude that the stated reasons for 

these approaches are valid and selecting the most appropriate spring pulse flow approach 

necessitates balancing environmental benefits against the effects on available storage in 

Lake McClure for use during the primary irrigation season.

Our analysis in section 3.3.1.2 supports a gradual spring increase of flows to a 2 or 

3-day maximum followed by a gradual decrease in flows to stimulate germination of 

cottonwood and other riparian vegetation with the goal of up to 9 days of floodplain 

inundation. This concept is recommended by NMFS and would apply to wet, above 

normal, and below normal water years. This spring pulse flow would also serve to 

stimulate salmonid outmigration prior to stressful summer flows and temperature

conditions, if timed appropriately, provide some geomorphic functions, and enable 

salmonids to gain access to food sources and cover when flows exceed 1,000 cfs (the 

flow at which flows begin inundating the floodplain). We recognize that there is natural 

variability in the magnitude of spring pulse flows during different water years and 

mimicking this variability would be ideal. However, the lower Merced River is regulated 

and if the floodplain inundation and channel maintenance objectives can be achieved with 

a release of 30,000 acre-feet (the below normal water year NMFS recommendation), we 

are not convinced that the additional 20,000 to 30,000 acre-feet recommended by NMFS 

for above normal and wet water years, respectively, would warrant the additional loss of 

Lake McClure water storage.

We also agree with the agencies and Conservation Groups that during dry or 

critically dry water years, when spring floodplain inundation flows are not the goal of 

pulse flow releases, a short-term pulse flow would likely stimulate salmonid emigration 

from the lower Merced River prior to stressful summer conditions. The range of 

critically dry water year flows to achieve this objective offered by stakeholders is broad: 

10,000 acre-feet by NMFS, 20,000 acre-feet by the Conservation Groups, and 30,942 by 
408

California DFW. We expect that if a critically dry water year pulse flow is effective in 

stimulating salmonid outmigration, a similar release during dry water years would 

achieve the same outcome. We have no data to support which of these flows would 

result in a meaningful stimulation of salmonid outmigration. Monitoring outmigration, as 

we recommend (discussed in detail in a following subsection) would provide a measure 

of effectiveness and a basis for adjusting future dry and critically dry water year pulse 

releases. 

For these reasons, we recommend that Merced ID release a spring pulse flow 

consisting of 30,000 acre-feet during wet, above normal, and below normal water years 

that would consist of flows equal to or above 1,000 cfs for 9 days, and peak flows that 

hold for 2 or 3 days, with a gradually ascending and descending hydrograph. To 

conserve Lake McClure storage, we recommend that this volume include the volume 

released in accordance with the minimum flow that may be included in a new license. 

Our recommended monitoring of spring salmonid outmigration, discussed later, would 

provide a basis for assessing the effectiveness of the spring pulse flow in stimulating 

outmigration and enable adjustments to be made, if necessary. During dry and critically 

dry water years, we recommend a spring pulse flow release of 10,000 acre-feet (which 

would equate to 1,040 cfs for about 5 days). After a minimum of two dry or critically dry 

water years, Merced ID, in consultation with the technical advisory committee, would 

make recommendations in a report to the Commission regarding whether anadromous 

fish outmigration data support increasing the volume of the spring pulse flow or 

continuing the 10,000 acre-feet spring pulse flow release to achieve outmigration 

stimulation. The specific timing of the beginning of the spring pulse flows and the 

configuration of the specific flow releases (as long as the recommended total volume is 

released) during all water year types would be determined by the technical advisory 

committee and approved by the Commission. The cost of the spring pulse flows are 

included in the cost of the minimum flow proposal. Although there would be some 

additional loss of generation capability and water for irrigation with our recommendation, 

we consider the benefits to juvenile Chinook salmon and potential benefits to federally 

listed Central Valley steelhead to be worth any such costs.

General Drought Management Plan

The Water Board [preliminary WQC condition 9] specifies that Merced ID submit 

a drought plan within 1 year of license issuance. The plan would provide overarching 

guidance for operation during an emergency drought and/or multiple critically dry years 

and would be created in consultation with the technical advisory committee. The plan 

would include Commission license or water quality certification variances that Merced 

ID may request. 

Merced ID proposes and we recommend (in section 5.1.1.1) that during years in 

which drought conditions can be predicted, a drought management plan specific to that 

year should be developed, because it would ensure prompt notification of drought 

concerns to the resource agencies, and effective consultation and development of 
409

appropriate emergency operational plans tailored to the specific circumstances of each 

drought. However, as we recommend below, some elements of drought management can 

be determined regardless of the specific circumstances associated with a particular year. 

As we note in section 3.3.1.2, we prefer this proactive approach rather than waiting until 

a drought is imminent or in progress to develop all of the details regarding how each 

drought would be managed. Consequently, we recommend that Merced ID, in 

consultation with the technical advisory committee, develop a general drought 

management plan. The plan would include, but not be limited to: (1) the measures that 

would be considered to address droughts when they occur; (2) decision paths regarding 

how management options for a specific drought would be decided; and (3) a listing of 

any Commission license conditions, BLM 4(e) conditions, and WQC conditions that 

would require variances with each of the potential drought management measures 

identified in item (1). We estimate that the levelized annual cost to develop this plan 

would be $760 but the time saved and associated public benefit in developing, gaining 

approval, and implementing effective site-specific drought management plans would be 

worth this relatively minor cost. 

Merced National Wildlife Refuge Water Delivery Plan

Merced ID proposes a continuation of the existing measure to annually provide 

15,000 acre-feet of water to the Merced NWR. Both FWS and California DFW 

recommend specific monthly deliveries to the Merced NWR with maximum deliveries 

occurring from September through December to facilitate winter refuge flooding. 

Merced ID, in its letter filed on September 5, 2014, states that water is available for 

delivery to the Merced NWR only during the irrigation season (March 1 through October 

31), and that providing water to the NWR from November through February is not 

possible because of the need for flood control (water levels in Yellowstone Lake, 

upstream of Lake McClure are kept low in the winter to capture spring high flows), 

dewatering the canals for maintenance, and health and safety considerations.

On May 22, 1992, the Commission ordered Merced ID to implement a plan for 

installing a water delivery system to provide 15,000 acre-feet to the entire refuge as 

required by article 45 of the current license.59 Included in the order was a provision to 

construct a 0.5-mile-long canal from Deadman Creek to the northeast corner of the 

Merced NWR. According to FWS, this canal was only used for one season and was 

ineffective in providing water to the refuge. FWS installed lift pumps on Deadman Creek 

to address the shortfall of water to this portion of the refuge; however, during years when 

capital to operate the pumps is unavailable, the northeast portion of the refuge does not 

receive water. FWS reported that from 2006 through 2013, actual deliveries to the 

Merced NWR never reached the 15,000 acre-feet specified in the current license and 

 

59 59 FERC 62,195
410

ranged from 9,130 to 12,271 acre-feet (average of 10,501 acre-feet). In addition, FWS 

reported that Merced ID sold an average of 4,929 acre-feet of water per year to the U.S. 

Bureau of Reclamation and FWS for delivery to the San Luis NWR during September 

through February. FWS states that at least some of this water originated from 

Yellowstone Lake and that some of it passed to the San Luis NWR through the Snobird 

Unit of the Merced NWR. FWS points to this as evidence that it is possible for Merced 

ID to provide water for Merced NWR’s purposes during periods outside the irrigation 

season. We note that if the water delivery data provided by FWS is accurate, the amount 

of water sold to the San Luis NWR would have enabled full delivery to be achieved if it 

had been delivered to the Merced NWR.

The agencies and Merced ID also differ in how deliveries should be adjusted in 

drier water years. The agencies include a provision for a reduction in water provided to 

Merced NWR in critically dry water years but with Merced ID reimbursing FWS for the 

cost of pumping groundwater to make up for the shortfall. Merced ID makes no such 

provision in its proposed measure, but in its response to the agencies’ 10(j) 

recommendations, states that if Merced ID reduces water deliveries to irrigators during 

dry and critically dry water years, deliveries to the Merced NWR should also be reduced 

in an equal proportion.

The groundwater resources in the Central Valley are under increasing demand 

because of the limited availability of surface water (California DWR, 2014). We 

consider it uncertain that groundwater would be available to compensate for reduced 

deliveries by Merced ID during dry or critically dry water years, or that groundwater use 

for compensation would be recommended in future years. We note that if irrigation 

water available for delivery by Merced ID to farmers is decreased because of increased 

flows to the Merced River downstream of Crocker-Huffman diversion dam, it would 

likely result in increased demand for groundwater by farmers to make up for this 

shortfall. 

There is no disagreement between the agencies and Merced ID that Merced ID 

should continue to provide 15,000 acre-feet of water to the Merced NWR as required 

under the current license and we recommend this measure in section 5.1.1.1 , because it 

would continue to mitigate for wildlife habitat inundated by Lake McClure. However, 

there remains disagreement regarding whether it is possible or feasible to deliver a 

portion of this total outside of the irrigation season. As indicated in section 3.3.1.2, we 

agree with the agencies’ rationale that providing water to the refuge throughout the year 

would have environmental benefits. One of the factors that influences whether or not 

water can be delivered to the refuge outside of the irrigation season involves assessing a 

complex system of irrigation conduits that are currently outside of the Commission’s 

jurisdiction. It is also unclear to us based on the available information whether the 

agency recommendation to provide “a device for delivering water to the Snobird Unit of 

Merced NWR along Bear Creek” would be necessary to achieve the goal of delivering 

15,000 acre-feet of water to the refuge. We conclude that the most effective means to 

resolve this disagreement is for the entities most familiar with the system—Merced ID, 
411

FWS, and California DFW—to further consult regarding the feasibility of providing 

water to the Merced NWR outside of the irrigation season. It is also evident that for 

license compliance purposes, there is a need to enhance documentation of how much 

water is delivered each year to the Merced NWR and the basis for the delivery estimates. 

Consequently, we recommend that Merced ID develop a Merced NWR water 

delivery plan, in consultation with FWS and California DFW, to ensure to the extent 

reasonably practical, the delivery of 15,000 acre-feet to the refuge during times of the

year when this water would provide the most benefit to wildlife. Elements in the plan 

would include the following:

 Provisions to conduct a feasibility study for providing the recommended 

monthly volumes of water to the Merced NWR on a year-round basis, 

including an assessment of adverse and beneficial effects, estimated costs for 

any needed infrastructure changes, and a report with a recommendation 

regarding proposed actions. 

 An assessment of whether an enhancement of water delivery to the Snobird 

Unit of the Merced NWR is needed to achieve the overall annual or monthly 

water delivery objectives.

 A clear statement regarding where water delivery to the Merced NWR would 

be measured and the means for measuring and reporting monthly deliveries to 

the agencies and the Commission.

 An evaluation of the environmental effects on the refuge if monthly deliveries 

are curtailed during dry or critically dry water years and make-up water is 

obtained via groundwater, and the ramifications if there are future restrictions

on the use of groundwater in the Central Valley.

Development of this plan and the associated feasibility report described in the first 

bullet would provide a basis for the Commission to approve a practical means of 

providing our recommended 15,000 acre-feet of water to the Merced NWR in a way that

optimizes benefits to wildlife habitat. It would also provide the Commission with 

enhanced ability to maintain oversight over this important environmental measure. We 

estimate that the annual levelized cost of developing this plan and associated report 

would be $4,300, but we conclude that the cost of providing clarity and documentation of 

issues that are now disputed is warranted.

Developing and gaining Commission approval for modifications to the water 

delivery process that would result from our recommended Merced NWR water delivery 

plan and feasibility study would take time, and we expect Merced ID to continue to 

provide 15,000 acre-feet of water to the Merced NWR until any such modifications are 

approved. Consequently, as an interim measure, we recommend that Merced ID 

implement its proposed measure to deliver water to the Merced NWR (WR2), which is 

essentially a continuation of the current process. We also recommend that Merced ID 
412

report the amount of water delivered to the refuge on an annual basis. Any costs 

associated with this interim measure would be minimal.

Anadromous Fish Monitoring Plan

Merced ID proposes to, and we recommend that Merced ID monitor anadromous 

salmonids downstream of Crocker-Huffman diversion dam (measure T&E2). The 

Merced ID monitoring program would use one RST and one counting weir to be located 

based on recommendations from the technical advisory committee and contingent on land 

owner approval. The counting weir would operate annually from October 1 through 

December 31 to monitor adult Chinook salmon and O. mykiss migrating upstream into 

the Merced River and would acquire data on time, direction of migration, size, sex, and 

marks such as adipose fin clips. For all other fish species passing through the weir, 

Merced ID would collect data on time, direction of movement, number, species, and size. 

The RST would be operated annually from January 1 through May 31 to monitor juvenile 

Chinook salmon and O. mykiss migrating downstream from the spawning reaches in the 

lower Merced River and would acquire data on individual size, weight, and life stage 

from a representative sample of the catch.

The Water Board [preliminary WQC condition 20] specifies that Merced ID 

develop an anadromous fish monitoring plan that includes: (1) a statement of the goals 

and objectives; (2) a description of the proposed monitoring protocols; (3) a description 

of factors that could adversely affect California and federally listed species and whether 

the factors are related to project operation; (4) a monitoring and reporting schedule; (5) a 

plan for corrective actions if monitoring shows the project is adversely affecting 

anadromous fish or their habitat; and (6) protective measures. California DFW, as part of 

10(j) recommendation 3F, recommends that Merced ID monitor salmonid habitat and 

populations and if stressful conditions are documented, implement fish rescue measures 

comparable to the emergency response that California DFW conducted in the spring and 

summer of 2014.

Although the proposed and staff-recommended measure provides reasonable 

monitoring for adult and juvenile anadromous salmonids, Merced ID does not specify the 

locations of the upstream or downstream monitoring stations because they would not be

identified until after a license is issued and consultation with the technical advisory 

committee had occurred. Therefore, we have no basis to evaluate the reason for 

placement of the monitoring stations at specific locations and whether they would 

appropriately identify potential project-related direct and indirect effects. Developing an 

anadromous fish monitoring plan to include the first four elements specified by the Water 

Board, in consultation with the technical advisory committee, would provide 

documentation of specific monitoring, consultation, and reporting procedures that would 

be implemented.

We recognize that monitoring is an important component for protecting 

anadromous fish; however, it does not in and of itself provide for adequate protection 
413

from project-related effects. Monitoring anadromous fish, combined with water 

temperature monitoring in the project-affected reach could form the basis for establishing 

immediate and long-term protection strategies for anadromous fish as developed by the 

technical advisory committee. Such strategies could include adjustments to project 

operation. We expect the need for adjustments to hydroelectric project operation or 

facilities would be identified within the first 10 years of a new license, unless substantial 

changes to project operation occur within that period. Protection strategies considered 

should also include a provision for fish rescue when water temperatures in the reach 

between Crocker-Huffman diversion dam and Shaffer Bridge become overly stressful. 

We conclude that not all stressful conditions are directly related or only partially related 

to hydroelectric project operation, Consequently, items (3), (5), and (6) of the Water 

Board specified plan link corrective actions to project effects. We agree that Merced ID 

should only be responsible for supporting fish rescue efforts if there is a linkage to 

project operation and that Merced ID should not bear the entire cost of any such fish 

rescue efforts. Therefore, we conclude that the entities responsible for each element of a 

fish rescue program should be identified. 

Consistent with the Water Board condition, we recommend that Merced ID 

develop, in consultation with the technical advisory committee, an anadromous fish 

monitoring plan that includes the following: (1) a statement of the goals and objectives; 

(2) a description of the proposed monitoring locations, the rationale for selecting these 

locations, and the proposed monitoring protocols; (3) a description of factors that could 

adversely affect Chinook salmon and Central Valley steelhead in the lower Merced River 

from Crocker-Huffman diversion dam to Shaffer Bridge and whether these factors are 

related to project operation; (4) a monitoring and reporting schedule; (5) provisions for 

making recommendations for corrective actions if monitoring shows the project is 

adversely affecting anadromous fish or their habitat and reporting any such 

recommendations and associated costs to the Commission for approval; and 

(6) identification of the process that would be used for identifying Merced ID’s 

responsibilities during any fish rescue effort that is linked to project operation. We 

estimate that the levelized annual cost of developing an anadromous fish monitoring plan 

would be $1,500, but the value that such monitoring would have in interpreting other 

measures, such as the effectiveness of the instream flow measures, and the clarity that 

would be established regarding actions that could be taken based on the monitoring 

results, would be worth the cost.

Gravel Augmentation Plan

Gravel trapped behind project dams reduces the amount of gravel available for 

salmonid spawning in the lower Merced River. However, other factors such as gravel 

and placer mining have also contributed extensively to the current lower Merced River 

conditions. The agencies and Conservation Groups recommend various quantities of 

gravel to augment salmonid spawning habitat in the lower Merced River. NMFS 

recommends that Merced ID add 20,000 tons annually downstream of Crocker-Huffman 
414

diversion dam over an approximate 30-year period, followed by 3,000 tons per year after 

the initial large-scale augmentation as an annual maintenance supply intended to balance 

out the transport capacity of the regulated flow regime. NMFS also recommends that 

PG&E add 2,500 tons of gravel to the reach between Merced Falls dam and CrockerHuffman diversion dam. California DFW recommends initially adding 50,000 cubic 

yards (~42,000 tons) downstream of Crocker-Huffman diversion dam and then placing 

2,600 cubic yards (~2,200 tons) per year thereafter for annual replenishment. FWS’ 

recommendation includes annual augmentation of 2,600 cubic yards (~2,200 tons) 

downstream of Crocker-Huffman diversion dam but not a larger initial amount. The 

Conservation Groups’ recommendation includes an initial placement of 20,000 cubic 

yards (~17,000 tons) downstream of Crocker-Huffman diversion dam followed by annual 

augmentation so that there is no net loss of spawning habitat thereafter (estimated to be 

from 2,600 to 10,400 cubic yards or ~2,200 to 8,800 tons). 

Our analysis in sections 3.3.1.2 indicates that gravel augmentation amounts equal 

to at least the transport capacity of the supply-limited lower reaches, estimated to be 

2,600 cubic yards (~2,200 tons) per year, would offset the ongoing coarse-sediment 

entrapment behind the Merced River Project dams that has a direct effect on spawninghabitat quantity. A larger initial placement of coarse sediments in the lower reaches 

would potentially benefit spawning habitat; however, doing so would address legacy 

effects not necessarily attributed wholly to past project effects and certainly not 

influenced by future project-related operation, construction, and maintenance activities. 

We also conclude that the contribution of the Merced Falls Project to the paucity of 

spawning gravel downstream of the Merced Falls is negligible. 

Obtaining the gravel to be placed in the lower reaches from the existing dredgertailing piles along the river, as recommended by California DFW and the Conservation 

Groups, would potentially make implementation relatively efficient, as opposed to 

importing gravels from outside of the project area, which could result in off-site 

environmental effects at the harvest site. Harvesting gravels on publicly owned land 

adjacent to the lower Merced River would also create an opportunity to develop a more 

natural floodplain that would facilitate the establishment of riparian vegetation and offer 

more valuable rearing habitat for anadromous and resident fish if grading following 

harvesting is properly implemented. We agree that monitoring and mapping existing and 

augmented spawning gravels, as recommended by FWS, California DFW, and the 

Conservation Groups, would provide an indication of the performance of the 

augmentations and inform the need for future augmentation projects.

To address project-related effects related to reduced spawning habitat availability 

for salmonids, we recommend that Merced ID develop, in consultation with the technical 

advisory committee, a gravel augmentation plan that provides for the annual placement of 

2,600 cubic yards of gravel in the lower Merced River. The plan would address, at a 

minimum, the following: (1) the range of particle sizes to be used for augmentation; 

(2) identification and mapping of potential gravel harvest sites adjacent to the lower 

Merced River on Merced ID, state, or federally owned land and the expected sequence of 
415

annual harvesting (i.e., which sites would be harvested first and why); (3) provisions for 

restoring land to what would be expected on natural riparian floodplains following gravel 

harvesting; (4) the protocol for selecting locations between Merced Falls dam and Shaffer 

Bridge for annual gravel augmentation based on consultation with the technical advisory 

committee; (5) provisions for monitoring and mapping augmented gravel after placement 

in the lower Merced River channel; and (6) provisions for annual reporting of the location 

of gravel harvesting and placement, and monitoring results. We estimate the levelized 

annual cost for this plan would be about $127,280, but considering the known spawning 

of Chinook salmon and potential for the federally listed Central Valley steelhead to 

spawn in the lower Merced River, we consider the benefits of implementing this plan to 

be worth the cost.

Vegetation Management

Merced ID proposes to implement its Vegetation Management Plan to minimize 

effects of project operation and maintenance on vegetation. Project operation and 

maintenance activities, such as facility maintenance, treatment of invasive weeds, and 

construction of any new facilities, could disturb vegetation resources through excavation, 

grading, topsoil stripping, or other similar activities. The plan includes specific measures 

for revegetation, general vegetation management, reporting, and protection of sensitive 

plant species. BLM [preliminary 4(e) condition 9] specifies that Merced ID develop a 

vegetation and non-native invasive plant management plan to protect terrestrial resources. 

In our analysis in section 3.3.2.1, Terrestrial Resources, we conclude that Merced 

ID could improve its plan by including details about the specific BMPs to be 

implemented. This modification would provide the agencies with information to evaluate 

the effectiveness of the BMPs and would allow Merced ID to implement additional 

BMPs, if necessary, to further protect terrestrial resources. We estimate the costs of this

modification to provide detail that is pertinent to the management and protection of 

terrestrial species to be $15,870.

Invasive Weeds

To minimize the spread of invasive weeds, Merced ID proposes to implement its 

Invasive Species Management Plan. In preliminary 4(e) condition 9, BLM specifies that 

Merced ID develop a vegetation and non-native invasive plant management plan to 

protect terrestrial resources. California DFW’s 10(j) recommendation 10 recommends 

that Merced ID develop a plan for integrated pest management and pesticide use 

notification to control undesirable woody and herbaceous vegetation in addition to 

aquatic plants, insects, and rodents to minimize the use of pesticides. BLM [preliminary 

4(e) condition 40] specifies that Merced ID request approval prior to using pesticides to 

control undesirably woody and herbaceous vegetation, aquatic plants, and other pests on 

BLM lands. 

In section 3.3.2.1, Terrestrial Resources, we find that project construction of any 

new facilities and improvements to recreation resources requiring excavation, grading, 
416

and topsoil stripping could contribute to the spread of invasive weeds. Facility and 

vegetation maintenance could cause disturbance to the soil, increasing the potential for 

weed colonization. We also find that an Invasive Species Management Plan would 

provide protocols for annual employee training, provisions for conducting surveys for 

invasive weeds, reviewing weed lists, and measures to prevent the spread of weeds into 

and within the project boundary. We also discuss the benefits of Merced ID’s proposed 

plan as well as the consistency of the plan with agency recommendations. However, we 

conclude that Merced ID could improve its plan. Modifying the proposed Invasive 

Species Management Plan to stipulate that the measures in the plan apply to all lands 

within the project boundary and including specific details of the BMPs that Merced ID 

proposes to implement would more directly address project-related effects from invasive 

weeds and allow BMPs to be evaluated and/or adjusted based on their effectiveness as 

necessary, thereby further reducing potential effects of invasive plant management on 

other terrestrial and aquatic resources. Integrating a component for pest management and 

pesticide use notification to address agency requirements of notification prior to use 

would further protect both terrestrial and aquatic resources from the effects of herbicides. 

We recommend implementing the proposed Invasive Species Management Plan with the 

modifications above. We estimate the costs of the plan with the modifications to be a 

levelized annual cost $55,030, and we consider the benefits of the plan to be worth the 

additional cost.

Bald Eagle Management Plan

Merced ID proposes to implement the Bald Eagle Protection Plan, as proposed in 

its license application and amended on September 22, 2014. In preliminary WQC 

condition 5, the Water Board specifies that Merced ID prepare a monitoring plan for bald 

and golden eagles consistent with the most current National Bald Eagle Management 

Guidelines provided by FWS that includes goals and objectives, measurable criteria, a 

monitoring and reporting schedule, a plan for corrective measures if goals are not 

achieved, and minimum monitoring requirements. BLM preliminary 4(e) condition 10 

specifies that Merced ID implement a bald eagle management plan and consult with 

BLM, California DFW, FWS, and the Water Board before submitting the plan for 

Commission approval. FWS [10(j) recommendation 9] recommends that Merced ID 

consult with resource agencies within 1 year of license issuance before implementing the 

revised Bald Eagle Management Plan, which would include the edits made to the plan by 

FWS and filed with its recommendation. 

In section 3.3.2.1, Terrestrial Resources, we discuss the inconsistencies between Merced 

ID’s proposal and FWS’ recommended plan, such as the frequency of shoreline surveys, 

distance of surveys from the shoreline, buffer distances around active nests, and 

protective measures for wintering bald eagles. In our discussion, we conclude that 

implementing the plan with the specific measures required by FWS would afford more 

protection to bald eagles and minimize project effects on bald eagles nesting, wintering, 

and roosting in the project area. These effects include noise caused by vegetation 
417

management activities and facility and road maintenance, and disturbances caused by 

recreation users, including hikers and boaters. Vegetation management activities could 

also result in the removal of nest or roost trees. 

In our analysis, we conclude that Merced ID’s proposed plan would further protect 

bald eagles by including protective measures for wintering bald eagles and information 

on public information boards to reduce disturbance to roosting and foraging eagles. We 

also discuss the benefits of identifying and describing any emergency activities that 

would be exempt from the restrictions provided in the Bald Eagle Management Plan. We 

recommend implementing the Bald Eagle Management Plan with the above 

modifications. With these modifications, we estimate the costs of implementing the plan 

to be $3,220, which is worth the cost of protecting bald eagles in the project area. 

Limestone Salamander Sensitive Areas Management Plan

Merced ID proposes to implement its Limestone Salamander Sensitive Areas 

Management Plan, which provides protection measures for limestone salamanders and 

associated habitat areas. In preliminary 4(e) condition 15, BLM specifies that Merced ID 

obtain its approval before submitting and implementing the plan, conduct studies of 

limestone salamanders every 7 years beginning in year one of license issuance, and 

inventory all suitable but unconfirmed habitats on BLM lands for the presence of 

limestone salamanders. In addition, BLM disagreed with some of Merced ID’s other 

proposed measures in its proposed plan. In response, Merced ID amended its proposal on 

September 22, 2014, to be consistent with BLM preliminary 4(e) condition 15. 

California DFW [10(j) recommendation 8] specifies that the Limestone Salamander 

Sensitive Areas Management Plan provide mapping of known occurrences of limestone 

salamanders and sensitive habitat, avoid sensitive areas, hold annual meetings with 

California DFW and BLM to review activities that may affect sensitive areas, and 

identify BMPs to be implemented as part of the plan. 

In our analysis in section 3.3.2.1, Terrestrial Resources, we find that the project 

could affect limestone salamanders through mortality caused by the effects of 

recreational activities, such as hiking. The activities could cause rock slides or otherwise 

degrade habitat; therefore, we find that future development of hiking trails associated 

with the project could affect limestone salamander habitat. We also find that Merced ID 

should specify and provide details about the proposed BMPs to improve the plan and 

reduce project effects on limestone salamanders and their habitats as well as other 

sensitive species. We also analyze the potential for effects of recreation on limestone 

salamanders, and conclude that any new hiking trails or modifications to existing hiking 

trails should be sited outside limestone salamander sensitive habitat to protect these 

habitats from degradation. We recommend implementing the Limestone Salamander 

Sensitive Areas Management Plan with the above modifications. We estimate the costs 

of the plan with the modifications to be a levelized cost of $2,260. We consider the plan

worthwhile to protect limestone salamanders and their habitats within the project area.
418

Protection Plan for Western Pond Turtles

Merced ID does not propose a protection plan for western pond turtles though 

Merced ID amended its proposal to include measures for the western pond turtle, 

consistent with BLM preliminary 4(e) condition 16. Merced ID proposes to train staff to 

identify western pond turtles so that staff could document western pond turtles 

incidentally observed on lands administered by BLM while conducting other 

environmental work. Merced ID proposes to record relevant data, including GPS 

locations, and develop written reports to be submitted annually to BLM (consistent with 

BLM preliminary 4(e) condition 1) and the Commission. BLM preliminary 4(e) 

condition 16 includes objectives for the conservation of special-status species, habitat 

maintenance or improvement, and proactive conservation measures to minimize the 

likelihood of and need for federal listing of the species. 

In our analysis in section 3.3.2, Terrestrial Resources, we find that project 

operation could affect western pond turtles by causing water level fluctuations, thereby 

affecting habitat for basking and nesting, as well as habitat for juvenile western pond 

turtles. We also find that traffic associated with project maintenance and recreation, and 

maintenance activities such as pesticide applications, also may affect the species. 

Because a project nexus exists, we recommend revising the proposal to record incidental 

observations of western pond turtles in the entire project area, rather than limiting data 

collection to just BLM lands. Under the proposal, Merced ID would submit reports to 

BLM and the Commission.

The western pond turtle is a special-status species, designated as a species of 

special concern by the state of California and as a species of concern by FWS. Thus, we 

recommend consulting with California DFW and FWS, in addition to BLM, to prepare a 

plan to protect western pond turtles to be implemented on all project lands. We estimate 

the plan would have a levelized annual cost of $2,000. We consider the cost of the plan 

to be worthwhile, given the potential for the plan to reduce project-related effects on the 

western pond turtle. 

Protection Plan for the California Red-legged frog, Foothill Yellow-legged 

Frog, and Western Spadefoot

Merced ID does not propose any measures to protect the federally listed California 

red-legged frog, nor does Merced ID propose measures to protect the foothill yellowlegged frog and western spadefoot, both of which are special-status species currently 

under review by FWS. FWS [10(j) recommendation 7] recommends that Merced ID, in 

consultation with FWS and BLM, develop and implement a watershed management and 

protection plan for the California red-legged frog in the Piney Creek core area of the 

recovery plan. BLM specifies in preliminary 4(e) condition 1 that Merced ID consult 

with BLM, FWS, the Water Board, and California DFW to develop a management plan 

for the California red-legged frog. BLM’s preliminary 4(e) condition 14 also specifies 

that Merced ID develop a management plan for the foothill yellow-legged frog. In 
419

preliminary 4(e) condition 40, BLM specifies that Merced ID avoid pesticide use within 

500 feet of known locations of foothill yellow-legged frogs and other special-status 

animals and plants. The Water Board [preliminary WQC condition 10] specifies that 

Merced ID develop a monitoring and conservation plan for the California red-legged 

frog, foothill yellow-legged frog, and western spadefoot.

In section 3.3.3.2, Threatened and Endangered Species, we analyze project effects 

on the California red-legged frog, and find that project operation and maintenance 

activities could adversely affect the California red-legged frog. We concur with the 

agencies’ recommendations for protective measures, such as including measures to 

control bullfrogs in the project reservoirs and adjacent areas, reducing population-level 

impacts from the frog-killing Batrachochytrium dendrobatidus fungus to reduce 

mortality of frogs within the project boundary and in the critical habitat area overlapping 

the project boundary, identifying areas where non-native predators occur within the 

project boundary, including control and eradication measures for non-native species and 

predators, identifying a habitat mosaic containing both breeding and dispersal habitat in 

the project area, monitoring water temperature at the confluence of Sherlock Creek and 

the Merced River to determine if project operation affects water temperature, and 

avoiding pesticide use within 500 feet of known locations of foothill yellow-legged frogs.

These measures would reduce predation and mortality on the California red-legged frog. 

Because other species, including the foothill yellow-legged frog and western spadefoot, 

are also affected by changes in water temperature caused and pesticide use, broadening 

the measures to include other special-status species, such as the foothill yellow-legged 

frog and the western spadefoot, would bestow similar protective benefits to those species. 

Therefore, we recommend that Merced ID develop and implement a protection plan for 

federally listed and special-status amphibian species, including the California red-legged 

frog, foothill yellow-legged frog, and western spadefoot. We estimate the cost of the 

protection plan to be $2,000. We consider the plan to be worth the cost, given the 

benefits to these federally listed and special-status species, while also ensuring the 

project’s compliance with state and federal laws governing federally listed and specialstatus species. 

Protection Plan for the California Tiger Salamander

Merced ID does not propose a protection plan for the California tiger salamander, 

though it does propose to avoid the use of burrow fumigants and rodenticides in 

California tiger salamander habitat. FWS [10(j) recommendation 6(a)G] recommends 

prohibiting the use of burrow fumigants or rodenticides in the habitat of California tiger 

salamanders. The Water Board [preliminary WQC condition 7] specifies the 

development of a monitoring and conservation plan to protect the California tiger 

salamander from the effects of pesticide use and recreation and construction activities.

In our analysis in section 3.3.2, Terrestrial Resources, we discuss potential project 

effects, including pesticide use on California tiger salamander. We agree with Merced 
420

ID’s proposed measure to avoid the use of pesticides in California salamander habitat and 

recognize that other plans could include measures that may protect California tiger 

salamanders. However, we find that protocol level surveys would be necessary to 

identify the habitats where California tiger salamanders occur and the migratory routes 

they use. Therefore, we recommend developing and implementing a protection plan for 

the California tiger salamander with provisions for protocol level surveys, identification 

of habitats and migratory routes used, and avoidance of burrow fumigants and 

rodenticides in habitat of the California tiger salamander. We estimate the plan would 

have a levelized annual cost of $2,000 and would be worth the cost to ensure that the 

project would not affect the California tiger salamander. 

Protection Plan for Vernal Pool Fairy Shrimp and its Habitat

Merced ID does not propose any species-specific measures to monitor or protect 

fairy shrimp in the project area, nor does it propose a protection plan for fairy shrimp or 

its associated habitat. The Water Board [preliminary WQC condition 6] specifies that 

Merced ID develop and implement a monitoring and conservation plan for vernal pool 

and Conservancy fairy shrimp. Per the Water Board, monitoring would be conducted

annually for the first 4 years, and thereafter every 3 years and prior to construction or 

ground-disturbing activities. FWS commented that although no documented occurrences 

of fairy shrimp are known in the project area, Merced ID did not conduct protocol level 

surveys. FWS notes that the project area overlaps with about 1 acre of critical habitat for 

the vernal pool fairy shrimp. FWS states that levee breaches spill water into vernal pool 

critical habitat in the dry summer months, and the project road that transects the critical 

habitat is likely to cause long-term degradation of the habitat adjacent to the road, despite 

the fact that the road itself does not contain any primary constituent elements. 

In our analysis in section 3.3.3.2, Threatened and Endangered Species, we note

that the presence of vernal pool fairy shrimp should be assumed because protocol level 

surveys have not been conducted. We also discuss the fact that critical habitat for vernal 

pool species overlaps with the project area. Thus, we recommend developing a 

protection plan for the vernal pool fairy shrimp and its habitat. Merced ID would develop 

the plan in consultation with FWS, the Water Board, California DFW, and BLM. The 

plan would include any measures required by the agencies’ conditions and

recommendations, as well as those developed in consultation. We estimate the plan 

would have a levelized annual cost of about $2,500 and would be worth the cost to ensure 

that the project would not affect vernal pool fairy shrimp or its habitat. 

Protection Plan for Federally Listed Plants

Merced ID does not propose a protection plan for federally listed plants. FWS 

[10(j) recommendation 6(b)] recommends annual consultation to identify newly listed 

species that could be affected by the project, the development of studies, and preparation 

of a biological assessment that includes protection measures. The Water Board

[preliminary WQC conditions 12 and 13] specifies annual consultation and reviews to 
421

protect newly listed federally listed and special-status species. BLM [preliminary 4(e) 

condition 1] specifies annual consultation to discuss, in part, necessary protection 

measures for federally listed species. BLM [preliminary 4(e) condition 3] specifies 

review of federally listed and special-status species, assessment of newly listed species,

and annual employee training to train employees to identify federally listed species. 

In our analysis in section 3.3.3.2, Threatened and Endangered Species, we note

that, given the lack of protocol level surveys for federally listed plants potentially

occurring in the project area, the occurrence and locations of federally listed plants 

remain unknown and therefore these plants cannot be adequately protected by any other 

plans. Thus we recommend developing a protection plan for federally listed plants in 

consultation with FWS, the Water Board, California DFW, and BLM. The plan would, at 

a minimum, include the following for each federally listed plant species potentially 

occurring in the project area: (1) study methodologies and protocols sufficient to produce 

adequate survey results; (2) a list of peak bloom times and identifying features; (3) the 

timing and frequency of the surveys; (4) maps and written descriptions of habitat areas to 

be surveyed; (5) references to measures contained in other plans that could protect 

federally listed plants; (6) protection and mitigation measures; and (7) reporting 

requirements. We estimate the plan would have a levelized annual cost of $2,500 and 

would be worth the cost to ensure that the project would not affect federally listed plants, 

including Keck’s checkerbloom, Layne’s butterweed, Chinese Camp brodiaea, Mariposa 

pussypaws, and California vervain, or their habitats. 

Protection Plan for the San Joaquin Kit Fox

Merced ID proposes to avoid the use of rodenticides and burrow fumigants in San 

Joaquin kit fox habitat. FWS [10(j) recommendation 6(a)F] recommends prohibiting the 

unauthorized use of burrow fumigants or rodenticides on federal land and 10(j) 

recommendation 6(a)G recommends prohibiting the use of burrow fumigants or 

rodenticides in habitat of the San Joaquin kit fox until section 7 ESA consultation is 

completed or a permit is issued under section 10 of the ESA. In preliminary WQC 

condition 18, the Water Board specifies that Merced ID develop a pesticide use plan to 

prevent pesticides from affecting federally and state-listed species in the project area or 

downstream of the project area. BLM specifies in preliminary 4(e) condition 40 that the 

use of pesticides be restricted and require written approval by BLM. California DFW 

[10(j) recommendation 10] recommends that Merced ID develop an integrated pest 

management and pesticide use notification plan, which includes a provision for Merced 

ID to obtain approval prior to using pesticides, including rodenticides. 

In our analysis in section 3.3.3.2, Threatened and Endangered Species, we discuss 

project effects on the San Joaquin kit fox, such as the use of pesticides, and maintenance 

activities and recreation resulting in noise that could disturb kit fox. We also explain that 

surveys would be necessary to identify habitats where the use of rodenticides and burrow 

fumigants would be avoided. In section 3.3.3.3, Threatened and Endangered Species, 

Cumulative Effects, we identify the San Joaquin kit fox as a species subject to cumulative 
422

effects from the project combined with other activities in the basin. To protect San 

Joaquin kit fox from project effects, including any contribution that project effects would 

have to cumulative effects, we recommend that Merced ID develop a protection plan for 

the San Joaquin kit fox that would include the following: (1) study methodologies and 

monitoring protocols to identify San Joaquin kit fox habitats within the project boundary; 

(2) an assessment of potential project effects on San Joaquin kit fox in the project 

boundary; (3) protection and mitigation measures; and (4) descriptions of any exceptions 

to the prohibited use of rodenticides that would be considered emergencies and allowed 

by agencies and an explanation of why the emergency situations would supersede 

protection measures for the San Joaquin kit fox. We estimate the plan would have a 

levelized annual cost of $2,500 and would be worth the cost to ensure that the project 

would not affect the San Joaquin kit fox. 

Recreation Facilities Plan

The project provides numerous recreation opportunities, and Merced ID 

appropriately proposes extensive development, rehabilitation, and management of these 

facilities in its proposed Recreation Facilities Plan. However, the proposed plan lacks 

sufficient detail on some project facilities, including extending the proposed paved bike 

lane 2.8 miles short of the length of the project’s Lake McClure Road, identifying the

location and condition of the three floating restrooms on Lake McClure, and including an 

assessment of water systems at the project over the term of the license. Further, Merced 

ID’s proposed implementation schedule for the rehabilitation and construction of 

recreation facilities included in the plan does not appear to prioritize those facilities with 

immediate rehabilitation needs (i.e., facilities within the Bagby recreation area) over the 

construction of new facilities where a need was not identified (i.e., park model cabins). 

Extending the bike lane along the entire length of Lake McClure Road, providing more 

detailed information on the location and future operation and maintenance of the three 

floating restrooms provided at Lake McClure and all project water systems, and revising 

the implementation schedule to prioritize those facilities in need of immediate 

rehabilitation would not only improve access to the project in the near future but would 

ensure all project facilities are maintained over the term of a new license. 

Merced ID’s plan also includes provisions for the management and protection of 

recreation areas, including providing a campground host site at the Horseshoe Bend 

recreation campground. While providing a campground host and host site at the 

Horseshoe Bend recreation area campground could potentially improve public safety and 

campground management, the Commission cannot ensure public safety would be 

improved as a result of providing a host site. The responsibility for recreation facility 

management is that of the licensee; therefore, we do not recommend a host site. 

We recommend Merced ID implement the Recreation Facilities Plan with the 

above staff recommended modifications. Our recommended Recreation Facilities Plan 

would have an estimated levelized annual cost of about $9,200,000, and we conclude the 

benefits of our recommended plan would be worth the cost.
423

Fish Stocking

Angling is one of the primary recreational activities associated with the project. 

Merced ID proposes to stock the following in Lake McClure: 32,000 to 70,000 

catchable-size rainbow trout with a 5-year running average target number of 48,000 fish; 

4,000 to 20,000 fingerling kokanee with a 5-year running average target number of 

15,000 fish; and 35,000 to 75,000 fingerling Chinook salmon with a 5-year running 

average target number of 45,000 fish. In McSwain reservoir, Merced ID proposes to 

stock 1,000 to 2,000 catchable-sized rainbow trout with a 5-year running average target 

of 1,500 fish. Merced ID states it would consult with California DFW and use angler 

data from recreation monitoring to make decisions on stocking throughout the term of the 

license. California DFW recommends and the Water Board specifies similar stocking 

numbers for the first 2 years of license issuance, however they recommend Merced ID 

develop a fish stocking plan that would implement fish stocking at the project reservoirs

for the remainder of the license term based on recreational use, angling demand, 

availability of hatchery fish, and future California DFW fish stocking management 

targets. The Conservation Groups propose similar stocking numbers to Merced ID and 

the agencies’ proposals for McSwain reservoir; however, they propose stocking numbers 

that are significantly higher than what has historically been stocked in Lake McClure. 

Although Merced ID’s proposal to stock both Lake McClure and McSwain reservoir 

would ensure that the recreational fishery is maintained at historic levels, it is unclear if 

these stocking numbers would be adequate to meet angling demand over the term of a 

new license. Alternatively, the Conservation Groups’ proposed stocking numbers for 

Lake McClure seem excessive in comparison. Developing and implementing a fish 

stocking plan in consultation with the agencies and the Conservation Groups would 

provide the flexibility to stock project reservoirs at levels that meet both recreational 

demand and state fish stocking management targets over the term of a new license. We 

recommend Merced ID develop and implement a fish stocking plan in consultation with 

California DFW, the Water Board, NMFS, and the Conservation Groups and file the plan 

with the Commission for approval to include, at minimum, the species, size, and number 

of fish to be stocked in Lake McClure and McSwain reservoir for the first 3 years within 

license issuance, a consultation schedule to discuss fish stocking in Lake McClure and 

McSwain reservoir over the term of a new license, and stipulations for the acquisition of 

fish (e.g., native, cold water species from facilities free of invasive species). We estimate 

that the annualized cost of developing and implementing a fish stocking plan would be 

$35,000, and conclude the benefits of this measure would be worth the cost.

Transportation Management Plan

Merced ID proposes to implement its proposed Transportation Management Plan 

to provide guidance to rehabilitate and maintain project roads over the term of a new 

license. However, Merced ID’s plan does not include any details regarding road 

conditions and approaches for monitoring use over the term of the license, nor does it 

identify BMPs that would be implemented to improve road conditions. The Water Board 
424

specifies in preliminary WQC condition 21 that Merced ID develop a transportation 

management plan that includes the aforementioned missing details as well as measures to 

improve maintenance and conditions of project roads, comparable to the most current

Forest Service BMPs Road Management Activities. As discussed in section 3.3.5.2,

Management of Project-Related Roads, the current conditions of roads are at the project

are unclear. Further, it is uncertain whether those project roads would continue to be 

maintained to meet the need for safe public recreational access over the term of a new 

license. Implementing a Transportation Management Plan, as proposed by Merced ID, 

would provide the mechanism to address operation, maintenance, monitoring, and road 

use within the project boundary. It would also ensure safe public access to project lands 

and project waters over the license term. We agree that the Merced ID’s proposed 

Transportation Management Plan needs to be revised to include more detail; however, 

because the Water Board did not provide specific information on the Forest Service’s 

BMPs Road Management Activities, it is unclear how those BMPs would improve the

plan. Further, there are no Forest Service roads or lands within the project boundary. We 

recommend Merced ID revise its Transportation Management Plan to include, at 

minimum, an inventory of all project roads and their current road conditions, a detailed 

schedule of maintenance based on the inventory of road conditions, relevant BMPs that 

would be implemented to improve and maintain road conditions, and a detailed approach 

for monitoring use over the term of the license. Our recommended Transportation 

Management Plan would have an estimated levelized annual cost of about $97,000, and 

we conclude the benefits of our recommended plan would be worth the cost.

5.1.1.3 Measures Not Recommended by Staff

Staff finds that some of the measures recommended by other interested parties 

would not contribute to the best comprehensive use of the Merced River water resources, 

do not exhibit sufficient relationship to project environmental effects, or would not result 

in benefits to non-power resources that would be worth their cost. The following 

discusses the basis for staff’s conclusion not to recommend such measures.

New Minimum Instream Flow Compliance Gage

NMFS recommends the Merced ID install a new gage capable of measuring up to 

6,000 cfs at Shaffer Bridge to document compliance with the flow regime that may be 

specified in a new license. Although we consider Shaffer Bridge to be an appropriate 

compliance point for a minimum flow regime, NMFS does not elaborate on why a new 

compliance gage capable of measuring up to 6,000 cfs would be necessary to measure 

project-related flows. No entity has offered a flow-related measure with a maximum 

flow provision. The existing gage at Shaffer Bridge has served to document required 

minimum flows and would continue to be sufficient to monitor flows that may be 

included in a new license for this project. The maximum lower Merced River flow in any 

staff recommendation is 1,040 cfs. Therefore, installing a new gage with the capacity to 
425

measure flows up to 6,000 cfs in place of the existing gage at this location would not be 

worth the estimated levelized annual cost of $11,400.

Two-Day Spring Pulse Flow

California DFW [10(j) recommendation 3D] recommends a spring floodplain 

inundation flow in ranging from 2,000 to 4,000 cfs over a 2-day period between March 

14 and March 28 in below normal, above normal, and wet water year types, with no 

requirement in dry and critically dry years. The stated purpose of this brief pulse flow is 

to provide young salmonids with at least some access to floodplain cover and food 

sources. The California DFW spring floodplain inundation flow volume (as converted 

from cfs) varies by water year type and includes: 15,840 acre-feet (4,000 cfs per day) in 

wet years, 11,880 acre-feet (3,000 cfs per day) in above normal years, and 7,920 acre-feet 

(2,000 cfs per day) in below normal years. In addition, California DFW’s minimum flow 

recommendation, discussed in the previous section, includes an extended pulse flow of 

from 2 to 6 weeks, which we discussed previously under our recommended spring pulse 

flow.

Although California DFW’s recommended 2-day pulse flow in March would 

provide young salmonids with access to floodplain cover and food sources, we conclude 

that a short-term pulse flow could also expose fish that occupy the floodplain to stranding 

as flows recede into the channel proper. We find that the benefit of providing limited 

floodplain access to young salmonids would not be worth the potential cost of stranding 

mortality following limited pulse flows. A more extended pulse flow later in the spring, 

which we recommend, would provide young salmonids with floodplain cover and food 

sources, and, because they would have better swimming ability, they would be better 

suited to avoid stranding.

Ramping Rates

Rapid changes in streamflow (both increases and decreases) can affect fish 

behavior, which in turn can reduce survival or growth. Limits governing the rate and 

timing of project-induced river stage changes (ramping rates) are often established to 

protect aquatic organisms from these project-related effects. For the Merced River 

Project, pulse flow releases and flood control releases are most likely to result in rapid 

changes in river flows that may warrant establishment of ramping rates.

NMFS [10(j) recommendation 1.1B(7)] recommends that minimum instream flow 

upramping and downramping rates occur evenly over a 24-hour period, with a maximum 

of 500 cfs per 24-hour period in all water years, with the exception of spring pulse flows 

in above normal and wet water years, when downramping rates are recommended to 

occur evenly over a 24-hour period at a maximum of 100 cfs per day (about 1 inch per 

day) to promote riparian seedling survival. The compliance point is not specified. FWS 

[10(j) recommendation 3A1] also recommends this gradual downramp of 100 cfs per day 

as measured at Shaffer Bridge in late May or early June during above normal and wet 

water years.
426

California DFW [10(j) recommendation 3G] recommends a ramping rate for 

increasing flows that restricts the rate of change to not more than double the amount of 

the release during any 1-hour period. This is the same as Merced ID’s proposed 

upramping rate. For decreasing flows, California DFW recommends the rate of change 

be no more than 2 inches per hour as measured at the existing gage near Snelling Bridge, 

downstream of Crocker-Huffman diversion dam, and at flows above 200 cfs, the rate of 

change in any one 24-hour period, the flow rate should not drop by more than 500 cfs.

Flow releases for hydroelectric project operation occur at New Exchequer and 

McSwain dams. These releases flow directly into impoundments, which minimize 

adverse effects typically associated with upramping and downramping in riverine habitat. 

The rate of change in flows downstream of Crocker-Huffman diversion dam is influenced 

by both hydroelectric project flow releases from McSwain dam and diversions for 

irrigation into the Main Canal, a facility not related to hydroelectric operation. Therefore, 

California DFW and FWS’ recommended downramping compliance point downstream of 

the diversion dam, and any other ramping rate compliance point downstream of the 

Crocker-Huffman diversion dam would measure both the rate of change of releases from 

McSwain dam, which would be related to hydropower operation, and gate operation at 

the Main Canal (and, in the case of FWS’ compliance point, other diversions upstream of 

Shaffer Bridge) in response to changing flows, which would not be related to hydropower 

operation.

The benefits of the upramping rate recommended by NMFS (a maximum increase 

of 500 cfs evenly spread over a 24-hour period) are difficult to evaluate because as 

worded, it would only pertain to changes in minimum instream flows and the compliance 

point is not specified. Few increases in the minimum flows proposed or recommended 

by any entity change by more than 500 cfs between any designated release periods. We 

therefore have no basis to recommend NMFS’ recommended upramping rate.

California DFW recommends a downramping rate of no more than 2-inches per 

hour as measured immediately downstream of Crocker-Huffman diversion dam. To 

support its recommended ramping rate, California DFW relies on Hunter (1992), which 

concludes that in unregulated river systems, aquatic biota are rarely exposed to drops in 

stage of more than 2-inches per hour and therefore are not adapted to more excessive 

stage changes. In addition, California DFW notes that a controlled downramping rate in 

late spring that approximates a natural recession rate promotes recruitment of willows 

and cottonwoods to riparian floodplains. Both California DFW and NMFS’ 

recommended spring downramping rates would achieve this goal. California DFW states 

that under Merced ID’s proposed downramping rate, using the maximum release of 6,000 

cfs allowed by the current Corps’ flood control rules, flows could be dropped by 3,000 

cfs in 1 hour and by 1,500 cfs during the next hour with no ecological rationale.

Controlling downramping rates can reduce the potential for aquatic biota stranding 

and, in the spring, stimulate the growth of riparian trees and shrubs. However, the 

downramping rates that occur in Merced River downstream of Crocker-Huffman 
427

diversion dam are a function of releases from McSwain powerhouse and operation of the 

gates for irrigation purposes at the Main Canal. Only releases from the McSwain 

powerhouse are within the Commission’s ability to regulate. Our review of typical 

releases from McSwain powerhouse during a normal and dry water year indicates that the 

maximum range of decreases in flow during a relatively short period of time is from 650 

to 1,000 cfs (see figures 3-5 and 3-7). Therefore, the scenario that California DFW 

presents is unlikely to occur except in emergency situations. Implementing Merced ID’s 

proposed and staff recommended downramping rate, listed in section 5.1.1.1, would 

provide control over flows that reach Crocker-Huffman diversion dam. The ramping 

rates further downstream would be influenced by the rate of additional flow diversions 

and returns associated with non-project facilities and natural attenuation of flows, making 

it more difficult to establish a direct relationship with the downramping protocol when 

compared to using the existing gage near Snelling. However, we have no data to assess 

how this translates into downramping rates downstream of the diversion dam. We 

therefore have no basis to recommend the downramping rates recommended by NMFS, 

FWS, and California DFW given that both project and non-project flows cause 

downramping in the lower Merced River. Monitoring flows and the downramping rate at 

the existing gage near Snelling immediately downstream of the Crocker-Huffman 

diversion dam, as recommended by California DFW, would provide the Commission 

with data regarding how the downramping rate measured at McSwain dam translates to 

the downramping rates immediately downstream of Crocker-Huffman diversion dam, 

which are influenced by both hydroelectric operation and irrigation diversions. These

data, along with input from the Merced ID proposed and staff-recommended technical 

advisory committee,60 also listed in section 5.1.1.1, regarding the measured downramping 

rates, would serve to inform the Commission regarding the adequacy of the downramping 

protocol and whether adjustments to that protocol may be needed in the future to reduce 

stranding risk and stimulate floodplain revegetation. 

Increased Lake McClure Minimum Pool Level

The volume of water required in Lake McClure affects Merced ID’s ability to

address water supply, carryover storage, and power generation needs associated with 

managing the project reservoirs. The volume of water in Lake McClure also affects 

Merced ID’s ability to achieve minimum instream flows, pulse flows, and water 

temperature objectives. Establishing a minimum pool elevation sets the minimum 

volume of water available for downstream water uses.

 

60 The staff recommended technical advisory committee would invite the 

following entities to participate: NMFS, FWS, California DFW, the Water Board, BLM, 

Park Service, and a representative from a non-governmental organization.
428

FWS [amended 10(j) recommendation 3(A1)] recommends Merced ID maintain a 

minimum pool of 130,000 acre-feet (an elevation of about 650 feet) in Lake McClure. 

Once the minimum pool storage drops below 130,000 acre-feet, all irrigation diversions 

would cease and the only flow releases from Lake McClure would be to maintain 

designated minimum instream flows. The Conservation Groups make a similar 

recommendation.

California DFW [10(j) recommendation 3F] recommends Merced ID maintain 

Lake McClure as high as possible from April through October, with a target minimum 

pool of no less than 200,000 acre-feet (an elevation of about 680 feet) on September 30 

of each year, by maintaining a minimum pool of no less than 265,000 acre-feet (an 

elevation of about 710 feet) at all times by ceasing all irrigation diversions, except for 

drawdowns as necessary to maintain minimum instream flows. Additionally, California 

DFW recommends that Merced ID submit an annual draft plan to the Commission 

describing planned operation to maintain Lake McClure levels, including the estimated 

delivery pattern needed to achieve a 200,000 acre-feet minimum pool target by the end of 

September, with a final operation plan submitted annually to the Commission by May 15. 

Merced ID provided model results that compare water supply, carryover storage, 

and power generation for its proposed measure and the stakeholder recommended flow 

regimes and minimum pool elevations to existing baseline conditions. The Merced ID 

model runs were developed without considering any additional flow measures that could 

be necessary to meet either NMFS, FWS, or California DFW water temperature 

objectives. Water supply shortages increase when Lake McClure is operated under 

California DFW’s recommended minimum pool volume of 200,000–265,000 acre-feet 

compared with operation under the baseline volume of 115,000 acre-feet (which is also 

Merced ID’s proposed and staff-recommended minimum pool). The Conservation 

Groups’ flow regime builds into the measure irrigation delivery restrictions based on 

water year type and results in the greatest total water delivery shortage of any alternative 

proposed or recommended. Carryover storage in Lake McClure is substantially reduced 

under all recommended minimum pool and flow regime scenarios compared with 

baseline conditions. 

Under baseline conditions and Merced ID’s proposed measure, Lake McClure 

reaches maximum storage (the reservoir is filled) ten times over the 36-year period of 

record. Based on Merced ID’s modeling results, this total is predicted to be reduced to 

six under FWS’ flow and minimum pool recommendation, five under the NMFS flow 

recommendation, four under California DFW’s flow and minimum pool 

recommendation, and Lake McClure would not fill in any of the 36 years under the 

Conservation Groups’ flow and minimum pool recommendation. 

Average annual power generation under existing conditions is about 387 GWh. 

With Merced ID’s proposed flow and minimum pool levels, annual generation is 

predicted to increase to about 389 GWh. The flow and minimum pool recommendations 

of stakeholders would decrease predicted average generation to the following amounts: 
429

FWS—377 GWh (a decrease of 3 percent from existing conditions); Conservation 

Groups—360 GWh (a decrease of 7 percent); California DFW—354 GWh (a decrease of 

9 percent); and NMFS—347 GWh (a decrease of 10 percent). 

Increasing the minimum pool as recommended by the agencies and Conservation 

Groups would serve to retain more coldwater pool in Lake McClure that would enable 

somewhat cooler temperatures to be maintained downstream of Crocker-Huffman 

diversion dam compared to existing conditions or Merced ID’s proposed and staffrecommended measure. Predicted water temperatures immediately downstream of the 

diversion dam and at the Snelling Bridge are 3 to 5°F cooler from mid-July to midOctober compared to Merced ID’s proposed measure. However, water temperatures 

during this time frame would still be well above the 18.0°C (64.4°F) 7DADM EPA 

guideline for adult steelhead rearing and juvenile rearing and emigration and the 16.0°C

(60.8°F) guideline for juvenile over-summer rearing.

Maintaining the recommended higher Lake McClure storage level would have an 

effect on the water available for delivery to irrigators. To illustrate this effect, we 

reviewed Lake McClure storage volumes for summer 2014, a critically dry water year 

within a severe drought (letter from H. EITal, Deputy General Manager, Water 

Supply/Rights, Merced ID, to T.J. LoVullo, FERC, Chief, Aquatic Resources Branch, 

Division of Hydropower Administration and Compliance, filed on October 10, 2014). 

Our analysis only provides a general concept of the effect on irrigation diversions 

because in 2014, Merced ID released the minimum flow of 15 cfs required by the current 

license. Releases of higher minimum flows as recommended by the agencies would 

result in the storage meeting the trigger for cessation of irrigation flows sooner. The 

Conservation Groups’ recommended minimum flow would have irrigation diversions 

equal to 30 to 40 percent of demand in 2014, and this would serve to preserve some 

storage in Lake McClure but at the expense of irrigators. Under California DFW’s 

recommendation, irrigation diversions would have stopped after July 4, 2014, and under 

the FWS and Conservation Groups’ recommendations, after September 23, 2014. 

Deliveries of irrigation water would have continued through September with Merced ID’s 

proposed minimum pool trigger for curtailing irrigation diversions. 

Dry, warm summers create stressful conditions for salmonids in the lower Merced 

River and for irrigators that depend on the water supply that had been provided by 

Merced ID long before the project was operated for hydroelectric power generation. We 

acknowledge that preserving the cold pool in Lake McClure could be used to create 

slightly less stressful water temperature conditions for salmonids in the lower Merced 

River. Irrigation diversions have the most value to irrigators during the driest years. 

Curtailing all irrigation diversions at the beginning of the summer would have a 

substantial effect on irrigated cropland and the associated agricultural community. 

Whether this adverse economic effect would be worth a marginally enhanced water 

temperature regime in the lower Merced River is questionable. Completely shutting 

down irrigation diversions when a target storage level is reached transfers all of the costs 

of any environmental benefits that such an approach would achieve to the irrigators. We 
430

therefore conclude that the limited benefits of the higher minimum pool elevations 

recommended by the agencies and Conservation Groups would not warrant the 

substantial cost to irrigators of the lost irrigation water. The recommended approach of 

the Conservation Groups would entail a reduction in irrigation deliveries that escalates 

during dry years but is never reduced to less than 30 percent of demand. Consequently, 

the irrigators would not bear the entire cost of enhanced lower Merced River habitat 

enhancements that relate to available water storage in Lake McClure. However, we still 

conclude that the benefits of the Conservation Groups’ approach to managing available 

water do not warrant the cost to irrigators.

California DFW recommends that Merced ID annually submit a draft operation 

plan to the Commission by March 1 and a final operation plan by May 15 that includes 

the estimated delivery pattern needed to achieve the 200,000 acre-feet end of September 

minimum pool target. If a minimum pool level should be specified in a new license, we 

would expect Merced ID to comply with any such condition. How Merced ID operates 

its project to comply with a minimum pool requirement would be up to them. However, 

if Merced ID is not able to meet a minimum pool requirement, the Commission would 

expect a report to be filed documenting the reasons for not meeting a specified minimum 

pool. Consequently, we find that there would be no need to file an annual operation plan 

with the Commission as California DFW recommends and we do not recommend that 

this measure be included in any new license that may be issued for this project. For the 

reasons described above, we do not recommend an increased Lake McClure minimum 

pool level.

Development of a Long-term Temperature Management Plan

NMFS [10(j) recommendation 1.1A(3c)] recommends developing a long-term 

water temperature improvement plan that includes a feasibility study of potential options 

for decreasing water temperature downstream of Crocker-Huffman diversion dam, 

including: (1) installing an underground pipe for New Exchequer dam that bypasses 

McSwain reservoir and/or Merced Falls reservoir; (2) modifying the Lake McClure outlet 

structure to allow water withdrawal from varying depths; and (3) developing engineering 

alternatives that do not require large volumes of water. The actual cost of this measure 

would not be known until a feasible option is identified. Merced ID conducted a 

feasibility study of engineering options and concludes that no feasible engineering 

options exist to decrease water temperature downstream of the Crocker-Huffman 

diversion dam (Merced ID, 2014e). The estimated cost for modifying the Lake McClure 

outlet structure ranged from $60 to $120 million.

California DFW [10(j) recommendation 4] also recommends that Merced ID 

prepare a long-term water temperature management plan. The plan would include: 

(1) developing a long term strategy for meeting seasonal temperature objectives for 

Chinook salmon and O. mykiss ranging from 13.0°C (55.4°F) to 18.0°C (64.4°F) during 

the time frames included in the recommendation; (2) a feasibility study on submerged 

pipes capable of delivering at least 200 cfs to a location downstream of Crocker-Huffman 
431

diversion dam; (3) measures to prolong and stabilize the irrigation delivery season; 

(4) measures to restore the natural channel morphology, floodplain habitats, and riparian 

forest in the approximately 10-mile reach downstream of the Crocker-Huffman diversion 

dam; (5) provisions to provide coldwater refugia when water temperatures exceed 

objectives for more than 14 days; and (6) evaluating the effects on instream flow releases 

of implementing alternatives, and the estimated funding and schedule needed for the 

alternatives.

FWS [10(j) recommendations 3(A3) and 5 (G and H) recommends that Merced ID 

conduct a riparian microclimate study and collect data for calibrating a HEC-5Q water 

temperature model analysis to determine the optimum length and width of riparian forest 

in the 10 miles from Merced Falls dam to a point 1.2 miles downstream of the Snelling 

Road bridge needed to achieve temperature objectives downstream of Crocker-Huffman 

diversion dam. FWS states that until site-specific modeling and analysis is completed, 

the expected cost per acre of riparian forest restoration is unknown. However, FWS 

notes that other riparian and floodplain restorations in the Central Valley ranged from 

$5,000 per acre for riparian plantings to $530,000 per acre for a small highly engineered 

restoration that included removal of dredge tailings from the site and riparian plantings. 

To develop a range of potential costs associated with restoring the riparian forest 

in the 10 miles downstream of Merced Falls dam, we assumed a 30-yard-wide restoration 

zone on each side of the river, which would result in the restoration of about 218 acres 

under the FWS and California DFW recommended measures. With these assumptions, 

the estimated costs for implementing 110 miles of floodplain restoration would range 

from $1,090,900 to $115,540,000. Merced ID states that the expected cost of riparian 

floodplain restoration would be well in excess of $100,000,000, and this falls within the 

range of our estimated costs.

The Water Board [preliminary WQC condition 8] specifies that Merced ID 

develop a fish passage or habitat restoration plan in consultation with a technical advisory 

committee. We address fish passage in a separate subsection. The habitat restoration 

plan would be developed within 1 year of license issuance and designed to decrease water 

temperatures in and downstream of the project.

The long-term water temperature improvement plans recommended by NMFS and 

by California DFW contain some elements pertaining to engineering options to deliver 

colder water from Lake McClure to downstream of Crocker-Huffman diversion dam that 

have already been studied by Merced ID and presented in its reservoir water temperature 

management and feasibility study (Merced ID, 2014e). The options evaluated were 

found by Merced ID to be infeasible and we concur with this conclusion. Therefore, the 

benefit of repeating this analysis are unclear. As we note previously, the cost of 

implementing any engineering options would not be known until a feasible option is 

identified.

Although establishing a riparian forest canopy adjacent to the Merced River from 

Crocker-Huffman diversion dam to Shaffer Bridge, as embedded in the FWS and 
432

California DFW recommendations, could help to decrease water temperatures compared 

to existing conditions, we conclude that the primary reason for the absence of a riparian 

forest is in-channel and floodplain dredger and aggregate mining, not operation of the 

hydroelectric project. Consequently, conducting modeling to determine the optimal 

configuration for a restored floodplain forest would be more like a research study not 

directly related to hydropower operation. The timing of our recommended spring pulse 

flow would create optimal conditions for germination of riparian cottonwood trees, which 

eventually would provide shading and some water temperature relief. Enhanced 

floodplain configuration could also result from implementation of our recommended 

gravel augmentation plan, which could also serve to foster establishment of riparian 

vegetation. Both of these measures would address project-related cumulative effects, 

whereas establishing the ideal riparian forest width may or may not lead to meaningful 

water temperature enhancements.

With regard to California DFW’s recommendation that Merced ID evaluate the 

feasibility of prolonging and stabilizing the irrigation delivery season to provide the 

benefit of shorter residence times, we note that Merced ID did evaluate reducing the 

residence time downstream of Lake McClure by releasing larger volumes of water from 

New Exchequer dam (Merced ID, 2014e). California DFW does not provide sufficient 

detail for us to analyze how prolonging and stabilizing irrigation deliveries by using 

irrigation storage capacity downstream of the project would enhance the temperature 

regime of the lower Merced River. Therefore, we have no basis to recommend that 

Merced ID evaluate the feasibility of this measure.

Our recommended anadromous fish monitoring plan would include provisions for 

Merced ID to participate in fish rescue operations with other appropriate entities when 

water temperature monitoring indicates that stressful conditions exist when anadromous 

fish are present. This would partially address California DFW’s recommendation that 

Merced ID provide coldwater refugia for salmonids. However, as noted in our discussion 

of our recommended anadromous fish monitoring plan, we do not conclude that Merced 

ID should be solely responsible for any fish rescue efforts.

The Water Board preliminary WQC condition 8 would have Merced ID develop a 

plan for decreasing water temperatures in the lower Merced River without necessarily 

establishing a relationship to project operation. As we note in our discussion of our the 

recommended water temperature monitoring plan, we find that the Water Board’s 

approach specified in preliminary WQC condition 19 bases corrective actions on 

monitoring results and a linkage to project operation to be reasonable. We therefore 

recommend that preliminary WQC condition 19 be included in any new license that may 

be issued for this project, but not preliminary WQC condition 8. However, we recognize 

that the Water Board’s preliminary WQC condition 8 would be included as a mandatory 

condition in any license issued for the project.

The costs of the agency recommended and specified plans and studies are difficult 

to estimate and would largely be dependent on which aspects of the plans and feasibility 
433

study recommendations Merced ID would be expected to implement. However, we 

expect the implementation costs would be substantial (within $1 million to more than 

$100 million) and the incremental benefits over the staff alternative would not be worth 

the costs.

Fish Passage Upstream of Crocker-Huffman Diversion Dam

Crocker-Huffman diversion dam represents the upstream barrier to resident and 

anadromous fish in lower Merced River. Merced ID owns and operates CrockerHuffman diversion dam and the Main Canal as part of its water supply system and both 

facilities are not related to hydropower operation. Crocker-Huffman diversion dam is 

equipped with a fish ladder that has been non-operational since 1971 and would require 

replacement or retrofit to meet current standards for fish passage. 

The Water Board (preliminary WQC condition 8) specifies that Merced ID either 

develop a fish passage plan to allow for passage upstream of Crocker-Huffman, 

McSwain, and New Exchequer dams, or, develop a habitat restoration plan to decrease 

water temperatures in and downstream of the project. 

FWS [10(j) recommendation 2] recommends Merced ID, in coordination with 

PG&E, develop a salmonid conservation, rescue, and passage plan to include: 

(1) planning, permitting, design, scheduling, costs, construction implementation, and 

monitoring of anadromous and resident salmonid passage at Crocker-Huffman diversion 

dam; (2) screening at the Merced ID Main Canal; (3) water filtration for the existing 

hatchery; (4) refrigeration facilities at the existing hatchery for protecting salmonids from 

sub-lethal and lethal water temperatures resulting from project operation; and 

(5) cooperating with California DFW in trapping and hauling local wild fish when 

temperatures in the lower Merced River are expected to be stressful. 

NMFS [10(j) recommendation 1.1A(3c)] recommends that until a long-term water 

temperature improvement plan is developed, Merced ID should provide fish with access 

to the cold water habitat upstream of the Crocker-Huffman diversion dam. California 

DFW [10(j) recommendation 6] makes a similar recommendation but adds the option of 

using self-contained water temperature controlled holding units.

The Conservation Groups recommend that Merced ID: (1) open the CrockerHuffman fish ladder on a temporary basis for seasonal use by O. mykiss when fall-run 

Chinook salmon are not present and develop monitoring and reporting protocols to 

quantify fish passage at this dam; (2) develop a plan for infrastructure needed for longterm upstream and downstream O. mykiss passage at Crocker-Huffman diversion dam 

including transporting adult anadromous fish upstream of Lake McClure and young 

anadromous fish from upstream of Lake McClure to downstream of the diversion dam; 

(3) evaluate the suitability of habitat in the upper Merced River Watershed for 

reintroducing spring-run Chinook salmon and steelhead, including a literature review, 

field studies to fill data gaps, and a habitat feasibility evaluation report; (4) conduct an 

engineering study to define capture and transport options for moving adult and juvenile 
434

anadromous fish to and from habitat upstream of Lake McClure; and (5) develop a plan 

for reintroduction of anadromous fish to the upper Merced River Watershed, including 

project description, conceptual drawing of facilities, costs, known and potential funding 

sources, and a time line for implementation.

Anadromous fish do not pass upstream of the Merced Falls dam, which is 

downstream of the first project dam, McSwain dam, and therefore are not present in Lake 

McClure or the upper Merced River. The Crocker-Huffman diversion dam and any 

associated features, including the Main Canal, are not related to hydropower operation 

and are not included in the existing license. 

The Conservation Groups made similar requests in 2009 and 2011 to study habitat 

in the upper Merced River for anadromous fish reintroduction suitability. In its April 1, 

2011, study plan determination letter, Commission staff determined that there is no 

relationship of Merced River Hydroelectric Project operation on fish habitat upstream of 

Lake McClure. Commission staff further noted that the suitability of upstream habitat for 

anadromous salmonids, as it relates to recovery planning under NMFS guidelines, 

pertains to management decisions and actions that most appropriately fall under NMFS’ 

jurisdiction. We agree with the previous staff findings and, consequently, do not 

recommend specific measures that would enable fish passage at Crocker-Huffman 

diversion dam to the Merced Falls reach or the Merced River water shed upstream of 

Lake McClure, or studies to evaluate the potential for such reintroduction. However, we 

recognize that the Water Board’s preliminary WQC condition 8 would be included as a 

mandatory condition in any license issued for the project.

Measures Related to Lower Merced River Habitat Restoration

Habitat restoration and enhancement projects have the potential to benefit aquatic 

biota as well as terrestrial vegetation and improve geomorphic processes in the lower 

Merced River. Some of these measures are discussed previously under additional staffrecommended measures or in subsections pertaining to measures we do not recommend. 

FWS [amended 10(j) recommendations 3(A2) and 3(A3)] recommends habitat 

restoration and enhancement measures for the lower Merced River. For the 10-mile 

reach between Merced Falls dam and RM 45.2 (1.2 miles downstream of Snelling Road), 

FWS recommends that Merced ID restore a dense, riparian tree canopy in at least a 30-

meter-wide zone on each side of the river to reduce water temperature by planting root 

stock, cuttings, or nursery stock using native tree species from the riparian corridor; 

protecting the plantings from beaver depredation; and, for restoration on lands not 

federally or state-owned, obtaining conservation easements and conveying them to an 

FWS-approved entity. For the reach from Shaffer Bridge to the confluence with the San 

Joaquin River, FWS recommends that Merced ID enhance at least 10 miles of habitat 

based on recommendations of a technical advisory committee and where conservation 

easements can be acquired to protect the restored habitat. FWS gives examples of 

potential habitat restoration projects, including addition of LWM, floodplain and riparian 
435

restoration, removal of riprap, and restoration of gravel mine pits. In 10(j) 

recommendations 5(I) and 9(9), FWS and California DFW recommend that Merced ID

conduct long-term monitoring of riparian vegetation at floodplain restoration sites. The 

Conservation Groups make an identical recommendation. 

NMFS [10(j) recommendation 6] recommends that Merced ID implement NMFS’ 

Ecosystem Adaptive Management Process and actions related to habitat enhancements 

from Crocker-Huffman diversion dam to Shaffer Bridge. This process would entail 

collating the annual reports specified in applicable license conditions, and in consultation 

with a technical advisory committee, holistically assessing the information to determine if 

respective goals and objectives have been achieved; and, if goals and objectives are not 

achieved, determining adjustments needed to achieve anadromous fish habitat restoration 

goals. In addition, in 10(j) recommendation 7.1(C), NMFS recommends that Merced ID 

establish a restoration implementation fund and use an independent financial advisor to 

manage, track, and report on the fund’s progress. Interest from the fund would be used to 

support habitat restoration projects recommended by a technical advisory committee.

We do not dispute the environmental benefit to aquatic and riparian habitat of 

restoring a dense riparian tree canopy along the Merced River. However, we conclude 

that existing information indicates that non-project-related dredger and aggregate mining 

has elevated the floodplain downstream of Crocker-Huffman diversion dam from its 

original position, indicating that non-project variables affect the establishment of overfloodplain flows, which serve an important function in maintaining floodplain vegetation. 

In addition, Commission staff noted that the extensive aggregate mining both in the 

floodplain and the channel have created in-channel or captured mining pits.

In its April 1, 2011, study plan determination, Commission staff also found that 

the effects of hydroelectric project operation are outweighed by other non-project factors 

downstream of Shaffer Bridge. We find no basis to recommend that Merced ID be 

responsible for any habitat enhancement measures downstream of Shaffer Bridge. 

Although FWS gives examples of the types of projects that could be considered in this 

downstream reach, it does not specify the activities that would actually take place. 

Therefore, we have no basis to evaluate the environmental benefits of this aspect of 

FWS’ recommendation or the associated costs. 

The NMFS recommendation that Merced ID be responsible for implementing the 

Ecosystem Adaptive Management Process seems to reiterate the purposes of the staffrecommended technical advisory committee. Major functions of such a committee 

include review of information pertaining to environmental measures that may be included 

in a new license, including those that pertain to enhancement of anadromous fish habitat, 

and developing recommendations for future actions to be considered by other 

stakeholders. The Commission would ultimately determine if any conditions of a new 

license need to be adjusted based on recommendations from Merced ID and other 

stakeholders to more effectively achieve the stated goals of environmental measures. We 

do not consider it appropriate to recommend this measure for inclusion in any new 
436

license that may be issued for this project, because with our recommended technical 

advisory committee, listed in section 5.1.1.1, there is no need to recommend an 

Ecosystem Adaptive Management Process. 

NMFS recommends that Merced ID establish a restoration implementation fund 

and use the interest from the fund for activities recommended by a technical advisory 

committee at a future date. This recommendation does not identify specific 

environmental measures for us to assess and consider pursuant to sections 4(e) and 10(a) 

of the FPA; therefore, we have no justification for adopting the recommendation under

the staff alternative. 

Supplemental Anadromous Fish Monitoring

Existing California DFW monitoring of fish populations in project-affected waters 

is currently focused on anadromous salmonids occurring in the lower Merced River 

downstream of the Crocker-Huffman diversion dam (RM 52.0). California DFW 

continues to monitor fall-run Chinook salmon escapement, including carcass surveys, 

spawning distribution, scale and otolith collection and analysis, length, sex, coded-wiretag, and fecundity data and analysis, as it has been doing since 1970.

NMFS, FWS, and California DFW [10(j) recommendations 4, 5(A-F), and 9(1-6), 

respectively] and the Conservation Groups recommend similar measures pertaining to 

anadromous fish monitoring. Compared with our recommended anadromous fish 

monitoring measure, these measures would include an expanded set of monitoring 

activities. The primary differences include: (1) continuing existing California DFW 

carcass surveys, including data collection and analysis of scales, otoliths, length, sex, 

wire tags, and fecundity for fall-run Chinook salmon; (2) conducting RST sampling at 

both currently monitored upstream and downstream sites (although the Conservation 

Groups only recommend RST sampling at one location); and (3) conducting annual 

snorkel surveys of the O. mykiss population. 

We recognize the additional value that conducting carcass surveys, scale and 

otolith analysis, and fecundity determinations of adult anadromous fish would provide for 

resource management purposes, but we do not see how this information relates to the 

hydroelectric project operation or how it could be used to inform any project 

modifications. Merced ID estimates the annual cost of conducting carcass and otolith 

surveys to be about $350,000, and we consider this to be a reasonable estimate of 

expected costs. Therefore, we do not consider the benefits of gathering this additional 

information to warrant the likely substantial cost of doing so. 

In our analysis of the need for anadromous fish monitoring, we conclude that one 

RST monitoring station would be sufficient to document the number of outmigrating 

salmonids from project-affected waters of the lower Merced River. Merced ID estimates 

that the annual cost of operating the agency-recommended second RST monitoring site 

would be about $150,000, and we consider any benefits of this second monitoring site not 

to warrant the expected annual cost.
437

Similarly, conducting additional snorkel surveys to monitor the O. mykiss

population would supplement the monitoring proposed by Merced ID and recommended 

by staff. However, during six seasonal fish sampling efforts conducted between summer 

2006 to spring 2008 using snorkel surveys, seining, and backpack and boat-mounted 

electrofishing units, a total of 110 O. mykiss were observed. This included 73 O. mykiss

observed in the Crocker-Huffman diversion dam impoundment, which were most likely 

resident because there are no upstream passage facilities at the diversion dam and 37 

O. mykiss observed downstream of the diversion dam, which could have been either

anadromous or resident (Stillwater Sciences, 2008). Of the 37 O. mykiss observed by all 

collection methods in the reach downstream of the diversion dam, 30 were observed 

during snorkel surveys (an average of 5 per survey). The anadromy of any observed 

O. mykiss during snorkel surveys could not be determined, and we expect that very few 

O. mykiss would be observed based on the results of previous studies. Therefore, it is 

unclear how snorkel surveys could further inform decisions regarding the status of lower 

Merced River steelhead beyond what would be achieved by Merced ID’s proposed RST 

and counting weir monitoring, which would detect upstream and downstream migrating 

fish. We therefore conclude that the benefit of conducting snorkel surveys in the lower 

Merced River would not be justified by the estimated annual cost of $150,000.

Merced River Fish Hatchery Management

The Merced River Fish Hatchery has been operational since 1970 and is managed 

by California DFW. The initial construction of the hatchery was funded by California 

DFW, California DWR, and Merced ID, and its ongoing operation is cooperatively 

funded by California DFW in collaboration with state water contractors. The current 

population of Chinook salmon in the Merced River is supported by fish produced at the 

hatchery. Salmon produced at the hatchery are also routinely used for studies conducted 

within the San Joaquin River Watershed. The hatchery reports recent average annual 

hatchery production of Chinook salmon (2004 to 2009) to be 972,344 fish. 

California DFW [10(j) recommendation 5] recommends that Merced ID prepare a 

hatchery master plan in consultation with California DFW, FWS, and NMFS. The plan 

would include provisions for an initial design study to determine site capabilities and 

costs associated with operating the hatchery. The recommended plan would also address 

11 potential hatchery upgrades to be provided at the existing hatchery and provisions to 

assess the possible relocation of facilities to a site immediately below New Exchequer 

dam to meet the guidelines of the California Hatchery Scientific Review Group. 

California DFW states that Merced ID should be responsible for the annual hatchery 

release of 5 million fall-run Chinook salmon smolts with a single year maximum of 7.5 

million juveniles, and the annual release of 250,000 steelhead juveniles with a single year 

maximum of 425,000 juveniles. 

The Conservation Groups recommend that Merced ID develop and implement a 

Merced River fish management plan to design, construct, and operate a fish propagation 

facility for the production of native salmonids. The initial capacity would be a 5-year 
438

running average of 60,000 eyed eggs, fry, or fingerling Chinook salmon per year and 

multiple age class broodstock (capacity of 1,000 to 2,000 pounds). Initial capacity would 

also include up to a 5-year running total of 667,200 rainbow trout annual production, 

commensurate with the need to outplant fish in tributaries of the Merced River. The 

Conservation Groups identify a 22-acre site on Merced ID land immediately below New 

Exchequer dam as a potential location for this new facility.

The current annual production goal of the Merced River Fish Hatchery is to take 2 

million fall Chinook salmon eggs and release 1 million Chinook salmon smolts 

(California HSRG, 2012). California DFW states that the current goal is based on facility 

constraints. The continued operation of the Merced River Fish Hatchery would support 

the Chinook salmon population in the lower Merced River until such time as natural 

reproduction in the river channel is sufficient to sustain or enhance the existing 

population. However, no aspect of the hatchery is included in the current license and the 

hatchery is not related to the ancillary use of project water for hydropower generation. 

The Crocker-Huffman diversion dam, which blocks upstream anadromous fish passage, 

was constructed in 1910, well before the Merced River Project received its hydroelectric 

license from the Commission. We do not dispute the assertion that upgrading and 

expanding the existing hatchery and assessing the potential relocation of the hatchery to a 

more favorable site could benefit efforts to artificially sustain Chinook salmon 

populations in the lower Merced River by stocking Chinook salmon smolts. We also 

recognize that the project plays a part in cumulative effects in the lower Merced River. 

However, other factors, such as instream mining and irrigation diversions, have had a 

much greater proportional effect than those associated with hydropower operation. To 

mitigate the effects of the project, we have recommended measures that could benefit 

Central Valley fall-run Chinook salmon populations by enhancing natural in-river 

production, such as an improved flow regime, reduced water temperatures to the extent 

controllable by the project, and spawning habitat enhancements.

The cost of California DFW recommended measures relating to a fish hatchery are 

difficult to quantify, because it is not clear how many of the elements Merced ID would 

be expected to implement. We estimate that implementing the recommended 

enhancements to the existing hatchery or constructing a new hatchery in proximity to 

New Exchequer dam would cost millions of dollars. Nevertheless, given the lack of a 

connection to hydroelectric project operation, we have no justification for adopting the 

recommended hatchery measures under the staff alternative.

Benthic Macroinvertebrate Monitoring

BMI assemblages are an important part of the aquatic ecosystem and provide a 

fundamental food source for many resident fish. The description and characterization of 

BMI can also be used to provide an indication of the general health and condition of a 

stream.
439

Previous study results showed at least two EPT taxa (intolerant of water quality 

impairment) included in the top five numerically dominant taxa at each monitoring site in 

the lower Merced River, with the majority of dominant taxa likely available as a food 

source for juvenile Chinook salmon (Stillwater Sciences 2008, 2006). Tolerance metrics 

indicated moderately tolerant BMI assemblages under existing conditions. 

FWS [10(j) recommendation 8] recommends that Merced ID develop a BMI 

monitoring plan describing sampling to be conducted in the project-affected bypass 

reaches to assess the effects on BMI under new flow regimes and other changes that may 

be included in a new license.

The recent BMI studies on the lower Merced River provide an adequate baseline 

for evaluating effects under any potential change to the flow regime. The instream flow 

measures offered by various stakeholders and recommended by staff would result in no 

decrease to the current flow schedule over all water year types and would, at a minimum, 

maintain existing conditions in the lower Merced River. Results of recent BMI studies 

indicate a moderately tolerant BMI assemblage that can be expected to be used as food 

by fish in the lower river. Additionally, if instream channel enhancements downstream 

of Crocker-Huffman diversion dam should be included in a new license, it would

improve conditions for the BMI community. Although continued sampling of BMI in the 

lower Merced River would enable trends to be evaluated over time, we cannot envision a 

scenario where project hydroelectric operation with our recommended protection and 

enhancement measures would result in a declining trend in BMI density and EPT taxa. 

Consequently, the benefits of this recommended monitoring are unclear and we do not 

recommend provisions for such monitoring be included in a new license for this project.

Operation, Maintenance, and Administration

BLM specifies in preliminary 4(e) condition 21 that Merced ID enter into an 

agreement to provide annual funding to BLM for the operation, maintenance, 

management, and administration costs of BLM-administered lands in and around the 

Merced River Project.

BLM did not disclose the amount of funding to be provided each year. Merced ID 

is ultimately responsible for operating and maintaining all project facilities and lands 

within the project boundary. Further, it is unclear how these funds would accomplish a 

project purpose. Therefore, we do not recommend Merced ID provide annual funding for 

the operation and management of lands and facilities at the project. 

Annual Consultation and Review

Merced ID proposes to conduct an annual review of federally listed and specialstatus species lists, assess newly added species occurring on federal land, and if necessary 

consult with agencies to develop and implement protection measures. Preliminary WQC

condition 12 and BLM preliminary 4(e) condition 1 both specify annual consultation to 

review the project status and plans, results of studies, necessary modifications to plans, 
440

and protection measures for newly listed species. Preliminary WQC condition 13 and 

BLMs preliminary 4(e) condition 11 also both specify that Merced ID review the lists of 

federally listed and special-status species and evaluate potential project effects on newly 

listed species. In its 10(j) recommendation 6(a), FWS recommends under item A, 

consultation prior to construction of new project features or the implementation of nonroutine maintenance activities that may affect federally listed and candidate species and 

their habitat, and directs the licensee to develop a draft biological assessment for 

potentially affected species. Under item B, FWS states the draft biological assessment 

should evaluate potential impacts of the proposed actions on species and their habitats, 

and the licensee should submit the plan to FWS and BLM for comments to be 

incorporated into a final biological assessment. Under item C, FWS recommends the 

contents of the draft biological assessment, and under items D and E, FWS recommends 

the licensee conclude consultation for a particular set of species and habitats, in the event 

of new construction or non-routine maintenance activities. 

Our analysis in section 3.3.3.2, Threatened and Endangered Species, 

Environmental Effects, indicates that although we agree that consultation prior to new 

construction and non-routine maintenance would protect federally listed species and their 

habitats over the term of the license, the Commission typically includes in its licenses a 

standard license article providing such protection. This license article contains a fish and 

wildlife reopener provision that could be used to require changes to project facilities or 

maintenance plans upon Commission motion or as recommended by the appropriate state 

and federal fish and wildlife agencies after notice and opportunity for hearing. This 

standard reopener provision retains authority for the Commission to implement any 

measures that may be needed to protect threatened or endangered species or other fish 

and wildlife resources over the term of the license issued for the project. Although we 

have no objection to Merced ID conducting this agency consultation, the standard license 

article would provide a similar level of protection as the proposed measure. We 

recognize, however, that these annual review and consultation measures are included in 

the Water Board preliminary WQC conditions and BLM preliminary 4(e) conditions, so 

the measures would be included as mandatory conditions of any license issued for the 

project. 

5.1.2 Merced Falls Project

This section contains the basis for, and a summary of, our recommendations for 

relicensing the Merced Falls Project. We weigh the costs and benefits of our 

recommended alternative against other proposed measures.

Based on our independent review of agency and public comments filed on this 

project and our review of the environmental and economic effects of the proposed project 

and its alternatives, we select the staff alternative as the preferred alternative. This 

alternative includes elements of the applicant’s proposal, section 4(e) conditions, section 

401 WQC conditions, resource agency recommendations, alternative conditions under the 

Energy Policy Act of 2005, and some additional measures. We recommend this 
441

alternative because: (1) issuance of a new hydropower license by the Commission would 

allow PG&E to operate the project as an economically beneficial and dependable source 

of electrical energy for its customers; (2) the 3.4 MW of electric energy generated 

capacity comes from a renewable resource that does not contribute to atmospheric 

pollution; (3) the public benefits of this alternative would exceed those of the no-action 

alternative; and (4) the recommended measures would protect and enhance fish and 

wildlife resources and would provide improved recreation opportunities at the project.

Finally, for the reasons outlined below, we recommend that certain conditions 

specified by the Water Board not be included in the staff alternative. The conditions we 

are not recommending include a fish passage plan and a gravel augmentation plan. We 

recognize, however, that the Commission must include these conditions in any license 

due to their mandatory nature.

5.1.2.1 Measures Proposed by PG&E

Based on our environmental analysis of PG&E’s proposal discussed in section 3

and the costs discussed in section 4, we recommend including the following 

environmental measures proposed by PG&E in any license issued for the project. Our 

recommended modifications to PG&E s proposed measure are shown in italic.

Aquatic Resources

 Develop and implement a water quality monitoring program.

 Develop an annual fish sampling plan in the Merced Falls reach in 

consultation with the technical advisory committee.

 Continue to perform intake cleaning of LWD. Cleaning and subsequent 

downstream placement of LWD should be dictated by an LWD management 

plan, created in consultation with the technical advisory committee.

Recreation

 Continue to operate and maintain existing recreation facilities at the 

Merced Falls impoundment area, including the River’s Edge Fishing 

Access area and the car-top boat launch at Merced Falls Fishing Access 

area.

 Develop and post directional and safety signage at the informal canoe 

portage trail.

 Continue to monitor recreation use and recreation facility capacity through 

the FERC Form 80 every 6 years.
442

 Develop a fish stocking plan in consultation with California DFW that 

includes stocking 11,000 adult-sized rainbow trout at the Merced Falls 

impoundment for the first 2 years following license issuance and a plan for 

stocking (schedule and type and amount of fish) for the rest of the license 

term.

Cultural Resources

 Implement the final HPMP upon license issuance. 

5.1.2.2 Additional Measures Recommended by Staff

In addition to PG&E’s proposed measures listed above, we recommend including 

the following staff-recommended measure in any license issued for the Merced Falls 

Project: 

Aquatic Resources

 Participate in a Merced River technical advisory committee in conjunction 

with Merced ID.

 In conjunction with Merced ID, develop a coordinated operation plan for 

the Merced River and Merced Falls Projects in consultation with the 

technical advisory committee.

 Develop a LWD management plan in consultation with the technical 

advisory committee.

 Develop an annual fish sampling plan in the Merced Falls reach in 

consultation with the technical advisory committee.

Terrestrial Resources

 Develop a control plan for noxious weeds and invasive plants, integrated 

with a component for pesticide use and notification.

 Develop and implement a management plan for the bald eagle in 

consultation with FWS, California DFW, and the Water Board.

Threatened and Endangered Species

 Develop a protection plan, in consultation with BLM, FWS, California 

DFW, and the Water Board for the valley elderberry longhorn beetle.

 Develop a protection plan in consultation with BLM, FWS, California 

DFW, and the Water Board for the San Joaquin kit fox.

 Develop a protection plan in consultation with BLM, FWS, California 

DFW, and the Water Board for the California red-legged frog, foothills 

yellow-legged frog, and western spadefoot.
443

Recreation

 Operate and maintain all recreation facilities at the Merced Falls Fishing 

Access area, including one sign, restroom, parking area, and car-top boat 

launch, the informal angler trail along the northern shoreline, the two 

informal parking areas on either side of Hornitos Bridge, and the informal 

canoe portage trail at the south end of Merced Falls dam.

Project Boundary

 Modify the project boundary to include the informal canoe trail on the 

south side of Merced Falls dam.

Below, we discuss our rationale for our additional staff-recommended measures.

Technical Advisory Committee

The Merced Falls Project area experiences many of the environmental effects of 

the upstream Merced River Project because of its proximity and operational dependence 

on the upstream Merced ID facilities. Downstream of Merced Falls dam, the 

environmental effects of both the Merced River and Merced Falls Projects are highly 

interrelated, although the incremental effects of the PG&E project are minor, as discussed 

in section 3.3.1.2. 

California DFW [10(j) recommendation 1] recommends that PG&E establish an 

ecological resource committee in conjunction with Merced ID for the purpose of 

consulting annually with resource agencies and other interested stakeholders on the 

implementation of license measures, implementation of monitoring plans, review and 

evaluation of monitoring data, and review and evaluation of required facility 

modifications. Similarly, NMFS [10(j) recommendation 7] recommends Merced ID 

establish an anadromous fish committee in conjunction with Merced ID that includes a 

technical advisory plan that defines membership, meeting responsibilities, ground rules 

for consensus-based decision making, and a process for implementing the decisions. The 

Water Board [preliminary WQC condition 7] specifies that PG&E hold a pentennial 

meeting with resource agencies to provide an update of all monitoring and data required 

by the new license and WQC. PG&E indicates that participation in regular consultation 

is unnecessary, given the minimal environmental impact of the Merced Falls Project. 

Establishing a committee to assess ongoing study results and project operation 

would provide an effective forum for making decisions regarding future project operation 

within the constraints of a new license. Due to the close proximity, operational 

dependence, and combined environmental effects of the Merced River and Merced Falls 

Projects, PG&E’s participation in a technical advisory would be valuable to ensure the 

timeliness, efficacy, and consistency in the application of any operational and 

environmental measures required of Merced ID and/or PG&E in the Merced Falls Project 

area and downstream. 
444

We note that Merced ID proposes to establish a Merced River technical advisory 

committee.

61

 Under the Merced River Project staff alternative, Merced ID would 

establish a technical advisory committee that is not constrained to measures that pertain 

only to anadromous fish downstream of Crocker-Huffman diversion dam; establish 

guidelines for conducting meetings; and add BLM and the Park Service to the entities 

invited to participate on the committee because Lake McClure water management affects 

resources within the jurisdiction of these two agencies. As such, PG&E’s investment in a 

technical committee would be limited to participation—significantly reducing the cost 

and effort associated to the measure, and thus being commensurate with the Merced Falls 

Project’s minor incremental environmental effects.

NMFS [10(j) recommendation 6] recommends that Merced ID implement NMFS’ 

Ecosystem Adaptive Management Process and actions related to habitat enhancements 

from Merced Falls dam to the Crocker-Huffman diversion dam. We find that this 

recommendation seems to reiterate the purposes of a technical advisory committee, 

previously discussed. Major functions of such a committee include review of 

information pertaining to environmental measures that may be included in a new license, 

including those that pertain to enhancement of anadromous fish habitat, and developing 

recommendations for future actions to be considered by other stakeholders. The 

Commission would ultimately determine if any conditions of a new license need to be 

adjusted based on recommendations from PG&E and other stakeholders to more 

effectively achieve the stated goals of environmental measures.

The Water Board [preliminary WQC condition 7] also specifies that PG&E review 

lists of endangered and special-status species to identify newly listed species that could 

be adversely affected by the project. For any newly listed species identified as 

potentially affected by the project, the Water Board further specifies that PG&E should 

consult with FWS, California DFW, the Water Board, and NMFS to develop a speciesspecific study plan. The Commission typically includes a standard license article 

providing such protection in its licenses. This license article contains a fish and wildlife 

reopener provision that could be used to require changes to project facilities or 

maintenance plans upon Commission motion or as recommended by the appropriate state 

and federal fish and wildlife agencies after notice and opportunity for hearing. This 

standard reopener provision retains authority for the Commission to implement any 

measures that may be needed to protect threatened or endangered species or other fish 

and wildlife resources over the term of the license issued for the project.

We consider PG&E’s participation in a technical advisory committee an effective 

approach to ensuring coordination between the licensees for the Merced River and 

Merced Falls Projects and adaptively managing resources during the term of the licenses. 

We estimate this measure would have an annualized cost of $2,200. Given the benefits 

 

61 See section 5.2.1.1 and section 3.3.1.2 for corresponding analysis.
445

of the staff’s recommended alternative as described above, we consider this cost to be 

warranted.

Coordinated Operation Plan

PG&E proposes to continue operating the project run-of-river and proposes no 

specific mechanism for coordinating project activities, such as operations and 

maintenance activities with the upstream Merced River Project.

Merced ID proposes to develop a coordinated operations plan for the Merced 

River and Merced Falls Projects. Under the Merced River Project staff alternative, 

Merced ID would develop the plan in consultation with the Water Board, BLM, FWS, 

California DFW, NMFS, and the Park Service.

California DFW [10(j) recommendation 2] recommends that PG&E develop a 

coordinated operation plan in consultation with Merced ID and file it with the 

Commission, California DFW, the Water Board, FWS, and NMFS within 90 days of 

license issuance.

Under the staff alternative, PG&E would develop a coordinated operation plan in 

consultation with Merced ID and file it with the Commission, California DFW, the Water 

Board, FWS, and NMFS within 90 days of license issuance.

As discussed in section 3.3.1.2, flows released from the Merced River Project for 

environmental and irrigation purposes must pass through the Merced Falls Project before 

reaching the irrigation diversion point at Crocker-Huffman diversion dam. Although the 

Merced Falls Project operates in a run-of-river mode, where inflow to the project equals 

outflow, there are circumstances that could occur, such as routine maintenance events,

that could have a bearing on the multi-purpose releases from the Crocker-Huffman 

diversion dam to the lower Merced River and irrigation flows into the Main Canal. 

Although developing this plan is likely to entail technical discussions about the fine 

points of project operations, inviting interested parties to provide input on the draft plan 

could provide valuable insights that enhance its effectiveness.

We estimate that developing a coordinated operations plan as recommended by 

staff would have an annualized cost of $1,000. Because operational coordination 

between the licensees would be valuable to ensure the timeliness, efficacy, and 

consistency in the application of any operational measures in the Merced Falls Project 

area and downstream in the lower Merced River, we conclude the benefits of the program 

are worth the costs.

Large Woody Debris Management

LWM provides habitat structure in streams and can influence sediment storage and 

channel morphology through its effects on flow, water velocity, and sediment transport. 

LWM provides cover and holding habitat for fish, serves as substrate for the growth of 

algae and invertebrates (which are important components of the aquatic food web), and 
446

affects patterns of sediment deposition and scouring. Loss of LWM can result in reduced 

complexity of aquatic habitat and reduced carrying capacity for aquatic biota. 

PG&E proposes to continue periodically perform intake cleaning, wherein woody 

debris lodged against the intake is raked off, placed on a debris chute, and passed 

downstream. PG&E also notes that woody debris can continue downstream periodically 

when project gates are opened. PG&E does not provide details regarding the timing or 

quantity of LWD/LWM removal and therefore, it is difficult to evaluate the biological 

significance, if any, of PG&E’s LWD/LWM intake cleaning procedures. 

Identical to its recommendation for the Merced River Project, NMFS [10(j) 

recommendation 3] recommends that in conjunction with Merced ID, PG&E implement 

LWD enhancements in four river reaches between Crocker-Huffman diversion dam and 

Shaffer Bridge (RMs 52.0–32.8). The Merced Falls project area consists primarily of 

annual grasses, with a relatively small percentage of woody vegetation that could 

contribute to the recruitment of LWM and LWD. The recruitment of LWM and LWD in 

the reach downstream of Merced Falls and the lower Merced River depends primarily 

sources upstream of the project. As previously discussed, pre-application studies indicate 

that LWM is uncommon at upstream the New Exchequer dam, most likely because LWM 

transported into Lake McClure (most often during storm flows) sinks or washes up on the 

reservoir shoreline before reaching the dam. Loss of LWM due to storage in Lake 

McClure is unavoidable. LWM input from the adjacent oak woodlands downstream of 

Lake McClure is also limited, and hardwood recruited to stream channels tends to be 

relatively small and short-lived in the channel. Therefore, the Merced Falls Project’s 

incremental effect on the lack of LWD in Merced Falls reach or the lower Merced River 

is negligible compared to the effect of the upstream dams. For these reasons, the breadth 

and scale of the LWM management activities recommended by NMFS are unwarranted. 

Development of an LWD plan specific to the Merced Falls Project, as described above 

would emphasize mitigation of the project’s effects on LWD in the project area. 

However, we note that we recommend Merced ID develop a LWM and debris 

management plan that describes existing locations of LWM collection in Lake McClure 

and McSwain reservoir, potential options for moving the LWM collected to the Merced 

River downstream of Crocker-Huffman diversion dam, and suitable locations where 

LWM and debris can be placed in the active channel.62

We estimate that PG&E’s proposal would have an annualized cost of $8,800. We 

estimate that developing a LWD management plan as recommended by staff would have 

an annualized cost of $13,800. Because staff’s recommended measure would provide a 

benefit to aquatic species in the Merced Falls reach, we conclude the benefits of the 

program are worth the additional costs.

 

62 See section 5.2.1.1 and section 3.3.1.2 for corresponding analysis.
447

Fish Population Monitoring

Fish population monitoring could form the basis for establishing immediate and 

long-term protection and enhancement strategies for fish in the project area. PG&E 

proposes to monitor O. mykiss populations in the reach of the Merced River downstream 

of the Merced Falls dam and upstream of Crocker-Huffman dam (Merced Falls reach)

annually during the fall. California DFW [10(j) recommendation 6] recommends that 

PG&E develop an annual monitoring plan and conduct O. mykiss surveys in the Merced 

Falls reach during the spring and summer to determine abundance, size distribution, 

spawning distribution, and summer distribution. Specific methodology of the monitoring 

plan would be developed in consultation with a technical advisory committee. NMFS 

[10(j) recommendation 4] recommends that PG&E develop and implement an 

anadromous/resident fish monitoring plan in the Merced Falls reach in consultation with 

a technical advisory committee. The goals and timing of NMFS’ recommended plan are 

similar to those recommended by California DFW. Given the seasonally high spring and 

early summer flows in the Merced Falls reach, certain sampling techniques would not 

only be limited in their efficacy, but also dangerous to those responsible for conducting 

the sampling. While fall sampling efforts would ensure safer and more effective 

sampling conditions, specific data needs, such as spawning distribution or summer 

distribution, may not be fulfilled because the timing of discrete events in the life cycle of 

the species of interest may not coincide with fall sampling. The development of a fish 

monitoring plan for the Merced Falls reach in consultation with a technical advisory 

committee could resolve the necessity for specific data needs, such as spawning 

distribution or summer distribution with regard to local site conditions, and would assist 

in any potential adaptation of sampling techniques to address local site conditions. We 

estimate that PG&E’s proposed measure would have an annualized cost of $16,000. We 

estimate that the development and implementation of a fish monitoring plan as 

recommended by staff would have an annualized cost of $20,000. Because the staffrecommended measure would optimize the design and implementation of a fish 

monitoring program, we conclude the benefits of the plan are worth the costs.

NMFS [10(j) recommendation 4] also recommends PG&E: (1) conduct an annual 

pre-spawning mortality survey; (2) conduct carcass surveys, including data collection and 

analysis of scales, otoliths, length, sex, wire tags, and fecundity data; (3) conduct annual 

juvenile emergence and outmigration monitoring using two RSTs; (4) establish counting 

weirs to estimate Central Valley Chinook salmon and Central Valley steelhead 

escapement and provide data on the percentage of females and migration timing; and 

(5) conduct otolith analysis annually to estimate the contribution of naturally produced 

fry-, parr-, and smolt-sized migrants to the adult population. We note that NMFS’ 

additional recommendations 1-5 listed above are identical to its recommendations for the 

Merced River Project, and are primarily intended to gather monitoring data on 

anadromous species. As previously discussed, Crocker-Huffman diversion dam, located 

downstream of the Merced Falls Project, represents the upstream barrier to resident and 

anadromous fish in lower Merced River. Therefore, monitoring these species in the 
448

Merced Falls reach, using the recommended techniques, would represent a considerable 

expense, estimated to be as much as $35,000 annually, but would likely result in data of 

little value. For these reasons, we find that the cost of the additional measures is not 

worth the potential benefits. As discussed in section 5.1.1.2, Additional Measures 

Recommended by Staff, we recommend that Merced ID conduct anadromous fish 

monitoring in the lower Merced River. 

Integrated Management Plan for Noxious Weeds, Invasive Plants, Pest 

Management, and Pesticide Use 

Under a new license, PG&E proposes to continue its semi-annual treatment of 

noxious weeds and invasive plants, but it does not propose a formal management plan. 

The Water Board comments that the Basin Plan pertains to all levels of pesticide use and 

includes herbicides. Preliminary WQC condition 2 specifies that PG&E develop a 

pesticide use plan within 6 months of license issuance, in consultation with the Water 

Board, BLM, California DFW, FWS, and NMFS. California DFW [10(j) 

recommendation 7] recommends an integrated pest management and pesticide use 

notification plan to control undesirable woody and herbaceous vegetation, aquatic plants, 

insects, and rodents. FWS’ comments about the effects of rodenticide and pesticide use 

are discussed in section 3.3.3.2 and section 3.3.3.3. 

A formal plan detailing the methods, locations, timing, frequency of control 

treatments, and target species would allow PG&E to manage undesirable vegetation more 

effectively, while also reducing effects on sensitive species and habitats. Integrating a 

component for pest management and pesticide use notification into the Invasive Species 

Management Plan to address agency requirements of notification prior to use would 

further protect both terrestrial and aquatic resources from the effects of herbicides used to 

control undesirable vegetation and other pesticides. We therefore recommend PG&E 

develop a plan for the control of noxious weeds and invasive plants integrated with a 

component on pest management and pesticide use. The plan would be developed in 

consultation with FWS, the Water Board, California DFW, and BLM and include the 

measures required by the conditions and recommendations made by agencies. We 

estimate the plan would have a levelized annual cost of about $15,000. Such a cost 

outweighs the potential effects on sensitive species and habitats in the project vicinity. 

Bald Eagle Management

PG&E proposes to protect bald eagles according to site-specific and projectspecific management criteria, rather than developing a management plan consistent with 

the National Bald Eagle Management Guidelines. The Water Board specifies in 

preliminary WQC condition 5 that PG&E develop a monitoring and conservation plan for 

bald eagles, consistent with the most current guidelines provided by FWS. FWS [10(j) 

recommendation 5] recommends a bald eagle management plan either to be implemented 

in concert with Merced ID or to be developed and implemented by PG&E. 
449

Requiring a plan to protect bald eagle nests from operation and maintenance 

activities and recreation activities would reduce project-related effects on nesting bald 

eagles. In addition, requiring protection of winter roost trees from vegetation 

management and future construction activities would reduce potential habitat 

degradation. 

All survey protocols and protection and mitigation measures should be consistent 

with the guidelines provided in the National Bald Eagle Management Guidelines, rather 

than site- or project-specific. Implementing survey protocols and protection and 

mitigation measures inconsistently could conflict with the National Bald and Golden 

Eagle Protection Act and the Migratory Bird Treaty Act. Thus, we recommend 

developing a plan in consultation with FWS, California DFW, and BLM to ensure survey 

protocols and protection and mitigation measures are consistent with those required by 

the National Bald Eagle Management Guidelines. We estimate the plan would have a 

levelized annual cost of about $2,000.

Protection Plan for the Valley Elderberry Longhorn Beetle

PG&E does not propose a protection plan for the valley elderberry longhorn 

beetle. FWS comments that it considers exit holes in the bark of elderberry bushes to be 

extremely rare and to be evidence of occupation by the valley elderberry longhorn beetle. 

FWS [10(j) recommendation 3] indicates ESA consultation has not been concluded for 

this species. The Water Board [preliminary WQC condition 6] specifies a monitoring 

and conservation plan for the valley elderberry longhorn beetle.

In our analysis in section 3.3.3.2, we note that valley elderberry longhorn beetles

could occur in the project area. Project-related activities, such as the control of 

undesirable vegetation and increases in recreation could negatively impact valley 

elderberry longhorn beetles and their habitat. To prevent unforeseen damage or removal 

of the existing elderberry shrub and any elderberry shrubs identified in the future, we 

recommend developing a protection plan for the valley elderberry longhorn beetle and its 

habitat in consultation with FWS, BLM, California DFW, and the Water Board. The plan 

would include measures required by agency conditions and recommendations, as well as 

other measures recommended by agencies during consultation. We estimate the plan 

would have a levelized annual cost of $2,000 and would be worth the cost to ensure the 

protection of any elderberry shrubs and the valley elderberry longhorn beetle from project 

effects. 

Protection Plan for the San Joaquin Kit Fox

PG&E does not propose any measures to protect the San Joaquin kit fox nor has it 

provided information about project effects on the species. The Water Board [preliminary 

WQC condition 2] specifies that PG&E develop a pesticide use plan to protect state and 

federally threatened and endangered species, where pesticide use includes rodenticides. 

California DFW [10(j) recommendation 7] recommends an integrated pest management 

and pesticide use notification plan for undesirable vegetation, insects, and rodents. 
450

PG&E did not provide information about San Joaquin kit fox and potential 

project-related effects on San Joaquin kit fox to sufficiently assess potential effects on the 

species. Conducting surveys in the project area would be necessary to document San 

Joaquin kit fox use of habitat in the project area. Additionally, data collected during 

surveys may provide information on the effects of the project on the dispersal of kit fox. 

Including the surveys as a component of a protection plan would be formally document

study results so that project effects on kit fox can sufficiently be evaluated and 

appropriate protection and mitigation measures can be developed. As such, we 

recommend PG&E develop a protection plan for the San Joaquin kit fox in consultation 

with FWS, the Water Board, California DFW, and BLM. The plan would include: 

(1) study methodologies and monitoring protocols to identify San Joaquin kit fox habitats 

within the project area; (2) an assessment of potential project effects on San Joaquin kit 

fox in the project area; (3) protection and mitigation measures; (4) references to measures 

contained in other plans that would protect San Joaquin kit fox; and (5) descriptions of 

any exceptions to the prohibited use of rodenticides that would be considered 

emergencies and allowed by agencies and an explanation of why the emergency 

situations would supersede protection measures for the San Joaquin kit fox. We estimate 

the plan would have a levelized annual cost of $2,000 and would be worth the cost to 

ensure that the project would not adversely or cumulatively affect the San Joaquin kit 

fox. 

Protection Plan for the California Red-legged frog, Foothill Yellow-legged 

Frog, and Western Spadefoot

PG&E does not propose any protective measures for the California red-legged 

frog, or any other federally listed or special-status amphibian species. FWS [10(j) 

recommendation 4] recommends a conservation plan for the California red-legged frog. 

The Water Board [preliminary WQC condition 9] specifies a frog monitoring program for 

the California red-legged frog, foothill yellow-legged frog, and western spadefoot. 

In section 3.3.3.2, we discuss the potential for California red-legged frogs to occur 

in and near the project area and analyze project effects on the species. The protective 

measures recommended by FWS include: measures to control bullfrogs, reestablishing

populations of the California red-legged frog in the Piney Creek core area, and reducing 

population-level impacts from the frog-killing Batrachochytrium dendrobatidus fungus.

These measures would help reduce predation and mortality and enhance populations in 

the vicinity of the project. We also agree with Water Board’s recommendation to include

similar measures for the foothill yellow-legged frog and western spadefoot, both of which 

are special-status species currently under review by FWS. Broadening the measures to 

include other special-status species, such as the foothill yellow-legged frog and the 

western spadefoot, would bestow similar protective benefits to those species. Therefore, 

we recommend PG&E develop a plan to protect federally listed and special-status 

amphibian species, including but not limited to the California red-legged frog, foothill 

yellow-legged frog, and western spadefoot. We estimate the cost of the protection plan 
451

to be $2,000. We consider the plan to be worth the cost, given the benefits to these 

federally listed and special-status species, while also ensuring the project’s compliance 

with state and federal laws governing federally listed and special-status species.

Recreation

A number of formal and informal recreation sites exist at the project. Although 

PG&E proposes to continue to operate and maintain the recreation facilities at River’s 

Edge Fishing Access area and the car-top boat launch at Merced Falls, there is no 

assurance that the rest of the formal and informal recreation sites at the Merced Falls 

impoundment would be maintained or remain accessible to the public over the term of a 

new license. We find these facilities necessary for project purposes and therefore, 

recommend PG&E operate and maintain all formal and informal recreation facilities 

within the project boundary at the Merced Falls impoundment. The cost of this measure 

is included in the existing operation and maintenance costs.

Project Boundary

Currently, boaters are forced to portage around the south side of the dam on 

private property to access the stream reach below Merced Falls dam. Although the canoe 

portage trail receives low to moderate use, it is the only access to the Merced Falls 

impoundment on the south shoreline. Formalizing the canoe portage trail would ensure 

boaters have a clear and safe passageway around the dam and would decrease the chance 

of boaters unintentionally trespassing on private lands. 

5.1.2.3 Measures Not Recommended by Staff

Staff finds that some of the measures recommended by other interested parties 

would not contribute to the best comprehensive use of the Merced River water resources, 

do not exhibit sufficient nexus to project environmental effects, or would not result in 

benefits to non-power resources that would be worth their cost. The following discusses 

the basis for staff’s conclusion not to recommend such measures.

Fish Passage

The Merced Falls dam has a non-operational fish passage facility. The facility 

was decommissioned after construction of the upstream Merced River Project dams 

eliminated suitable habitat for anadromous species upstream of the Merced Falls dam. 

As previously discussed, Crocker-Huffman diversion dam (RM 52.0), located 

downstream of the Merced Falls Project, represents the upstream barrier to resident and 

anadromous fish in lower Merced River. Crocker-Huffman diversion dam is equipped 

with a fish ladder that has been non-operational since 1971 and would require 

replacement or retrofit to meet current standards for fish passage. PG&E does not 

propose any measures relating to fish passage.

The Conservation Groups recommend that PG&E reopen the fish ladder at Merced 

Falls, based on the “reasonably foreseeable” future reoperation of the fish passage facility 
452

at the downstream Crocker-Huffman diversion dam. Because anadromous fish are 

unable to achieve passage over Crocker-Huffman diversion dam and access the Merced 

Falls Project area, reoperation of the fish ladder at Merced Falls dam would provide no 

benefit to anadromous species in the Merced River at this time.

FWS [10(j) recommendation 1(1-3)] recommends PG&E, in coordination with 

Merced ID, develop a salmonid conservation, rescue, and passage plan to include: 

(1) planning, permitting, design, scheduling, costs, construction implementation, and 

monitoring of anadromous and resident salmonid passage at Crocker-Huffman diversion 

dam; (2) cooperating screening at any conveyance facilities out of the Merced Falls 

reservoir pool; (3) cooperating with California DFW in trapping and hauling local wild 

fish when temperatures in the lower Merced River are expected to be stressful. The 

Crocker-Huffman diversion dam and any associated features, including the Main Canal, 

are not related to hydropower operation and are not included in the existing license. 

Regarding canal entrainment, studies indicate that entrainment into the northside 

canal likely represents a negligible effect on the overall abundance of the fish 

assemblage. As such, FWS’s recommendation to screen water conveyance facilities out 

of the Merced Falls reservoir pool would provide only minor enhancement to existing 

fish populations. Furthermore, we note that PG&E is not proposing any operational 

changes to the project that could increase canal entrainment. Therefore, canal screening 

would not be a valid mitigation measure for any potential project effect.

The Water Board [preliminary WQC condition 4] specifies that if fish passage 

resumes at Crocker-Huffman diversion dam, PG&E consult with NMFS, CDFW, and 

FWS to determine if passage should resume at Merced Falls dam. In the event that 

passage is recommended after consultation, the preliminary condition specifies that 

PG&E develop a fish passage plan in consultation with the same parties. Similarly, FWS 

[10(j) recommendation 1(4&5)] recommends that PG&E (4) plan for opening of the 

existing fish ladder on Merced Falls dam; conduct an analysis of the measures that would 

need to be taken to bring the existing fish ladders up to NMFS standards; and (5) provide 

annual progress reports. We find that participation in a technical advisory committee, as 

described above, would facilitate the sharing of information regarding the status of 

anadromous fish passage at Crocker-Huffman, and therefore, the potential necessity of 

reevaluating passage scenarios at Merced Falls dam. Should fish passage be successfully 

restored upstream of the Crocker-Huffman diversion dam at some point in the future, the 

Commission’s standard reopener could be used to address any necessary changes to 

project facilities or environmental measures to accommodate anadromous species. We 

estimate screening the northside canal and developing a fish passage plan would have an 

annualized cost of $13,000. Because these measures would not provide any significant 

enhancement to resident or anadromous fish species, we find that the costs of the 

measures are not worth the potential benefits.
453

Minimum Instream Flows

PG&E proposes to continue operating the project run-of-river, where outflow 

equals inflow to the project.

California DFW [10j recommendation 3, parts A-D] recommends that PG&E 

calculate water year types annually and then implement and adaptively manage a flow 

schedule based on that water year type calculation. California DFW recommends that 

PG&E coordinate with Merced ID regarding implementation of its recommended 

instream flows. We note that the recommended flow schedule is identical to the flow 

schedule California DFW recommended for the Merced River Project. The Merced Falls 

Project does not alter the timing or quantity of flow and has limited operational capacity 

to do so. PG&E proposes to continue to operate the project as a run-of-river facility, 

completely dependent on inflow from the upstream Merced River Project facilities. 

Therefore, California DFW’s recommendation of a flow prescription for the Merced Falls 

project is unfounded. However, we note that the intent of California DFW’s 

recommendation was most likely to underscore the need for coordination between 

Merced ID and PG&E in the operation of both projects. We address that 

recommendation in the above sections, Coordinated Operations Plan and Technical 

Advisory Committee.

Water Temperature Monitoring and Mitigation

Water temperature data collected from 1998 to 2008 in the Merced Falls Project 

impoundment ranged between 49oF and 60oF (9.4oC and 15.5oC). Downstream of 

Merced Falls dam, temperatures generally met or exceeded state standards, ranging from 

57oF (13.8oC) to just over 60oF (15.5oC). The lower Merced River is listed under CWA 

section 303(d) as impaired for temperature. Under current conditions, warm water 

temperatures reduce habitat suitability for Chinook salmon and steelhead downstream of 

Crocker-Huffman diversion dam, particularly for spawning.

PG&E proposes to implement a long-term water quality monitoring program for 

periodic (10 year intervals) assessment of water temperature and DO downstream of the 

project dam. PG&E’s proposed long-term monitoring program would help identify any 

potential unforeseen effects on water quality parameters (temperature and DO) important 

to aquatic biota.

Identical to its recommendation for the Merced River Project, California DFW 

[10(j) recommendation 4] recommends that PG&E prepare a long-term water temperature 

management plan in conjunction with Merced ID. The plan would include: 

(1) developing a long-term strategy for meeting seasonal temperature objectives for 

Chinook salmon and O. mykiss; (2) a feasibility study on submerged pipes capable of 

delivering water to a location downstream of Crocker-Huffman diversion dam; 

(3) measures to prolong and stabilize the irrigation delivery season; (4) measures to 

restore the natural channel morphology, floodplain habitats, and riparian forest 

downstream of the Crocker-Huffman diversion dam; (5) provisions to provide coldwater 
454

refugia when water temperatures exceed objectives; and (6) evaluating the effects on 

instream flow releases of implementing alternatives, and the estimated funding and 

schedule needed for the alternatives. California DFW [10(j) recommendation 6(2)] also 

recommends that PG&E continuously monitor water temperatures between inflow into 

the Merced Falls impoundment and outflow into the Merced River downstream of the 

project.

FWS [10j recommendation 2] recommends that PG&E coordinate and cooperate 

with Merced ID for restoration of shaded riverine habitat and riparian floodplain in the 

lower Merced River. FWS recommends that PG&E participate in temperature modeling 

to determine the thermal contribution of the Merced Falls Project to warming in the lower 

Merced River and bear a commensurate share of the costs of downstream restoration 

based on the results of that modeling.

Identical to its recommendation for the Merced River Project, NMFS [10(j) 

recommendation 8] recommends that water temperature and flows be measured at ten 

locations ranging from RM 62.0 to a location between Shaffer Bridge and the confluence 

with the San Joaquin River.

As previously discussed, the Merced River Project is the primary influence on 

water temperatures in the main channel of the Merced River downstream to Shaffer 

Bridge during the off-irrigation season (November through February) and exerts 

significant influence on temperatures during the irrigation season. Water entering the

Merced Falls impoundment from the upstream Merced River project moves quickly 

downstream – typically within a day, and therefore, little warming occurs. Modeling 

studies estimated that the Merced Falls impoundment warmed only 0.54oF in the month 

of July. For these reasons, we can conclude that, when compared to the Merced River 

project, Merced Falls Project has a relatively insignificant incremental thermal influence 

within the project area and downstream in the lower Merced River. We estimate that 

PG&E’s proposed monitoring program would have an annualized cost of $500. We 

estimate that a water temperature and mitigation program consisting of the elements 

recommended by the agencies could cost as much as $45,000 annually. For these 

reasons, we conclude that the potential costs of implementation or funding of any 

potential temperature management, monitoring, or mitigation programs are not 

commensurate with the incremental effects of the project. PG&E’s proposed long-term 

monitoring program would identify any potential unforeseen effects on water quality 

parameters (temperature and DO) important to aquatic biota and provide information 

useful for the adaptive management of the project. As discussed in section 5.1.1.2, we 

recommend Merced ID develop a water temperature monitoring plan, which would 

include sites within the Merced Falls project area. We also recommend that Merced ID 

implement a flow schedule that would improve water temperature conditions downstream 

of the Merced River project for coldwater aquatic species during certain periods and 

produce conditions more suitable for the establishment of riparian shade vegetation in the 

lower Merced River.
455

Gravel Augmentation

The availability and composition of river gravels influences suitability of 

spawning habitat for anadromous and resident fish. Studies suggest that the Merced 

River downstream of the Merced River Project is starved of coarse sediment, and as such, 

the availability of gravel suitable for fish habitat is limited.

The Water Board [preliminary WQC condition 3] specifies that PG&E develop a 

gravel augmentation plan in consultation with California DFW, FWS, and NMES, and 

submit the plan to the Water Board’s Deputy Director within 1 year of license issuance. 

The Water Board also specifies that the amount of gravel augmented should be consistent 

with the amount of gravel annually trapped behind Merced Falls dam. No further details 

were provided about the content of the plan. 

NMFS [10(j) recommendation 2] recommends that Merced ID add 2,500 tons of 

coarse sediment to the Merced Falls reach. Following the initial large-scale gravel 

augmentations, an annual maintenance augmentation would be added to the river reach. 

Details of gravel-augmentation particle-size ranges, locations, and configurations in the 

river reaches would be developed in consultation with a technical advisory committee 

and coordinated with LWD enhancement actions.

The Conservation Groups recommends that PG&E provide a $50,000 annual 

payment to Merced ID for gravel augmentation.

As discussed in section 3.3.1.1, the two Merced River project dams have 

collectively intercepted the majority of sediment that has contributed in part to bed 

coarsening, channel narrowing and simplification, and spawning-habitat loss in 

downstream reaches. The banks of the Merced Falls impoundment are armored, the 

water level does not fluctuate dramatically, and there are no tributaries that enter the 

impoundment. Therefore, coarse sediment supply in the Merced Falls reach is likely very 

limited. Studies conducted by Merced ID estimated that the incremental effect of the 

Merced Falls project on sediment supply in the Merced Falls reach and lower Merced 

River are several orders of magnitude less than that of the upstream Merced River project 

dams. 

We estimate that the development and implementation of a gravel augmentation 

plan could cost as much as $80,000 annually. For these reasons, we conclude that the 

potential costs of implementation or funding of any potential gravel augmentation and/or 

monitoring, or mitigation programs are not commensurate with the minor incremental 

effects of the project. As discussed in section 5.1.1.2, we recommend Merced ID develop 

a gravel augmentation plan, with input from a technical advisory committee. The plan 

would consider the appropriate sources, quantities, composition, and augmentation sites 

of gravels to place in the lower reaches of the Merced River, including the Merced Falls 

reach, to ultimately benefit spawning habitat.
456

Proposed Project Boundary

PG&E proposes to remove 4.8 acres from the project boundary (75.6 to 70.8 

acres) at the northeastern shoreline of the Merced Falls impoundment. In accordance 

with regulations, the project boundary must enclose all principal project works and lands 

necessary for operation and maintenance of the project and other project purposes, such 

as recreation (18 CFR §4.51). PG&E states that these lands are not needed for project 

purposes. However, in section 3.3.4, Recreation Resources, we find that recreation 

features that serve the Merced Falls Project are located on the lands proposed for 

removal. Specifically, portions of the Merced Falls Fishing Access area and the informal 

angler trail are within the lands proposed for removal. Therefore, we do not recommend 

these lands be removed from the project boundary because they are currently serving a 

project purpose. 

5.2 UNAVOIDABLE ADVERSE EFFECTS

The continued operation of the Merced River and Merced Falls Projects would 

result in some minor unavoidable adverse effects on geologic, soil, geomorphic, and 

water quality resources, including some minor continued erosion associated with project 

operation and the renovation of recreational facilities, interruption of sediment transport 

at project reservoirs, and warming of water in the Merced River. Most of these effects 

would be reduced by recommended resource enhancement measures, including: 

(1) preparation and implementation of an erosion and sediment control plan, (2) 

preparation and implementation of LWD management plans; (3) preparation and 

implementation of a sediment management and gravel augmentation plan; and (4) the 

provision of a minimum instream flow, enhanced spring pulse flows, and a fall 

pulse flow.

Under the proposed action, the continued operation of the projects would continue 

to adversely affect some archaeological sites. The execution of PAs and implementation 

of the final HPMPs would ensure proper protection and management of significant 

cultural resources within the both project’s APEs and also would provide satisfactory 

resolution of any project-related adverse effects.

We have identified no other unavoidable adverse effects on resources influenced 

by the projects’ operations.

5.3 SUMMARY OF SECTION 10(j) RECOMMENDATIONS AND 4(e) 

CONDITIONS

5.3.1 Fish and Wildlife Agency Recommendations 

Under the provisions of section 10(j) of the FPA, each hydroelectric license issued 

by the Commission shall include conditions based on recommendations provided federal 

and state fish and wildlife agencies for the protection, mitigation, and enhancement of 

fish and wildlife resources affected by the project. 
457

Section 10(j) of the FPA states that whenever the Commission believes that any 

fish and wildlife agency recommendation is inconsistent with the purposes and the 

requirements of the FPA or other applicable law, the Commission and the agency will 

attempt to resolve any such inconsistency, giving due weight to the recommendations, 

expertise, and statutory responsibilities of such agency. 

5.3.1.1 Merced River Project

In response to our REA notice, the following fish and wildlife agencies submitted 

recommendations for the project: California DFW (letter filed July 21, 2014), FWS

(letter filed July 22, 2014), and NMFS (letter filed July 22, 2014). 

Table 5-4 lists the federal and state recommendations filed subject to section 10(j), 

and whether the recommendations are adopted under the staff alternative. Environmental 

recommendations that we consider outside the scope of section 10(j) have been 

considered under section 10(a) of the FPA and are addressed in the specific resource 

sections of this document and the previous section.

Of the 38 recommendations that we consider to be within the scope of section 

10(j), we wholly include 14, include 11 in part, and do not include 13. We discuss the 

reasons for not including those recommendations in section 5.1, Comprehensive 

Development and Recommended Alternative. Table 5-4 indicates the basis for our 

preliminary determinations concerning measures that we consider inconsistent with 

section 10(j).
458

Table 5-4. Fish and wildlife agency recommendations for the Merced River Hydroelectric Project (Source: staff).

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

1. Establish a Merced ecological 

resource committee to consult on 

implementation of license measures 

and monitoring plans, monitoring 

data and study plans, and facility 

modifications; the committee 

would meet quarterly for the first 5 

years, after which it may meet less 

frequently, but not less than

annually.

California DFW 

(recommendation 1)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$24,000 Yes

2. Establish a technical advisory 

committee to help manage flow 

releases, research, and habitat 

restoration to benefit native fish 

species by providing study plan and 

fishery report oversight and 

approving entities conducting field 

work.

FWS 

(recommendation 5)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$24,000 Yes, would be 

included in the 

committee 

referenced in 

item 1

3. Establish a Merced technical 

advisory committee to guide 

implementation of license terms 

that would protect anadromous and 

resident fish from Merced Falls 

dam to Shaffer Bridge. The 

committee would operate under a 

NMFS 

(recommendation 7)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$24,000 Yes, would be 

included in the 

committee 

referenced in 

item 1
459

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

technical advisory plan that defines 

membership, meeting 

responsibilities, ground rules for 

consensus-based decision making, 

and a process for implementing 

decisions.

4. Annually consult with FWS and 

BLM regarding special-status 

species that may have been added 

to state or federal lists and 

determine if any newly added 

species could be affected by the 

project and if so, determine actions 

needed to protect the species. 

NMFS restricts area to downstream 

of Crocker-Huffman diversion dam 

to Shaffer Bridge and expands 

consultation to include NMFS, 

California DFW, and the Water 

Board.

FWS 

(recommendation 

6[b]); NMFS 

(recommendation 

5[B])

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$8,000 No

5. Implement NMFS’ Ecosystem 

Adaptive Management Process for 

the reach from Crocker-Huffman 

diversion dam to Shaffer Bridge in 

consultation with the technical 

committee.

NMFS 

(recommendation 6)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

Not specific 

enough to 

estimate 

No
460

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

6. Develop a coordinated operations 

plan for the Merced River and 

Merced Falls Projects

California DFW 

(recommendation 2)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$5,880 Yes

7. Annually deliver 15,000 acre-feet 

of water to the Merced NWR in 

accordance with a specified 

monthly schedule at a rate of up to 

55 cfs. 

California DFW 

(recommendation 

12); FWS 

(recommendation 1)

Yes $873,000 Yes, for total 

annual; develop 

plan to address 

year-round 

monthly 

deliveries

8. Install a device for delivering water 

to the Snobird Unit of the Merced 

NWR along Bear Creek, which 

would be used when the areas 

serviced by the lift pumps on 

Deadman Creek are at capacity.

California DFW 

(recommendation 

12); FWS 

(recommendation 1)

No, not a 

specific measure

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

Cost included 

with #7

To be 

determined, 

would be 

addressed in the 

plan referenced 

in item 7
461

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

9. Include facilities for delivering 

water to the Merced NWR in the 

project boundary.

California DFW 

(recommendation 

12); FWS 

(recommendation 1)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$0 To be 

determined, 

depends on the 

plan contents

10. Use the Hughes method to 

determine water year type.

California DFW 

(recommendation 

3A); NMFS 

(recommendation 

1.1A[7])

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$0 Yes

11. Use the Merced ID method to 

determine water year type.

FWS (amended 

recommendation 

3(A1)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$0 No

12. Maintain a minimum flow of 25 cfs 

at all times downstream of 

Exchequer dam.

California DFW 

(recommendation 

3B[a])

Yes Included in 

existing O&M 

Yes
462

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

13. Maintain minimum instantaneous 

flows of from 140 to 2,330 cfs at 

Shaffer Bridge depending on water 

year type and time frame (15-day 

intervals).

California DFW 

(recommendation 

3B[b])

Yes $2,010,000 Partially, we 

recommend some 

but not all of the 

recommended 

minimum flows

14. Maintain target flows of from 100 

to 2,972 cfs at Shaffer Bridge 

depending on water year type and 

time frame (1 to 31 day intervals).

FWS (amended

recommendation 

3A1)

Yes $525,000 Partially, we 

recommend some 

but not all of the 

recommended 

minimum flows

15. Maintain minimum flows of from 

150 to 1,200 cfs at Shaffer Bridge 

depending on water year type and 

time frame (15-day intervals) if 

upstream fish passage at CrockerHuffman diversion dam is not 

provided. If fish passage is 

provided, maintain minimum flows 

from 150 to 1,000 cfs depending on 

water year type and time frame.

NMFS 

(recommendation 

1.1A[1])

Yes $2,393,000 Partially, we 

recommend some 

but not all of the 

recommended 

minimum flows
463

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

16. Measure minimum flows at a new 

gage as mean daily flows based on 

instantaneous flows measured at 

15-minute intervals. Allow 

instantaneous minimum flows to 

deviate below the specified flow by 

up to 10 percent or 3 cfs, whichever 

is less. The gage would be capable 

of measuring up to 6,000 cfs.

NMFS 

(recommendation 

1.1B[1-4])

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$11,400 No, the existing 

gage at Shaffer 

Bridge should be 

sufficient to 

measure 

minimum flows

17. Release a spring floodplain 

inundation flow for not less than 2 

days between March 14 and March 

28 of 2,000 cfs in below normal 

water years, 3,000 cfs in above 

normal water years, and 4,000 in 

wet water years as measured at 

Shaffer Bridge.

California DFW 

(recommendation 

3D)

Yes Included in 

minimum flow 

estimate

No, a short-term, 

high flow event 

could expose 

salmonids to 

stranding when 

the flow recedes
464

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

18. Release a spring floodplain 

inundation flow of 10,000 acre-feet 

in dry and critically dry water 

years, 30,000 acre-feet in below 

normal water years, 50,000 acrefeet in above normal water years, 

and 60,000 acre-feet in wet water 

years.

NMFS 

(recommendation 

1.1A[2])

Yes Included in 

minimum flow 

estimate

Partially, we 

recommend 

10,000 acre-feet 

in dry and 

critically dry 

water years and 

30,000 acre-feet 

in above normal

and wet water 

years instead of 

50,000 and 

60,000 acre-feet

19. Release a fall attraction flow 

between October 16 and November 

15 of 1,000 cfs as measured at 

Shaffer Bridge for 6 days in dry 

and critically dry water years, 9 

days in below normal water years, 

and 12 days in wet and above 

normal water years.

California DFW 

(recommendation 

3E)

Yes Included in 

minimum flow 

estimate

Partially, we 

recommend a fall 

attraction flow of 

1,000 cfs until a 

total of 12,500 

acre-feet is 

reached; this 

would take just 

over 6 days to 

achieve

20. Release a fall pulse flow of 12,500 

acre-feet; timing determined by the 

committee.

NMFS 

(recommendation 

1.1A[2])

Yes Included in 

minimum flow 

estimate

Yes
465

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

21. For all controllable flow rate 

changes above 200 cfs when 

releases are increasing, restrict the 

rate of change to not more than 

double the amount of release 

during any 1 hour period at the start 

of the change.

California DFW 

(recommendation 

3G)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

Included in 

minimum flow 

estimate

Yes

22. Allow incremental up-ramping 

steps to occur evenly over a 24-

hour period, with a maximum of 

500 cfs per 24-hour period.

NMFS 

(recommendation 

1.1b[7])

Yes Included in 

minimum flow 

estimate

No, but we 

recommend 

monitoring stage 

and flow in the 

lower Merced 

River, which 

would enable 

problematic 

ramping rates to 

be documented, 

and if needed, 

corrective action 

taken
466

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

23. When controllable flows are 

decreasing, the rate of change 

should be no more than 2-inches 

per hour as measured at the existing 

gage near Snelling, and should not 

drop by more than 500 cfs in any 

one 24-hour period.

California DFW 

(recommendation 

3G)

Yes Included in 

minimum flow 

estimate

No, but we 

recommend 

monitoring stage 

and flow in the 

lower Merced 

River, which 

would enable 

problematic 

ramping rates to 

be documented, 

and if needed, 

corrective action 

taken

24. Incremental down-ramping steps 

are to occur evenly over a 24-hour 

period, with a maximum of 500 cfs 

per 24-hour period. The exception 

is that at the cessation of spring 

pulse flows in above normal and 

wet water years, the steps would 

occur evenly over a 24-hour period 

at a maximum of 100 cfs per day to 

promote riparian seedling survival.

NMFS 

(recommendation 

1.1B[7])

Yes Included in 

minimum flow 

estimate

No, but we 

recommend 

monitoring stage 

and flow in the 

lower Merced 

River, which 

would enable 

problematic 

ramping rates to 

be documented, 

and if needed, 

corrective action 

taken
467

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

25. Required releases at CrockerHuffman diversion dam for Cowell 

diversions are in addition to all 

flow requirements.

NMFS 

(recommendation 

1.1A[5])

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

Included in 

minimum flow 

estimate

Yes

26. Maintain Lake McClure as high as 

possible from April through 

October to achieve a target 

minimum pool of no less than 

200,000 acre-feet on September 30 

of each year. To achieve this 

target, irrigation diversions should 

stop when the minimum pool is less 

than 265,000 acre-feet except for 

drawdowns needed to maintain 

minimum flows.

California DFW 

(recommendation 

3F)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

Included in 

minimum flow 

estimate

No, we consider 

the loss of water 

for irrigation to 

be too much

27. File a draft operations plan with the 

Commission by March 1 of each 

year describing planned operations 

to maintain the 200,000 acre-feet 

minimum pool. By May 15 of each 

year, file a final operations plan 

with the Commission. 

California DFW 

(recommendation 

3F)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$6,000 No
468

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

28. When a dry or critically dry water 

year is immediately preceded by a 

dry or critically dry water year, 

notify the agencies by June 1 of 

any potential concerns related to 

meeting the required Lake McClure 

minimum pool, and implement 

revised operations upon 

Commission approval.

California DFW 

(recommendation 

3F)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$4,000 Yes, would be 

encompassed by 

Merced ID’s 

proposed 

measure

29. If management of Lake McClure is 

modified in accordance with the 

previous measure, prepare, 

implement, and fund a fisheries 

protection management plan that 

includes provisions for monitoring 

flows, water temperature, and fish 

abundance, and a fish rescue 

component comparable to drought 

emergency plans implement by 

California DFW in the spring and 

summer of 2014.

California DFW 

(recommendation 

3F)

Yes $1,520 Yes, if the need 

for fish rescue is 

tied to project 

operation
469

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

30. By March 10 of the second or 

subsequent dry/critically dry water 

years, notify the agencies, and 

consult with the agencies by May 1 

regarding operational plans to 

manage the drought. After this 

consultation, file a drought 

management plan with the 

Commission.

NMFS 

(recommendation 

1.1A[8])

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$4,000 Yes

31. California DFW reserves the right 

to adaptively manage its instream 

flow recommendations in response 

to future amendments to relevant 

comprehensive plans, such as the 

2006 Bay-Delta Plan issued by the 

Water Board.

California DFW 

(recommendation 

3H)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$0 Not applicable,

the standard fish 

and wildlife 

reopener article 

allows for such 

requests to 

modify an 

existing license 

condition
470

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

32. Maintain a 7DADM of 13oC 

(55.4oF) from January 1 to 

February 14 at Shaffer Bridge (RM 

32.8) during wet and above normal 

water years, RM 38.0 in below 

normal water years, RM 45.0 in dry 

water years, and RM 46.5 

(Snelling) in critically dry water 

years. Maintain a 7DADM of 

16.0oC (60.8oF) from February 15 

through June 15 at Shaffer Bridge 

in wet and above normal water

years; from February 15 through 

May 31 at RM 38.0 in below 

normal water years; and RM 45.0 

in dry water years; and from 

February 15 through May 15 at RM 

46.5 in critically dry water years. 

California DFW 

(recommendation 

3C)

Yes Included in 

minimum flow 

estimate

Yes, to the extent 

controllable by 

the project; 

location of 

temperature 

monitoring 

stations would be 

determined by a 

technical 

advisory 

committee

33. Maintain the 7DADM below 18oC 

from April 1 through October 31 

between Crocker-Huffman 

diversion dam and Snelling Road 

Bridge to the extent possible.

FWS (amended

recommendation 

3A1a)

Yes Included in 

minimum flow 

estimate

Yes, temperature 

monitoring 

locations would 

be determined by 

a technical 

advisory 

committee
471

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

34. Maintain 7DADM below 18oC 

year-round at the Highway 59 

bridge (RM 42.0) if fish passage at 

Crocker-Huffman diversion dam is 

not provided and at the G Street 

bridge (RM 46.4) if fish passage is 

provided.

NMFS 

(recommendation 

1.1A[3a])

Yes Included in 

minimum flow 

estimate

Yes, to the extent

controllable by 

the project; 

temperature 

monitoring 

locations would 

be determined by 

a technical 

advisory 

committee; 

however, it may 

not be possible to 

meet the 

objectives of this 

recommendation

35. Include provisions in a monitoring 

plan for continuously monitoring 

water temperature at RMs 32.5, 

38.0, 42.0 (Highway 59 bridge), 

45.0, 46.5, 52.0 (below CrockerHuffman diversion dam), 56.0 

(below McSwain dam), and 62.0 

(below Exchequer dam).

California DFW 

(recommendations 

3C and 9[7])

Yes $5,000 No, we 

recommend water 

temperature 

monitoring at 

four to eight

locations to be 

determined by a 

technical 

advisory 

committee
472

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

36. Continuously monitor water 

temperature at about 5-mile 

intervals from Exchequer dam and 

Shaffer Bridge.

FWS 

(recommendation 

5[J])

Yes $5,000 No, we 

recommend water 

temperature 

monitoring at 

four to eight

locations to be 

determined by a 

technical 

advisory 

committee

37. Develop a plan to continuously 

monitor water temperature and 

flows at the following RMs: 1.0; 

32.8, 38.0; 42.0; 44.7; 46.4; 52.0; 

55.0; 56.0; and 62.0.

NMFS 

(recommendation 8)

Yes $5,000 No, we 

recommend water 

temperature 

monitoring at 

four to eight

locations to be 

determined by a 

technical 

advisory 

committee

38. Develop a long-term water 

temperature management plan that 

includes: (1) a strategy for meeting 

identified temperature objectives 

and the compliance locations; 

(2) an evaluation of potential 

California DFW 

(recommendation 4)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

$35,000 No
473

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

effectiveness and engineering and 

biological feasibility of the 

following: (a) a sequence of 

submerged pipes from the outlet of

the Exchequer dam to McSwain 

reservoir, the outlet of McSwain 

dam to Merced Falls impoundment, 

and the outlet at Merced Falls dam 

to Crocker-Huffman diversion dam 

with each pipe capable of 

delivering 200 cfs; (b) measures to 

prolong and stabilize the irrigation 

delivery season until at least 

September 30 of each year to 

minimize residence time in project 

reservoirs; (c) measures to restore a 

natural channel morphology, 

floodplain habitats, and a riparian 

forest in the 10-mile reach between 

Merced Falls dam and RM 45.2 to 

reduce water temperatures 

downstream of Crocker-Huffman 

diversion dam; and(d) access to 

native anadromous species to cold water refugia during periods when 

water temperature objectives at RM 

46.5 are exceeded for more than 14 

resources
474

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

consecutive days; (3) an evaluation 

of the effects of implementing 

long-term water temperature 

management alternative(s) on 

instream flow releases required to 

mitigate water temperature effects; (4) funding estimates necessary to 

implement the identified alternative(s); and (5) a schedule 

for achieving the temperature 

objectives at the identified 

locations.

39. Collect microclimate data in areas 

with mature riparian forests and in 

degraded areas between Merced 

Falls dam and Shaffer Bridge to be 

used for calibration of a HEC-5Q 

analysis. This analysis would focus 

on the effects of restored channel 

morphology, floodplain width, and 

riparian tree canopies on water 

temperature.

FWS 

(recommendation 

5[G&H])

No, this 

modeling study 

could have been 

done prior to 

license issuance

Not specific 

enough to 

estimate 

No
475

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

40. Develop a long-term water 

temperature improvement plan that 

includes a feasibility study of 

potential options for decreasing 

water temperature downstream of 

Crocker-Huffman diversion dam 

including: (1) installing an 

underground pipe from New 

Exchequer dam that bypasses 

McSwain reservoir and/or Merced 

Falls reservoir; (2) modifying the 

McClure outlet structure to allow 

water withdrawal from varying 

depths; and (3) developing 

engineering alternatives that do not 

require large volumes of water.

NMFS 

(recommendation 

1.1A[3c])

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$45,000 No

41. Provide fish access to cold water 

refugia upstream of CrockerHuffman diversion dam.

NMFS 

(recommendation 

1.1A[3c])

No, CrockerHuffman 

diversion dam is 

not within the 

Commission’s 

jurisdiction; 

therefore, there 

is no nexus to 

the hydroelectric 

project

$2,766,000 No
476

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

42. Develop a spawning gravel and 

floodplain habitat restoration plan 

that includes (1) initially adding 

50,000 cubic yards of cleaned 

spawning gravel downstream of 

Crocker-Huffman diversion dam 

(the source would be from dredger 

tailings located on either public 

lands or lands owned by Merced 

ID), (2) replenishing spawning-size 

gravel at a mean annual rate of 

2,600 cubic yards between 

Crocker-Huffman diversion dam 

and Shaffer Bridge following the 

initial augmentation; (3) harvesting 

aggregate in a manner that creates 

new floodplain areas and inchannel placement in a manner that 

increases local floodplain 

inundation; and (4) the schedule 

and sequence for habitat restoration 

actions.

California DFW 

(recommendation 6)

Yes $128,000 Yes, with 

modifications; we 

recommend 

development of a 

plan that provides 

for the annual 

placement of 

2,600 cubic yards 

between CrockerHuffman 

diversion dam 

and Shaffer 

Bridge
477

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

43. Restore natural channel 

morphology, floodplain habitat, 

and a riparian forest in the 10-mile 

reach between Merced Falls dam 

and RM 45.2 by using dredger 

tailings and grading the floodplain 

to allow inundation at a 1.5-year 

interval.

FWS (amended

recommendation 

3A2f)

Yes $128,000 

(with gravel 

augmentation)

No, however, we 

recommend 

gravel 

augmentation,

which would help 

restore channel 

morphology, 

enable some 

floodplain 

grading at harvest 

sites, and a spring 

pulse flow 

release, which 

would inundate 

floodplains and 

facilitate riparian 

forest growth

44. Add 20,000 tons of cleaned coarse 

sediment annually into four river 

reaches from Crocker-Huffman 

diversion dam to Shaffer Bridge; 

complete aggregate harvest to 

create new floodplain areas; and 

complete in-channel placement to 

increase local floodplain inundation 

by raising the channel bed.

NMFS 

(recommendation 2)

Yes $128,000 Yes with 

modifications; we 

recommend 

development of a 

plan that provides 

for the annual 

placement of 

2,600 cubic yards 

(about 2,200 

tons) between 
478

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

Crocker-Huffman 

diversion dam 

and Shaffer 

Bridge

45. Add about 2,600 cubic yards of 

spawning-size gravel annually 

between Crocker-Huffman 

diversion dam and Shaffer Bridge.

FWS 

(recommendation 4)

Yes $128,000 Yes

46. Include in a monitoring program 

provisions for monitoring sediment 

size between Crocker-Huffman 

diversion dam and Shaffer Bridge 

to help determine where future 

spawning gravel augmentation is 

needed; also include monitoring of 

spawner use of restoration sites and 

control sites for at least 5 years 

following completion of gravel 

augmentation projects. California 

DFW specifies development of a 

plan but FWS does not.

California DFW 

and FWS 

(recommendations 

9[8] and 5[K])

Yes Cost included 

in 

augmentation 

plan estimate

Yes, we 

recommend 

monitoring 

sediment size be 

addressed in the 

plan we 

recommend

47. Restore floodplain forests and 

associated habitats by plantings of 

root stock, cuttings, or nursery 

stock from trees along the Merced 

River riparian corridor; protect 

FWS (amended 

recommendations 

3A2[a-e and i])

Yes $7,600,000 No, however our 

recommended 

spring pulse flow 

would inundate 

floodplain 
479

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

plantings for beaver depredation for 

5 years; during above normal and, 

when possible in wet years, release 

flows that inundate floodplain 

surfaces for at least 5 days and then 

ramp down to base flows no faster 

than 100 cfs/day (1 inch/day of 

water surface in elevation) during 

late May or early June to promote 

recruitment of tree species; and, if 

the results of the HEC-5Q 

modeling suggest that only a 

portion of the dredger tailing reach 

needs to be restored to achieve the 

temperature objectives, restore 

riparian habitat in accordance with 

a prioritized list.

surfaces for up to 

9 days

48. Include in a monitoring program 

provisions for long-term 

monitoring of riparian vegetation at 

floodplain restoration sites. 

California DFW specifies 

development of a plan but FWS 

does not.

California DFW 

and FWS 

(recommendations 

9[9] and 5[I])

Yes, related to 

temperature 

enhancements 

for salmonids

Not specific 

enough to 

estimate

No
480

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

49. For floodplain restoration projects 

on land that is not federal or stateowned, obtain conservation 

easements and convey such 

easements to a FWS-approved 

entity.

FWS (amended

recommendation 

3A2g)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

Not specific 

enough to 

estimate

No

50. Enhance at least 10 miles of habitat 

between Shaffer Bridge and the 

confluence of the San Joaquin 

River by implementing projects 

approved by the committee and 

based on whether conservation 

easements can be acquired, such as 

addition of LWM, floodplain and 

riparian restoration, removal of 

riprap, and restoration of gravel 

mine pits.

FWS (amended

recommendation 

3A3)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

Not specific 

enough to 

estimate

No

51. Acquire LWD from project 

reservoirs, roads, and aggregate 

harvest sites downstream of 

Crocker-Huffman diversion dam; 

routinely survey Lake McClure by 

boat to corral and stabilize wood 

for future transport, removal, and 

stockpiling for later use at 

NMFS 

(recommendation 3)

Yes $12,400 Yes with 

modifications; we 

recommend 

development of a 

plan that 

addresses the 

environmental 

effects of 
481

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

downstream augmentation projects. 

Consult with the committee 

regarding placement of LWD 

downstream of Crocker-Huffman 

diversion dam to Shaffer Bridge. 

Maintain a GIS database that is 

updated annually of all LWD 

between RM 32.8 and 55.0; report

annually on status of LWD 

management and monitoring.

stockpiling large 

amounts of LWD

52. Develop a salmonid monitoring 

plan that includes provisions for: 

annual snorkel surveys; annual prespawning mortality surveys; annual 

carcass surveys during which 

scales, otoliths (for age analysis 

and to determine contribution of 

naturally produced fry, parr, and 

smolts to the adult population), 

length, sex, wire tags, and 

fecundity data would be collected; 

annual juvenile emergence and 

outmigration monitoring using two 

RSTs; counting weirs for adult 

salmonids; and reporting 

mechanisms.

California DFW, 

FWS, NMFS 

(recommendations 

9[1-6], 5[A-F], and 

NMFS 4.1[D])

Yes $1,520 Yes with 

modifications; we 

recommend 

Merced ID’s 

proposed 

measure, which 

would monitor 

upstream and 

downstream 

migration, but not 

all of the 

additional 

parameters 

recommended
482

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

53. Develop a hatchery master plan 

that establishes short- and longterm goals for the Merced River 

Hatchery; 11 needed upgrades to 

the existing hatchery are listed as 

elements of the plan as well as an 

evaluation of a new hatchery 

location immediately downstream 

of New Exchequer dam. The plan 

would also provide estimated 

needed operation and management 

funding, costs of upgrades, and 

provisions for periodic reviews of 

progress under the master plan. 

Provide for the annual release of 5 

million fall-run Chinook salmon 

smolts with a single year maximum 

of 7.5 million juveniles, and 

250,000 juvenile steelhead with a 

single year maximum of 425,000 

juveniles. 

California DFW 

(recommendation 5)

No, measure 

does not have a 

nexus to the 

hydroelectric 

project 

Not specific 

enough to 

estimate

No

54. Develop a salmonid conservation, 

rescue, and passage plan that 

includes provisions for planning, 

permitting, design, scheduling, 

costs, construction implementation, 

monitoring of fish passage, 

FWS 

(recommendation 2)

Yes $2,766,000 No, we include 

measures for fish 

rescue if linked to 

project operations
483

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

screening, water filtration, and 

refrigeration facilities for protecting salmonids from sub

-

lethal and lethal water temperatures 

resulting from project operation. 

Elements of the plan would include 

opening the fish ladder at Crocker-

Huffman diversion dam, installing 

a fish screen at the entrance of the 

Main Canal, installing a filtration 

device at the hatchery intake to 

protect it from New Zealand mud 

snails, maintaining a refrigeration 

device at the hatchery, cooperating 

with California DFW in trapping 

and hauling wild fish in the lower 

Merced River when conditions could cause thermal stress or 

mortality.
484

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

55. Implement Merced ID’s proposed 

Aquatic Invasive Species 

Management Plan.

California DFW 

(recommendation 

11)

Yes $2,280 Yes, with 

modifications

56. Develop a BMI monitoring plan. FWS 

(recommendation 8)

Yes $50,760 No

57. Develop a fish stocking plan for 

Lake McClure and McSwain 

reservoir that provides for stocking 

55,000 pounds of hatchery 

salmonids.

California DFW 

(recommendation 7)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$35,000 Yes

58. Establish a restoration 

implementation fund and use an 

independent third party financial 

advisor to manage, track, and 

report on the fund’s progress; 

interest from the fund would 

provide funding for implementing 

the terms of a new license.

NMFS 

(recommendation 

7.1[c])

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

Not specific 

enough to 

estimate

No
485

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

59. California DFW reserves the 

authority to modify its 10(j) 

recommendations if needed to 

respond to any final biological 

opinion by NMFS or FWS or WQC 

conditions specified by the Water 

Board.

California DFW 

(recommendation 

13)

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

$0 Not applicable, 

the standard fish 

and wildlife 

reopener article 

allows for such 

requests to 

modify an 

existing license 

condition

60. Prior to construction of new project 

features or non-routine 

maintenance activities that affect 

federally listed and candidate 

species and their habitat, prepare a 

draft biological assessment or other 

required documents and obtain any 

necessary permits or approvals 

from FWS and BLM. Complete 

consultation with FWS for the San 

Joaquin kit fox, California redlegged frog, valley elderberry 

longhorn beetle, conservancy fairy 

shrimp, vernal pool fairy shrimp, 

California tiger salamander, Keck’s 

checkerbloom, Layne’s ragwort, 

and Chinese camp brodiaea,

mariposa pussypaws, California 

FWS 

recommendation 

6(a)A-E

No, not a 

specific measure 

to protect, 

mitigate, or 

enhance fish and 

wildlife 

resources

Not specific 

enough to 

estimate

No; the standard 

fish and wildlife 

reopener article 

requires 

consultation for 

new construction
486

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

vervain and critical habitat for 

vernal pool fairy shrimp, 

conservancy fairy shrimp, 

succulent owl’s-clover, Hoover’s 

spurge, Colusa grass, and San 

Joaquin Valley orcutt grass. 

61. Avoid the unauthorized use of 

burrow fumigants or rodenticides 

on federal land.

FWS 

recommendation 

6(a)F

Yes $0 Yes

62. Avoid use of burrow fumigants or 

rodenticides in habitat of the San 

Joaquin kit fox and the California 

tiger salamander until either section 

7 consultation is completed or a 

section 10 permit is issued.

FWS 

recommendation 

6(a)G

Yes $0 Yes

63. Conduct annual consultation for 

newly added federally listed and 

special-status species that could be 

affected by the project.

FWS 

recommendation 

6(b)

Yes $4,000 No, the standard 

fish and wildlife 

reopener article 

requires 

consultation for 

project effects on 

federally listed 

species 
487

No. Recommendation Agency Within the 

Scope of 

Section 10(j)

Annual Cost Adopted?

64. Develop and implement a 

protection plan for the California 

red-legged frog, within 1 year of 

license issuance. 

FWS 

recommendation 7

Yes $3,000 Yes

65. Implement the Bald Eagle 

Management Plan. 

FWS 

recommendation 9

Yes $3,220 Yes

66. Develop and implement a 

management plan for limestone 

salamander sensitive areas.

California DFW 

recommendation 8

Yes $2,260 Yes

67. Develop an integrated pest 

management pesticide use plan.

California DFW 

recommendation 10

Yes Included with 

invasive weeds 

plan ($55,030)

Yes, modified to 

be a component 

of the noxious 

weed and 

invasive plants 

control plan 
488

5.3.1.2 Merced Falls Project

In response to our REA notice, the following fish and wildlife agencies submitted 

recommendations for the project: California DFW (letter filed July 21, 2014), FWS 

(letter filed July 22, 2014), and NMFS (letter filed July 22, 2014). 

Table 5-5 lists the federal and state recommendations filed subject to section 10(j), 

and whether the recommendations are adopted under the staff alternative. Environmental 

recommendations that we consider outside the scope of section 10(j) have been 

considered under section 10(a) of the FPA and are addressed in the specific resource 

sections of this document and the previous section.

Of the 14 recommendations that we consider to be within the scope of section 

10(j), we wholly include 5, include 3 in part, and do not include 6. We discuss the 

reasons for not including those recommendations in section 5.1, Comprehensive 

Development and Recommended Alternative. Table 5-5 indicates the basis for our 

preliminary determinations concerning measures that we consider inconsistent with 

section 10(j).
489

Table 5-5. Fish and wildlife agency recommendations for the Merced Falls Hydroelectric Project (Source: staff).

No. Recommendation Agency

Within the 

Scope of Section 

10(j)

Annual 

Cost Adopted?

1. Establish a Merced 

ecological resource 

committee to consult on 

implementation of license 

measures and monitoring 

plans, monitoring data and 

study plans, and facility 

modifications; the 

committee would meet 

quarterly for the first 5 

years, after which it may 

meet less frequently, but 

not less than annually.

California DFW 

recommendation 

1

No, not a specific 

measure to 

protect, mitigate, 

or enhance fish 

and wildlife 

resources

$2,200 Yes

2. Establish a Merced 

technical advisory 

committee to guide 

implementation of license 

terms that would protect 

anadromous and resident 

fish from Merced Falls dam 

to Shaffer Bridge. The 

committee would operate 

under a technical advisory 

plan that defines 

membership, meeting 

NMFS 

recommendation 

7

No, not a specific 

measure to 

protect, mitigate, 

or enhance fish 

and wildlife 

resources

$2,200 Yes, would be included in the 

committee referenced in item 1
490

No. Recommendation Agency

Within the 

Scope of Section 

10(j)

Annual 

Cost Adopted?

responsibilities, ground 

rules for consensus-based 

decision making, and a 

process for implementing 

decisions.

3. Develop a coordinated 

operations plan with 

Merced ID within 90 days 

after issuance of license.

California DFW 

recommendation 

2

No, not a specific 

measure to 

protect, mitigate, 

or enhance fish 

and wildlife 

resources

$1,000 Yes

4. Implement instream flow 

schedule. 

California DFW 

recommendation 

3

Yes NA No, Merced Falls proposes to 

operate as a run-of-river facility. 

Flows are dependent upon 

upstream Merced ID project 

facilities

5. Pass through flows 

provided by Merced ID, 

such that inflow equals 

outflow. When diversions 

are occurring out of 

PG&E’s reservoir, outflow 

should equal inflow, minus 

the amount of flow being 

diverted.

NMFS 

recommendation 

1

Yes NA No, recommendation is identical 

to PG&E’s proposed run-of-river 

operation
491

No. Recommendation Agency

Within the 

Scope of Section 

10(j)

Annual 

Cost Adopted?

6. Develop and implement a 

long term water 

temperature management 

plan in consultation with 

Merced ID, resource 

agencies and conservation 

groups.

California DFW 

recommendation 

4

Yes $20,000 No, Merced Falls’ incremental 

effects on water temperature are 

negligible. We recommend 

PG&E perform long-term water 

temperature monitoring 

downstream of Merced Falls 

dam.

7. Continuously monitor water 

temperatures between 

inflow into the Merced 

Falls impoundment and 

outflow into the Merced 

River downstream.

California DFW 

recommendation 

6(2)

Yes $10,000 No

8. Coordinate with Merced ID 

for restoration of shaded 

riverine habitat and riparian 

floodplain in the lower 

Merced River – PG&E 

should provide a 

commensurate share of 

costs of downstream 

restoration, based upon its 

effects on water 

temperature.

FWS 

recommendation 

2

Yes $15,000 No 
492

No. Recommendation Agency

Within the 

Scope of Section 

10(j)

Annual 

Cost Adopted?

9. Stock 11,000 adult-sized 

rainbow trout for the first 2 

years after license issuance; 

develop a reservoir fish 

stocking plan in 

consultation with California 

DFW.

California DFW 

recommendation 

5

No $1,400 Yes

10. Develop an integrated pest 

management and pesticide 

use plan.

California DFW 

recommendation 

7

Yes $15,000 Yes, modified to be a component 

of the Noxious Weeds and 

Invasive Plants Control Plan

11. Develop a salmonid 

conservation, rescue, and 

passage plan in consultation 

with Merced ID, including 

an analysis of measures that 

would be required to 

reoperate existing fish 

passage facilities at Merced 

Falls dam.

FWS 

recommendation 

1 (1&2, 4&5)

Yes $3,000 No, existing downstream 

anadromous fish barrier 

(Crocker-Huffman) renders fish 

passage at Merced Falls 

unnecessary at this time. The 

Commission’s standard reopener 

could be used to address any 

necessary changes to project 

facilities or environmental 

measures to accommodate 

anadromous species should 

passage be restored in the future.

.
493

No. Recommendation Agency

Within the 

Scope of Section 

10(j)

Annual 

Cost Adopted?

12. In coordination with 

Merced ID, screen any 

conveyance facilities out of 

the Merced Falls reservoir 

pool.

FWS 

recommendation 

1(3)

Yes $10,000 No, existing entrainment 

mortality is not significant. 

Proposed operations would not 

change baseline entrainment 

rates. Therefore, the cost of 

measure would not support 

potential minimal biological 

benefits.

13. Conclude ESA consultation 

for the San Joaquin kit fox, 

California red-legged frog, 

and valley elderberry 

longhorn beetle.

FWS 

recommendation 

3

No, not a specific 

measure to 

protect, mitigate, 

or enhance fish 

and wildlife 

resources

$3,000 Not applicable; discussed under 

ESA

14. Implement conservation 

measures for the California 

red-legged frog.

FWS 

recommendation 

4

Yes $3,000 Yes

15. Coordinate with Merced ID 

to implement its Bald Eagle 

Management Plan with 

FWS’ edits, or develop and 

implement a management 

plan specific to the Merced 

Falls Project.

FWS 

recommendation 

5

Yes $2,000 Yes
494

No. Recommendation Agency

Within the 

Scope of Section 

10(j)

Annual 

Cost Adopted?

16. Augment Merced Falls 

reach with 2,500 tons of 

coarse sediment. 

Determine additional 

maintenance augmentations 

in consultation with 

technical advisory 

committee.

NMFS 

recommendation 

2

Yes $80,000 No, we recommend Merced ID 

include the Merced Falls reach in 

its development of a gravel 

augmentation plan

17. In conjunction with Merced 

ID, acquire LWD from 

project reservoirs, roads, 

and aggregate harvest sites 

downstream of CrockerHuffman diversion dam; 

routinely survey Lake 

McClure by boat to corral 

and stabilize wood for 

future transport, removal, 

and stockpiling for later use 

at downstream 

augmentation projects. 

Consult with the committee 

regarding placement of 

LWD downstream of 

Merced Falls dam and 

Crocker-Huffman diversion 

dam to Shaffer Bridge. 

NMFS

recommendation 

3

Yes $13,800 Yes with modifications; we 

recommend PG&E develop a 

project-specific LWD 

management plan for the Merced 

Falls reach, in consultation with 

a technical advisory committee
495

No. Recommendation Agency

Within the 

Scope of Section 

10(j)

Annual 

Cost Adopted?

Maintain a GIS database 

that is updated annually of 

all LWD between RM 32.8 

and 55.0; report annually on 

status of LWD management 

and monitoring.

18. Conduct an annual 

monitoring program for 

O. mykiss in the Merced 

Falls reach. 

California DFW 

recommendation 

6(1)

Yes $10,000 Yes, with modifications; we 

recommend that PG&E consult 

with the technical advisory 

committee to determine sampling 

periodicity, techniques, and data 

to be collected 

19. Develop a salmonid 

monitoring plan, in 

conjunction with Merced 

ID, that includes provisions 

for: annual snorkel surveys; 

annual pre-spawning 

mortality surveys; annual 

carcass surveys during 

which scales, otoliths (for 

age analysis and to 

determine contribution of 

naturally produced fry, parr, 

and smolts to the adult 

population), length, sex, 

wire tags, and fecundity 

NMFS 

recommendation 

4

Yes $14,000 No, we recommend PG&E 

develop a project-specific annual 

monitoring plan for O. mykiss in 

the Merced Falls reach. We also 

recommend Merced ID conduct 

fish monitoring downstream of 

Crocker-Huffman diversion dam.
496

No. Recommendation Agency

Within the 

Scope of Section 

10(j)

Annual 

Cost Adopted?

data would be collected; 

annual juvenile emergence 

and outmigration 

monitoring using two 

RSTs; counting weirs for 

adult salmonids; and 

reporting mechanisms.
497

5.3.2 Land Management Agencies’ Section 4(e) Conditions

In sections 2.2.1.5 and 2.2.2.5, Modifications to Applicant’s Proposal—Mandatory 

Conditions, we list the preliminary 4(e) conditions submitted by BLM, and note that 

section 4(e) of the FPA provides that any license issued by the Commission “for a project 

within a federal reservation shall be subject to and contain such conditions as the 

Secretary of the responsible federal land management agency deems necessary for the 

adequate protection and use of the reservation.” Thus, any 4(e) condition that meets the 

requirements of the law must be included in any license issued by the Commission, 

regardless of whether we include the condition in our staff alternative. 

5.3.2.1 Merced River Project

Of BLM’s 50 preliminary conditions, we consider 25 of the conditions (conditions 

7 and 27 through 50) to be administrative or legal in nature and not specific 

environmental measures. We therefore, do not analyze these conditions in this EIS. 

Table 5-6 summarizes our conclusions with respect to the 25 preliminary 4(e) conditions 

that we consider to be environmental measures. We include in the staff alternative six 

conditions as specified by the agency, modify two condition to adjust the scope of the 

measure, and did not recommend two conditions; the measures not adopted in total are 

discussed in more detail in section 5.1, Comprehensive Development and Recommended 

Alternative.

Table 5-6. Bureau of Land Management preliminary section 4(e) conditions for the 

Merced River Hydroelectric Project (Source: staff).

Condition Annualized Cost Adopted?

No. 1: Annual consultation with BLM $10,500 No

No. 2: Consultation group specific to the 

Merced River Hydroelectric Project

$8,000 Yes

No. 3: Annual employee training $10,580 Yes

No. 4: Coordinated operations plan $5,880 Yes

No. 5: Erosion control and restoration 

plan

$2,000 Yes

No. 6: LWD material management plan $12,460 Yes

No. 8: Aquatic invasive species 

management and monitoring plan

$2,280 Yes

No. 9: Terrestrial protection measures $55,000 Yes

No. 10: Bald eagle management plan $3,220 Yes
498

Condition Annualized Cost Adopted?

No. 11: Annual review of special-status 

species lists and assessment of new 

species on federal land

$4,000 No

No. 12: Bat management $3,600 Yes, modified to 

require a 

protection plan

No. 13: Red-legged frog management 

plan for Piney Creek Core Area

$3,000 Yes

No. 14: Foothill yellow-legged frog 

management plan

$3,000 Yes

No. 15: Limestone salamander sensitive 

management areas plan and studies

$2,260 Yes

No. 16: Western pond turtle incidental 

observations

$2,000 Yes, modified to 

require a 

protection plan

No. 17: Riparian vegetation monitoring 

plan

$15,870 Yes

5.4 CONSISTENCY WITH COMPREHENSIVE PLANS

5.4.1 Applicable to Both Projects

Section 10(a)(2)(A) of the FPA, 16 U.S.C.§803(a)(2)(A), requires the Commission

to consider the extent to which a project is consistent with the federal or state 

comprehensive plans for improving, developing, or conserving a waterway or waterways 

affected by the project. We reviewed 17 comprehensive plans that are applicable to both 

the Merced River and Merced Falls Projects, located in California and no inconsistencies 

were found.

California Department of Fish and Game, U.S. Fish and Wildlife Service, National 

Marine Fisheries Service and Bureau of Reclamation. 1988. Cooperative

agreement to implement actions to benefit winter-run Chinook salmon in the

Sacramento River Basin. Sacramento, California. May 20, 1988. 10 pp.

California Department of Fish and Game. 2003. Strategic Plan for Trout Management: 

A Plan for 2004 and Beyond. Sacramento, California. November 2003.

California Department of Fish and Game. 2007. California wildlife: Conservation 

Challenges, California’s Wildlife Action Plan. Sacramento, California. 2007.
499

California Department of Parks and Recreation. 1980. Recreation outlook in Planning 

District 2. Sacramento, California. April 1980. 88 pp. 8

California Department of Parks and Recreation. 1980. Recreation outlook in Planning

District 3. Sacramento, California. June 1980. 82 pp.

California Department of Parks and Recreation. 1998. Public Opinions and Attitudes on 

Outdoor Recreation in California. Sacramento, California. March 1998.

California Department of Parks and Recreation. 1994. California Outdoor Recreation

Plan (SCORP). Sacramento, California. April 1994.

California Department of Water Resources. 1983. The California Water Plan: Projected 

Use and Available Water Supplies to 2010. Bulletin 160–83. Sacramento, 

California. December 1983. 268 pp.

California Department of Water Resources. 1994. California Water Plan Update. 

Bulletin 160–93. Sacramento, California. October 1994. Two volumes and 

Executive Summary.

California State Water Resources Control Board. 1975. Water Quality Control Plan 

Report. Sacramento, California. Nine volumes.

California State Water Resources Control Board. 1995. Water Quality Control Plan 

Report. Sacramento, California. Nine volumes.

National Marine Fisheries Service, Seattle, Washington. Pacific Fishery Management 

Council, Portland, Oregon. 1978. Fishery management plan for commercial and 

recreational salmon fisheries off the coasts of Washington, Oregon, and California 

commencing in 1978. Department of Commerce. March 1978. 157 pp.

Pacific Fishery Management Council. 1988. Eighth amendment to the fishery 

management plan for commercial and recreational salmon fisheries off the coasts 

of Washington, Oregon, and California commencing in 1978. Portland, Oregon. 

January 1988.

The Resources Agency. 1983. Department of Parks and Recreation. Recreation Needs 

in California. Sacramento, California. March 1983. 39 pp.

State Water Resources Control Board. 1999. Water Quality Control Plans and Policies 

adopted as part of the State comprehensive plan. April 1999.

U.S. Fish and Wildlife Service and Canadian Wildlife Service. 1986. North American 

waterfowl management plan. Department of the Interior. Environment Canada. 

May 1986.

U.S. Fish and Wildlife Service. Undated. Fisheries USA: The Recreational Fisheries 

Policy of the U.S. Fish and Wildlife Service. Washington, D.C.
500

5.4.2 Applicable Only to Merced River Project 

Section 10(a)(2)(A) of the FPA, 16 U.S.C.§803(a)(2)(A), requires the Commission

to consider the extent to which a project is consistent with the federal or state 

comprehensive plans for improving, developing, or conserving a waterway or waterways 

affected by the project. We reviewed 10 comprehensive plans that are applicable to the 

Merced River Project, located in California and. No inconsistencies were found.

California Advisory Committee on Salmon and Steelhead Trout. 1988. Restoring the 

Balance: 1988 Annual Report. Sausalito, California. 84 pp.

California Department of Fish and Game. 1990. Central Valley Salmon and Steelhead 

Restoration and Enhancement Plan. Sacramento, California. April 1990. 115 pp.

California Department of Fish and Game. 1993. Restoring Central Valley streams: A 

plan for action. Sacramento, California. November 1993. 129 pp.

California Department of Fish and Game. 1996. Steelhead Restoration and Management 

Plan for California. February 1996. 234 pp.

California Department of Fish and Game and U.S. Fish and Wildlife Service. 2010. 

Final Hatchery and Stocking Program Environmental Impact 

Report/Environmental Impact Statement. Sacramento, California. January 2010.

California State Water Resources Control Board. 2006. Water Quality Control Plan for 

the San Francisco Bay/Sacramento-San Joaquin Delta Estuary. Sacramento, 

California. December 13, 2006.

California Department of Water Resources. 2000. Final Programmatic Environmental

Impact Statement/Environmental Impact Report for the CALFED Bay-Delta 

Program. Sacramento, California. July 2000. CD Rom, including Associated 

Plans.

National Park Service. 1982. The Nationwide Rivers Inventory. Department of the

Interior, Washington, D.C. January 1982.

U.S. Fish and Wildlife Service. 1990. Central Valley Habitat Joint Venture 

Implementation Plan: A Component of the North American Waterfowl 

Management Plan. February 1990. 

U.S. Fish and Wildlife Service. 2001. Final Restoration Plan for the Anadromous Fish 

Restoration Program. Department of the Interior, Sacramento, California. January 

9, 2001.
501

6.0 LITERATURE CITED

American Whitewater. 2014. Merced, California River Description. Available at 

http://www.americanwhitewater.org/content/River/detail/id/6344/. Accessed July 

17, 2014.

American Whitewater. 2013. Merced, California, Redbud to Briceburg web page. 

Available at http://www.americanwhitewater.org/content/River/detail/id/246. 

Accessed September 18, 2013.

Barbour, M.T., J. Gerritsen, B.D. Snyder, and J.B. Stribling. 1999. Rapid bioassessment 

protocols for use in streams and wadeable rivers: Periphyton, benthic 

macroinvertebrates and fish. Second Edition. EPA 841‐B‐99‐002. U.S. 

Environmental Protection Agency; Office of Water; Washington, D.C.

BLM (U.S. Department of the Interior, Bureau of Land Management). 2008. Sierra 

Resource Management Plan and Record of Decision. U.S. Bureau of Land 

Management, Folsom Field Office. February 2008.

BLM. 1991. Merced Wild and Scenic River Management Plan. Final. U.S. Bureau of 

Land Management, Bakersfield District. March 1991.

Brown, L.R. and J.T. May. 2000. Benthic macroinvertebrate assemblages and their 

relations with environmental variables in the Sacramento and San Joaquin River 

drainages, California, 1993–1997. U.S. Geological Survey Water‐Resources 

Investigations Report 00‐4125, National Water‐Quality Assessment Program.

California DEC (California Data Exchange Center). 2013. California Data Exchange

Center available data for Dry Creek near Snelling (DSN) web page. Available at 

http://cdec.water.ca.gov/cgi-progs/selectQuery. Accessed September 25, 

2013. California Data Exchange Center.

California DFA (California Department of Food and Agriculture). 2014. Hydrilla, 

Egeria, and Elodea Weed Info Fact Sheet. Available at 

http://www.cdfa.ca.gov/plant/ipc/weedinfor/hydrilla.htm. Accessed September 5, 

2014.

California DFW (California Department of Fish and Wildlife). 2014a. Response to 

Notice of Ready for Environmental Analysis. Federal Power Act section 10(j) and 

10(a) recommendations; Merced River Hydroelectric Project (Project no. 2179-

042) Mariposa and Merced Counties. Filed on July 21, 2014.

California DFW. 2014b. Keep Me Wild: San Joaquin Kit Fox. Available at 

https://www.dfg.ca.gov/keepmewild/kitfox.html. Accessed October 29, 2014.

California DFW. 2014c. California Natural Diversity Database. State and Federally 

Listed Threatened and Endangered Animals of California. Available at 

https://www.dfg.ca.gov/biogeodata/cnddb/pdfs/TEAnimals.pdf. Accessed 

October 29, 2014.
502

California DPH (California Department of Public Health). 2008. Maximum contaminant 

levels and regulatory dates for drinking water, US EPA vs California. Available at 

http://www.cdph.ca.gov/certlic/drinkingwater/Documents/DWdocuments/EPAand

CDPH-11-28-2008.pdf. Accessed September 24, 2013. Updated November 28, 

2008. 

California DWR (California Department of Water Resources). 2014. Public Update for 

Drought Response Groundwater Basins with Potential Water Shortages and Gaps 

in Groundwater Monitoring. Available at 

http://www.water.ca.gov/waterconditions/docs/Drought_ResponseGroundwater_Basins_April30_Final_BC.pdf. Accessed September 22, 2014.

California DWR. 2004. Merced River gravel augmentation project, monitoring report. 

California DWR, San Joaquin District, River Management Section. Available at 

http://www.water.ca.gov/pubs/environment/restoration/merced_river_gravel_aug

mentation_project_monitoring_report/2004_merced_hatchery_monitoring.pdf. 

Accessed September 8, 2014.

California DWR. 1994. San Joaquin tributaries spawning gravel assessment: Stanislaus, 

Tuolumne, Merced rivers. California Department of Water Resources, Northern 

District, Red Bluff, CA.

California HSRG (California Hatchery Scientific Review Group). 2012. California 

hatchery review project appendix VIII: Merced River hatchery fall Chinook 

program report. June 2012. Available at http://cahatchery 

review.com/wp.content/uploads/2012/08/Merced%20Chinook%20Program%20Re

port%20June%202012.pdf. Accessed August 14, 2013. 

California OEHHA (California Office of Environmental Health Hazard Assessment). 

2013. Health advisory and guidelines for eating fish from Lake McClure 

(Mariposa County). July 2013 update. Available at 

http://www.oehha.ca.gov/fish/special_reports/pdf/071613McClureReport.pdf. 

Accessed September 25, 2013.

California OEHHA. 2012. Health advisory and guidelines for eating fish from Lake 

McSwain (Mariposa County). December 2012 update. Available at 

http://www.oehha.ca.gov/fish/special_reports/pdf/121812McSwainAdvisoryRpt.p

df. Accessed September 25, 2013.

California WHR (California Wildlife Habitat Relationship System). 2013a. Fringed 

myotis web page. Available at 

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=2325. Accessed July 31, 

2013. California Department of Fish and Game, California Interagency Wildlife 

Task Group.
503

California WHR. 2013b. Pallid bat web page. Available at 

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=2349. Accessed July 31, 

2013. California Department of Fish and Game, California Interagency Wildlife 

Task Group.

California WHR. 2013c. Spotted bat web page. Available at 

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=2345. Accessed July 31, 

2013. California Department of Fish and Game, California Interagency Wildlife 

Task Group.

California WHR. 2013d. Townsend’s big eared bat web page. Available at 

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=2347. Accessed July 31, 

2013. California Department of Fish and Game, California Interagency Wildlife 

Task Group.

California WHR. 2013e. Long-eared myotis web page. Available at 

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=2323. Accessed July 31, 

2013. California Department of Fish and Game, California Interagency Wildlife 

Task Group.

California WHR. 2013f. Western mastiff bat web page. Available at 

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentVersionID=18101. Accessed 

July 31, 2013. California Department of Fish and Game, California Interagency 

Wildlife Task Group.

California WHR. 2013g. Western small-footed myotis web page. Available at 

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=2331. Accessed July 31, 

2013. California Department of Fish and Game, California Interagency Wildlife 

Task Group.

California WHR. 2013h. Western red bat web page. Available at 

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=2339. Accessed July 31, 

2013. California Department of Fish and Game, California Interagency Wildlife 

Task Group.

California WHR. 2013i. Yuma myotis web page. Available at

https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=2319. Accessed July 31, 

2013. California Department of Fish and Game, California Interagency Wildlife 

Task Group.

Central Valley Water Board (Central Valley Regional Water Quality Control Board). 

2011. Water Quality Control Plan (Basin Plan) for the Sacramento River and the 

San Joaquin River Basins. Fourth Edition. Available at 

http://www.waterboards.ca.gov/centralvalley/water_issues/basin_plans/. Revised 

October 2011.
504

Claudi, R. and K. Prescott. 2011. Examination of calcium and pH as predictors of 

Dreissenid mussel survival in the California State Water Project. Prepared for the 

California Department of Water Resources, Division of Operations and 

Maintenance, Aquatic Nuisance Species Program.

CNPS (California Native Plant Society). 2014. Rare Plant Program. Inventory of Rare 

and Endangered Plants (online edition, v8-02). California Native Plant Society, 

Sacramento, CA. Available at http://www.rareplants.cnps.org. Accessed 

November 24, 2014.

CNPS. 2013a. Inventory of rare and endangered plants—tansy-flowered woolly 

sunflower. Available at http://www.rareplants.cnps.org/detail/1339.html. 

Accessed July 30, 2013. California Native Plant Society, Sacramento, CA. 

CNPS. 2013b. Inventory of rare and endangered plants—stinkbells web page. Available 

at http://www.rareplants.cnps.org/detail/820.html. Accessed July 30, 2013. 

California Native Plant Society, Sacramento, CA. 

CNPS. 2013c. Inventory of rare and endangered plants—foothill jepsonia web page. 

Available at http://www.rareplants.cnps.org/detail/1703.html. Accessed July 30, 

2013. California Native Plant Society. Sacramento, CA. 

EPA (U.S. Environmental Protection Agency). 2003. EPA Region 10 guidance for 

Pacific Northwest state and tribal temperature water quality standards. EPA 910-

B-03-002. U.S. Environmental Protection Agency, Region 10 Office of Water,

Seattle, WA.

FERC. 2009. Scoping document 2 for the Merced River Hydroelectric Project, 

California, Project No. 2179-042. Federal Energy Regulatory Commission, 

Washington, DC. April 2009.

Forest Service (U.S. Department of Agriculture, Forest Service). 2009. Vegetation 

descriptions—Central Valley Ecological Province, CALVEG Zone 5. March 12, 

2009. Available at 

http://www.fs.usda.gov/Internet/FSE_DOCUMENTS/fsbdev3_045936.pdf. 

Accessed July 26, 2013.

Forest Service. 2003. Sierra National Forest, California, MAP. U.S. Department of 

Agriculture, Forest Service. 

FWS (U.S. Fish and Wildlife Service). 2014a. Species profile: Layne’s butterweed. 

Available at 

http://ecos.fws.gov/speciesProfile/profile/speciesProfile.action?spcode=Q1O2. 

Accessed November 24, 2014. 

FWS. 2014b. Species profile: Keck’s Checker-mallow. Available at 

http://ecos.fws.gov/speciesProfile/profile/speciesProfile?spcode=Q1OS. Accessed 

November 24, 2014. 
505

FWS. 2014c. Species profile: San Joaquin kit fox. Accessed October 29, 2014.

FWS. 2014d. Recovery Plan for upland species of the San Joaquin Valley. 

http://ecos.fws.gov/docs/recovery_plan/980930a.pdf. Accessed October 29, 2014.

FWS. 2007. National Bald Eagle Management Guidelines. Available at 

http://www.fws.gov/southdakotafieldoffice/NationalBaldEagleManagementGuidel

ines.pdf. Accessed December 31, 2012.

FWS. 2002. Recovery Plan for the California Red-legged Frog (Rana aurora draytonii). 

U.S. Fish and Wildlife Service, Portland, Oregon. viii + 173 pp. Available at 

http://ecos.fws.gov/docs/recovery_plan/020528.pdf. Accessed November 6, 2014.

FWS. 1998. 63 FR 49022 49035: Endangered and threatened wildlife and plants; 

determination of threatened status for four plants from the foothills of the Sierra. 

Available at http://ecos.fws.gov/docs/federal_register/fr3303.pdf. Accessed 

November 24, 2014. 

Geotourism Mapguide. 2013. Sierra Nevada geotourism mapguide web page. Available 

at http://www.sierranevadageotourism.org/content/highway-49-the-golden-chainhighway/sie17643EEAD89F069E6. Accessed September 18, 2013.

Good, T.P., R.S. Waples, and P. Adams (eds.). 2005. Updated status of federally listed 

ESUs of West Coast salmon and steelhead. U.S. Department of Commerce,

NOAA Technical Memorandum NMFS-NWFSC-66. Available at 

http://swfsc.noaa.gov/publications/FED/00749.pdf. Accessed September 24, 

2013. 

Hannon, J. and B. Deason. 2008. American River steelhead spawning 2001–2007. U.S. 

Bureau of Reclamation, Central Valley Project, American River, California MidPacific Region, Sacramento, CA.

Hunter, M.A. 1992. Hydropower flow fluctuations and salmonids: A review of the 

biological effects, mechanical causes, and options for mitigation. Technical 

Report Number 119. State of Washington Department of Fisheries, Habitat 

Management Division, Olympia, WA.

Klasing, S. and R. Brodberg. 2008. Development of fish contaminant goals and advisory 

tissue levels for common contaminants in California sport fish: Chlordane, DDTs, 

dieldrin, methylmercury, PCBs, selenium, and toxaphene. California 

Environmental Protection Agency, Office of Environmental Health Hazard 

Assessment, Pesticide and Environmental Toxicology Branch. Available at

http://www.oehha.org/fish/gtlsv/crnr062708.html. Accessed September 24, 2013. 

Lindley, S.T., R.S. Schick, A. Agrawal, M. Goslin, T.E. Pearson, E. More, J.J. Anderson, 

B. May, S. Greene, C. Hanson, A. Low, D. McEwan, R.B. MacFarlane, C. 

Swanson, and J.G. Williams. 2006. Historical population structure of Central 

Valley steelhead and its alteration by dams. San Francisco Estuary and Watershed 

Science 4:1–19.
506

Markiewicz, D., K. Goding, V. de Vlaming, and J. Rowan. 2003. Benthic 

macroinvertebrate bioassessment of San Joaquin River tributaries: Spring and fall 

2002. California State Water Resources Control Board.

Mesick, C. 2010. The high risk of extinction for the natural fall-run Chinook salmon 

population in the Lower Merced River due to insufficient instream flow releases. 

November 30, 2010. Prepared for the California Sportfishing Protection Alliance.

Merced ID (Merced Irrigation District). 2014a. Amended application for new license, 

major project—existing dam, Merced River Hydroelectric Project. Merced 

Irrigation District, Merced, CA. Filed April 23, 2014.

Merced ID. 2014b. Merced ID’s response to comments, recommendations, preliminary 

terms and conditions, and preliminary fishway prescriptions, Merced River 

Hydroelectric Project. Merced Irrigation District, Merced, CA. Filed September 

5, 2014.

Merced ID. 2014c. Merced ID’s response to comments, recommendations, preliminary 

terms and conditions, and preliminary fishway prescriptions, Merced River 

Hydroelectric Project. Merced Irrigation District, Merced, CA. Filed November 

7, 2014.

Merced ID. 2014d. Merced ID’s response to comments, recommendations, preliminary 

terms and conditions, and preliminary fishway prescriptions, Merced River 

Hydroelectric Project. Merced Irrigation District, Merced, CA. Filed December 

5, 2014.

Merced ID. 2014e. Revised Technical Memorandum 2-5: Reservoir water temperature 

management and feasibility. Merced River Hydroelectric Project, FERC Project 

No. 2179-042. Merced Irrigation District, Merced, CA. March 2014.

Merced ID. 2014f. Proposed Measures and Errata to Application, as Amended. Merced 

River Hydroelectric Project, FERC Project No. 2179-042. Merced Irrigation 

District, Merced, CA. Filed September 22, 2014.

Merced ID. 2014g. Submission of Alternative 4(e) Conditions. Merced River 

Hydroelectric Project, FERC Project No. 2179-042. Merced Irrigation District, 

Merced, CA. Filed August 21, 2014.

Merced ID. 2013a. Technical Memorandum 3-5: Instream flow (PHABSIM) 

downstream of Crocker-Huffman dam. Merced Irrigation District, Merced, CA. 

January 2013. 

Merced ID. 2013b. Merced River Hydroelectric Project, FERC Project No. 2179-043—

California, final license application—additional information. Merced Irrigation 

District, Merced, CA. Filed September 13, 2013. 
507

Merced ID. 2013c. Amended historic properties management plan, Merced River 

Hydroelectric Project. Merced Irrigation District, Merced, CA. Filed December 

31, 2013.

Merced ID. 2012a. Application for new license, major project—existing dam, Merced 

River Hydroelectric Project. Merced Irrigation District, Merced, CA. Filed 

February 26, 2012. 

Merced ID. 2012b. Reply to FERC request deficiency notice, final license, Merced 

River Hydroelectric Project. Merced Irrigation District, Merced, CA. Filed 

September 10, 2012. 

Merced ID. 2012c. Technical Memorandum 2-3: Water quality, Merced River 

Hydroelectric Project, FERC Project No. 2179-042. Including Attachments A-D. 

Merced Irrigation District, Merced, CA. February 2012.

Merced ID. 2012d. Technical Memorandum 7-9: CESA-listed amphibians – limestone 

salamander second year surveys. Merced Irrigation District, Merced, CA. 

October 2012.

Merced ID. 2012e. Reply to additional information request, final license, Merced River 

Hydroelectric Project. Merced Irrigation District, Merced, CA. Filed October 10, 

2012.

Merced ID. 2011a. Reservoir water temperature profiles, Merced River Hydroelectric 

Project, FERC Project No. 2179. Draft Report. Merced Irrigation District, 

Merced, CA. October 2011.

Merced ID. 2011b. Merced stream and reservoir water temperature data. October 3, 

20111. Available at 

http://www.eurekasw.com/MID/Technical%20Memoranda/Forms/AllItems.aspx?

RootFolder=%2fMID%2fTechnical%20Memoranda%2fWater%20Temperature%

20Data&View=%7bEE86A90E%2dFFFC%2d4D66%2d96CC%2d9D93E2A14A

2F%7d. Accessed September 24, 2013. Merced Irrigation District, Merced, CA.

Merced ID. 2011c. Technical Memorandum 1-1: Channel armoring, Merced River 

Hydroelectric Project, FERC Project No. 2179. Merced Irrigation District, 

Merced, CA.

Merced ID. 2011d. Technical Memorandum 3-1: Reservoir fish populations. Merced 

Irrigation District, Merced, CA. March.

Merced ID. 2011e. Technical Memorandum 7.3: Endangered species act listed 

branchiopods—vernal pool fairy shrimp and Conservancy fairy shrimp. Merced 

Irrigation District, Merced, CA. September 2011.

Merced ID. 2011f. Technical Memorandum 8-1: Recreation use and visitor surveys. 

Merced Irrigation District, Merced, CA. August 2011.
508

Merced ID. 2010a. Merced River Project operations model: Documentation and 

validation. MBK Engineers, Sacramento, CA. May 27, 2010.

Merced ID. 2010b. Lake McClure houseboat policies. Merced Irrigation District, Parks 

Department, Merced, CA.

Moyle, P.B. 2002. Inland fishes of California; revised and expanded. University of 

California Press.

NatureServe. 2013. NatureServe Explorer plant/animal records—northern California 

black walnut web page. Available at 

http://www.natureserve.org/explorer/servlet/NatureServe?searchSciOrCommonNa

me=northern+california+black+walnut. Accessed July 31, 2013. NatureServe, 

Arlington, VA.

NERC (North American Electricity Reliability Corporation). 2014. 2014 long-term 

reliability assessment. North American Electricity Reliability Corporation. 

Atlanta, GA. November.

NMFS (National Marine Fisheries Service). 2014. Recovery plan for the evolutionarily 

significant units of Sacramento River winter-run Chinook salmon and Central 

Valley spring-run Chinook salmon and the distinct population segment of 

California Central Valley steelhead. California Central Valley area office. July 

2014. 

PG&E (Pacific Gas and Electric Company). 2014. Merced Falls Hydroelectric Project, 

FERC Project No. 2467, Historic properties management plan. Pacific Gas and 

Electric Company, San Francisco, CA. Filed October 7, 2014.

PG&E. 2012. Merced Falls Hydroelectric Project, FERC Project No. 2467, final license 

application. Pacific Gas and Electric Company, San Francisco, CA. Filed 

February 8, 2012.

PG&E. 2011a. Merced Falls Hydroelectric Project FERC Project No. 2467, licensee’s 

initial study report—Fish and aquatic resources report.

PG&E. 2011b. Merced Falls Hydroelectric Project FERC Project No. 2467, licensee’s 

updated study report—Recreation resources report. Filed September 16, 2011.

Pacific Fisheries Management Council. 1999. Description and identification of essential 

fish habitat, adverse impacts, and recommended conservation measures for 

salmon. Amendment 14 to the Pacific Coast Salmon Plan, Appendix A. Portland, 

Oregon.

PaddlingCalifornia.com. 2013. Lake McSwain web page. Available at 

http://www.paddlingcalifornia.com/Lake_McSwain.html. Accessed September 

11, 2013.
509

Park Service (National Park Service). 2013. Yosemite National Park web page. 

Available at http://www.nps.gov/yose/index.htm. Accessed September 18, 2013.

Parker, P.L. and T.K. King. 1998. National Register bulletin 38, guidelines for 

documenting and evaluating traditional cultural properties. U.S. Department of 

the Interior, National Park Service, National Register, History and Education, 

National Register of Historic Places. Washington, DC.

Payen, L.A. 1966. Prehistoric rock art in the Northern Sierra Nevada, California. M.A. 

thesis. Department of Anthropology, Sacramento State College, Sacramento, CA. 

(as cited by Merced ID 2013c)

Sawyer. J., and T. Keller-Wolf. 1995. Manual of California Vegetation. Available at 

http://davisherb.ucdavis.edu/cnpsActiveServer/index.html. Accessed 

September 16, 2014. 

Sousa, R., C. Antunes, and L. Guilhermino. 2008. Ecology of the invasive Asian clam, 

Corbicula fluminea (Muller, 1774) in aquatic ecosystems: an overview. Annals of 

Limnology—International Journal of Limnology 44(2):85–94.

S.P. Cramer and Associates. 2007. Using rotary screw traps to determine juvenile 

Chinook salmon out‐migration abundance, size and timing in the lower Merced 

River, California 2007. Annual Data Report. Anadromous Fish Restoration 

Program Grant No. 813326G009. Prepared for U.S. Fish and Wildlife Service, 

Stockton, CA. 

Stamp, M., and M. Golden. 2005. Evaluation of the need for fish passage at the Arizona 

Public Service and Fruitland Irrigation diversion structures. Grant Agreement No. 

04-FG-40-2160 PR 948-1. Prepared by BIO-WEST, Inc., Logan, Utah for San 

Juan River Basin Recovery Implementation Program, Salt Lake City, UT.

Stillwater Sciences. 2008. The Merced River Alliance Project, Volume II: Biological 

monitoring and assessment report. Final Report. Prepared for East Merced 

Resource Conservation District Merced, CA, and State Water Resources Control 

Board, Sacramento, CA. Stillwater Sciences, Berkeley, CA.

Stillwater Sciences. 2006. Baseline monitoring of the Merced River dredger tailings 

reach. Technical Memorandum 7, Merced River Corridor Restoration Plan. Phase 

IV: dredger tailings reach. Prepared for CALFED, Sacramento, CA. Stillwater 

Sciences, Berkeley, CA.

Stillwater Sciences. 2004. Technical memorandum 5: Mercury assessment of the 

Merced River Ranch. Prepared for CALFED, Sacramento, CA. Stillwater 

Sciences, Berkeley, CA.
510

Stillwater Sciences. 2002. Merced River corridor restoration plan. Stillwater Sciences, 

Berkeley, CA.

Stillwater Sciences. 2001. Merced River corridor restoration plan baseline studies,

Volume II: Geomorphic and riparian investigations. Prepared for CALFED, 

Sacramento, CA. Stillwater Sciences, Berkeley, CA.

Turlock Irrigation District. 2013. Don Pedro Lake web page. Available at 

http://www.donpedrolake.com/. Accessed September 11, 2013. 

University of California, Merced. 2013. Merced County events web page. Available at 

http://mercedcountyevents.com/great-boating/. Accessed September 18, 2013.

URS (URS Corporation). 2004. Hydraulic model of the Merced River dredger tailings 

reach. Prepared for Stillwater Sciences, Berkeley, CA.

USGS (U.S. Department of the Interior, Geological Survey). 2014. Web Interface, 

USGS surface-water statistics for California web page. Available at 

http://waterdata.usgs.gov/ca/nwis/dvstat/?referred_module=sw. Accessed October 

9, 2014. 

USGS. 2013. Nonindigenous aquatic species web page. Available at 

http://nas.er.usgs.gov. Accessed August 27, 2013. U.S. Geological Survey. 

Vick, J.C. 1995. Habitat rehabilitation in the lower Merced River: A geomorphological 

perspective. Thesis submitted in partial satisfaction of the requirements for a 

Master of Landscape Architecture in the graduate division of the University of 

California, Berkeley, CA.

Vogel, D.A. 2007. A feasibility investigation of reintroduction of anadromous 

salmonids above Crocker-Huffman dam on the Merced River. Natural Resource

Scientists, Inc., Red Bluff, CA. December 2007.

Water Board (State Water Resources Control Board). 2010. 2010 integrated report 

(Clean Water Act section 303(d) list / 305(b) report)—statewide. Available at 

http://www.waterboards.ca.gov/water_issues/programs/tmdl/integrated2010.shtml. 

Accessed California State Water Resources Control Board, Sacramento, CA. 

Water Board. 2006a. 2006 Clean Water Act section 303(d) list of water quality limited 

segments. Approved October 25, 2006. Available at 

http://www.swrcb.ca.gov/water_issues/programs/tmdl/303d_lists2006.shtml. 

Accessed September 24, 2013. 

Water Board. 2006b. Water quality control plan for the San Francisco Bay/ SacramentoSan Joaquin Delta Estuary. Sacramento, CA. Available at 

http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/wq_

control_plans/2006wqcp/docs/2006_plan_final.pdf. Accessed September 5, 2014.
511

Yoshiyama, R.M., E.R. Gerstung, F.W. Fisher, and P.B. Moyle. 2001. Historical and 

present distribution of Chinook salmon in the Central Valley drainage of 

California. In: R.L. Brown (ed.). Contributions to the Biology of Central Valley 

Salmonids. California Department of Fish and Game Bulletin 179, pages 71–176. 

Yoshiyama, R.M., F.W. Fisher, and P.B. Moyle. 1998. Historical abundance and decline 

of Chinook salmon in the Central Valley region of California. North American 

Journal of Fisheries Management 18:487–521.
512

This page intentionally left blank.
513

7.0 LIST OF PREPARERS

7.1 FEDERAL ENERGY REGULATORY COMMISSION

Matt Buhyoff—Project Coordinator, Geology and Soils, Water Quantity and 

Hydrology, Water Quality, and Fisheries Resources (Ecology and Environment; 

B.S., Fisheries Science; M.S. candidate)

Jim Fargo—Need for Power, Engineering, and Developmental Analysis (Civil 

Engineer; M.S., Engineering)

Shana Murray—Recreation, Land Use, Socioeconomics, and Aesthetics (Outdoor 

Recreation Planner; M.S., Recreation, Park, and Tourism Management)

Frank Winchell—Cultural Resources (Archeologist; B.A., M.A., Ph.D., Anthropology)

Jennifer Adams—Terrestrial and Threatened and Endangered Species (Wildlife 

Biologist; M.S., Biological Sciences; B.S., Agriculture)

7.2 LOUIS BERGER GROUP AND STILLWATER SCIENCES

Douglas Hjorth—Task Manager (Senior Aquatic Ecologist; M.A., Biology; B.S., 

Fisheries Biology)

Christine Champe—Deputy Task Manager (Senior Wildlife Biologist; M.S., Wildlife 

and Range Sciences; B.S., Biology and Environmental Studies)

Carol Efird—Recreation, Land Use, Socioeconomics, and Aesthetics (Senior 

Recreational Specialist; B.S., Forestry)

Kenneth Hodge—Need for Power, Engineering, and Developmental Analysis (Senior 

Engineer; B.S., Civil Engineering)

Noah Hume—Water Quality (Aquatic Ecologist, Senior Scientist; Ph.D., Civil and 

Environmental Engineering; M.S., Civil and Environmental Engineering; B.S., 

Mechanical and Ocean Engineering)

Coreen Johnson—Editorial Review (Technical Editor; B.A., English/Education) 

AJ Keith—Fisheries Resources and Threatened and Endangered Species (Aquatic 

Ecologist; M.A., Ecology and Systematic Biology; B.S., Environmental, 

Population, and Organismal Biology)

Alison Macdougall—Cultural Resources (Senior Environmental Manager; B.A., 

Anthropology)

Deborah Mandell—Editing (Senior Technical Editor; M.B.A, Finance and Marketing; 

B.A., Government)
514

Tyler Rychener—Terrestrial and Threatened and Endangered Species (Environmental 

Scientist/GIS; M.S., Plant Biology; B.S., Biology)

Jay Stallman—Geology and Soils (Geologist/Geomorphologist; M.S., Geology)
APPENDIX A

Draft License Articles for the Merced River Hydroelectric Project
This page intentionally left blank.
A-1

DRAFT LICENSE ARTICLES

I. ADMINISTRATIVE ARTICLES

Article 2XX. Administrative Annual Charges. The licensee must pay the United 

States annual charges, effective the first day of the month in which the license is issued, 

and as determined in accordance with provisions of the Commission’s regulations in 

effect from time to time, for the purposes of: 

(a) reimbursing the United States for the cost of administration of Part I of the 

Federal Power Act. The authorized installed capacity for that purpose is 101.25 

megawatts. 

(b) recompensing the United States for the use, occupancy, and enjoyment of 

3,154.9 acres of its lands (other than for transmission line right-of-way).

Article 2XX. Exhibit Drawings. Within 45 days of the date of issuance of this 

license, as directed below, the licensee must file two sets of the approved exhibit 

drawings, form FERC-587, and GIS data in electronic file format on compact disks with 

the Secretary of the Commission, ATTN: OEP/DHAC.

(1) Digital images of the approved exhibit drawings must be prepared in 

electronic format. Prior to preparing each digital image, the FERC Project-Drawing 

Number (i.e., P-2179-1001 through P-2179-###) must be shown in the margin below the 

title block of the approved drawing. Exhibit F drawings must be segregated from other 

project exhibits, and identified as (CEII) material under 18 CFR §388.113(c). Each 

drawing must be a separate electronic file, and the file name must include: FERC 

Project-Drawing Number, FERC Exhibit, Drawing Title, date of this license, and file 

extension in the following format [P-2179-####, G-1, Project Boundary, MM-DDYYYY.TIF]. 

Each Exhibit G drawing that includes the project boundary must contain a 

minimum of three known reference points (i.e., latitude and longitude coordinates, or 

state plane coordinates). The points must be arranged in a triangular format for GIS 

georeferencing the project boundary drawing to the polygon data, and must be based on a 

standard map coordinate system. The spatial reference for the drawing (i.e., map 

projection, map datum, and units of measurement) must be identified on the drawing and 

each reference point must be labeled. In addition, each project boundary drawing must 

be stamped by a registered land surveyor. All digital images of the exhibit drawings must 

meet the following format specification:
A-2

IMAGERY - black & white raster file 

FILE TYPE – Tagged Image File Format (TIFF), CCITT Group 4 

(also known as T.6 coding scheme)

RESOLUTION – 300 dpi desired, (200 dpi min)

DRAWING SIZE FORMAT – 22” x 34” (min), 24” x 36” (max)

FILE SIZE – less than 1 MB desired

A third set (Exhibit G only) and a copy of Form FERC-587 must be filed with the Bureau 

of Land Management office at the following address:

Bureau of Land Management

Branch of Adjudication and Records (CA-943.5)

2800 COTTAGE WAY SUITE W1623

SACRAMENTO CA 95825-1886

ATTN: FERC Withdrawal Recordation

Form FERC-587 is available through the Commission’s website at the following URL: 

http://www.ferc.gov/docs-filing/forms/form-587/form-587.pdf. Although instruction no.

3 requires microfilm copies of the project boundary maps in aperture card format, 

electronic copies that meet the digital specifications in this ordering paragraph should be 

substituted. If the FERC-587 cannot be downloaded from the Internet, a hard copy may 

be obtained by mailing a request to the Secretary of the Commission.

(2) Project boundary GIS data must be in a georeferenced electronic file format 

(such as ArcView shape files, GeoMedia files, MapInfo files, or a similar GIS format). 

The filing must include both polygon data and all reference points shown on the 

individual project boundary drawings. An electronic boundary polygon data file(s) is 

required for each project development. Depending on the electronic file format, the 

polygon and point data can be included in single files with multiple layers. The 

georeferenced electronic boundary data file must be positionally accurate to ±40 feet in 

order to comply with National Map Accuracy Standards for maps at a 1:24,000 scale. 

The file name(s) must include: FERC Project Number, data description, date of this 

license, and file extension in the following format [P-2179 boundary polygon/or point 

data, MM-DD-YYYY.SHP]. The filing must be accompanied by a separate text file 

describing the spatial reference for the georeferenced data: map projection used (i.e., 

UTM, State Plane, Decimal Degrees, etc.), the map datum (i.e., North American 27, 

North American 83, etc.), and the units of measurement (i.e., feet, meters, miles, etc.). 

The text file name must include: FERC Project Number, data description, date of this 

license, and file extension in the following format [P-2179, project boundary metadata, 

MM-DD-YYYY.TXT].

In addition, for those projects that occupy federal lands, a separate georeferenced 

polygon file(s) is required that identifies transmission line acreage and non-transmission 

line acreage affecting federal lands for the purpose of meeting the requirements of 18 
A-3

CFR §11.2. The file(s) must also identify each federal owner (e.g., Bureau of Land 

Management, Forest Service, U.S. Army Corps of Engineers, etc.), land identification 

(e.g., forest name, Section 24 lands, national park name, etc.), and federal acreage 

affected by the project boundary. Depending on the georeferenced electronic file format, 

the polygon, point, and federal lands data can be included in a single file with multiple 

layers.

Article 2XX. Headwater Benefits. If the licensee’s project was directly benefited 

by the construction work of another licensee, a permittee, or the United States on a 

storage reservoir or other headwater improvement during the term of the original license 

(including extensions of that term by annual licenses), and if those headwater benefits 

were not previously assessed and reimbursed to the owner of the headwater 

improvement, the licensee must reimburse the owner of the headwater improvement for 

those benefits, at such time as they are assessed, in the same manner as for benefits 

received during the term of this new license. The benefits will be assessed in accordance 

with Part 11, Subpart B, of the Commission’s regulations.

II. ENGINEERING ARTICLES

Article 3XX. Project Modification Resulting from Environmental 

Requirements. If environmental requirements under this license require modification that 

may affect the project works or operations, the licensee must consult with the 

Commission’s Division of Dam Safety and Inspections—San Francisco Regional 

Engineer. Consultation must allow sufficient review time for the Commission to ensure 

that the proposed work does not adversely affect the project works, dam safety, or project 

operation.

III. MANDATORY CONDITIONS 

On July 22, 2014, the U.S. Department of the Interior, Bureau of Land 

Management (BLM) filed 50 preliminary 4(e) conditions (appendix C). These conditions 

are described in section 2.2.1.5 of the environmental impact statement (EIS). We 

consider 25 (7 and 27 through 50) of the BLM preliminary conditions to be 

administrative or legal in nature and not specific environmental measures. Of the 25

conditions we consider to be environmental measures applicable to the Merced River 

Project, we include 211 of these conditions in the staff alternative as specified by BLM.

 

1 As explained in section 5 of the draft EIS, we recommend modifying the 

following conditions specified by BLM: 8, 13, 14, 16, 22, 25, and 26. We do not 

recommend the following condition: provide annual funding in a contributed funds 

account to offset operation, maintenance, management, and administration costs incurred 

by BLM.
A-4

We recognize, however, that the Commission is required to include valid 4(e) 

conditions in any license issued for the project. As such, each of the measures that staff 

recommend be modified in the staff alternative (as discussed in section 5.1.2,

Comprehensive Development and Recommended Alternative) would not be included in 

any license issued by the Commission. Instead, those conditions would be replaced with 

BLM’s corresponding conditions, as filed with the Commission.

On July 22, 2014, the California State Water Resources Control Board (Water 

Board) filed 49 preliminary water quality certification conditions (appendix D). We 

consider 20 (22, and 30 through 49) of the Water Board preliminary conditions to be 

administrative or legal in nature and not specific environmental measures. Of the 29 

conditions we consider to be environmental measures applicable to the Merced River 

Project, we include 272 of these conditions in the staff alternative as specified by the 

Water Board. We recognize, however, that the Commission is required to include valid 

401 Water Quality Certification (WQC) conditions in any license issued for the project. 

As such, each of the measures that staff recommend be modified in the staff alternative 

(as discussed in section 5.1.2, Comprehensive Development and Recommended 

Alternative) would not be included in any license issued by the Commission. Instead, 

those conditions would be replaced with Water Board’s corresponding conditions, as 

filed with the Commission.

IV. ADDITIONAL LICENSE ARTICLES RECOMMENDED BY 

COMMISSION STAFF

We recommend including the following license articles in any license issued for 

the project in addition to the mandatory conditions.

Article 4xx. Commission Approval, and Filing of Reports and Amendment

Applications.

(a) Requirement to File Plans for Commission Approval

Various conditions of this license found in the Bureau of Land Management’s 

(BLM’s) section 4(e) conditions (appendix C) and the California State Water Resources

 

2 As explained in section 5 of the draft EIS, we recommend modifying the 

following conditions specified by the Water Board: 8, 18, and 19. We do not 

recommend the following conditions: (1) annual consultation to review the project status 

and plans, results of studies, necessary modifications to plans, and protection measures 

for newly listed species; (2) a fish passage or habitat restoration plan that would result in 

fish passage over Crocker-Huffman, McSwain, and New Exchequer dams or decrease 

water temperature in and downstream of the project; and (3) review the lists of federally 

listed and special status species and evaluate potential project effects on newly listed 

species.
A-5

Control Board’s (Water Board) section 401 water quality certification (WQC) conditions 

(appendix D) require the licensee to prepare plans in consultation with other entities; 

some of these measures do not specify that Commission approval is required prior to 

implementation. Each such plan must also be submitted to the Commission for approval. 

These plans are listed below.

WQC 

Condition

Plan Name Due Date

4 Gravel augmentation plan Within 15 months 

of license issuance

5 Bald and golden eagle plan Within 15 months 

of license issuance

6 Vernal pool fairy shrimp plan Within 15 months 

of license issuance

7 Tiger salamander monitoring and conservation 

plan

Within 15 months 

of license issuance

8 Fish passage or habitat restoration plan Within 15 months 

of license issuance

9 Drought plan Within 15 months 

of license issuance

10 California red-legged frog, Foothills yellow-legged 

frog, and western spadefoot monitoring and 

conservation plan

Within 15 months 

of license issuance

11 Valley elderberry longhorn beetle monitoring and 

conservation plan

Within 15 months 

of license issuance

14 Large woody material plan Within 15 months 

of license issuance

16 Lake McClure and McSwain reservoir fish 

stocking

Within 6 months of 

license issuance

17 Aquatic invasive species management plan Within 15 months 

of license issuance

18 Pesticide use plan Within 15 months 

of license issuance

19 Water temperature monitoring plan Within 9 months of 

license issuance
A-6

WQC 

Condition

Plan Name Due Date

20 Anadromous fish monitoring plan Within 15 months 

of license issuance

21 Transportation management plan Within 15 months 

of license issuance

(b) Requirement to File Reports

Some BLM section 4(e) conditions and Water Board WQC conditions 

require Merced ID to file reports with other entities. These reports document compliance 

with requirements of this license and may have a bearing on future actions. Each such 

report must also be submitted to the Commission. These reports are listed in the 

following table.

BLM 

Condition

Description Due Date

12 Bat inspection documentation 15 months after license 

issuance

WQC 

Condition

Description Due Date

13 Annual review of Endangered Species Acts 

lists and special status lists and assessment of 

new species

Within 6 months of license 

issuance, annually 

thereafter

(c) Requirement to File Amendment Applications

Certain BLM 4(e) conditions and Water Board WQC conditions appear to 

contemplate these unspecified long-term changes to project operations or facilities based 

on new information or results of monitoring, but do not appear to require Commission 

approval for such changes (e.g., modification of minimum pool, anadromous fish 

introduction). Such changes may not be implemented without prior Commission 

authorization granted after the filing of an application to amend the license.

Article 4XX. Reservation of Authority to Prescribe Fishways. Authority is 

reserved to the Commission to require the licensee to construct, operate, and maintain, or 

to provide for the construction, operation, and maintenance of such fishways as may be 
A-7

prescribed by the Secretaries of the Interior and/or Commerce pursuant to section 18 of 

the Federal Power Act. 

Article 4XX. Site Specific Erosion Control and Restoration Plan. The licensee 

must develop site-specific erosion control and restoration plans required by Bureau of 

Land Management (BLM) condition no. 5. The plans must include, at a minimum, the 

following: (1) a description of best management practices for erosion control that would 

be applied in specific circumstances; (2) provisions for inspecting erosion control 

measures while they are in place; (3) emergency protocols for erosion and sedimentation 

control (e.g., steps that will be taken if control measures fail during a storm event); (4) 

techniques that will be used to stabilize sites once construction is completed; and (5) a 

description of when and what type of water quality monitoring of surface waters will

occur during and after ground-disturbing activities. Such plans must pertain to all 

project-related ground-disturbing activities within the project boundary and be developed 

in consultation with the California State Water Resources Control Board, California 

Department of Fish and Wildlife, and U.S. Fish and Wildlife Service, in addition to 

BLM, and filed with the Commission for approval at least 90 days in advance of 

initiating construction of recreation or other project facilities that require grounddisturbing activities. The licensee must include with each plan documentation of 

consultation, copies of comments and recommendations on the completed plan after it 

has been prepared and provided to the agencies, and specific descriptions of how the 

agencies’ comments are accommodated by each plan. The licensee must allow a 

minimum of 30 days for the agencies to comment before filing each plan with the 

Commission. If the licensee does not adopt a recommendation, the filing must include 

the licensee’s reasons, based on site-specific information.

The Commission reserves the right to require changes to each plan. Upon 

Commission approval, the licensee must implement each plan, including any changes 

required by the Commission.

Article 4XX. Site Specific Construction and Non-Routine Maintenance

Hazardous Materials Spill Prevention, Control, and Countermeasure Plan. The licensee 

must develop site-specific construction and non-routine maintenance hazardous material 

spill prevention, control, and countermeasure plans and file each plan with the 

Commission at least 90-days in advance of initiating construction or non-routine 

maintenance. The plans must include, at a minimum, the following: (1) a description of 

the best management practices for contaminant control that will be applied in specific 

circumstances; (2) emergency protocols for spill containment and remediation; (3) the 

location of emergency cleanup equipment in the event of contaminant release; 

(4) identification of the entities to be contacted in the event of a spill; (5) designated 

equipment refueling and maintenance areas; (6) provisions requiring equipment to be 

cleaned and inspected prior to entering a construction site to ensure it is in proper 

functioning condition; (7) post-spill water quality monitoring protocols to ensure 
A-8

remediation measures are effective; and (8) a listing of applicable local, state, and federal 

regulations that pertain to prevention of spills and protection of water quality. Such plans 

must pertain to all project-related ground-disturbing activities within the project boundary 

and be developed in consultation with the California State Water Resources Control 

Board, California Department of Fish and Wildlife, U.S. Fish and Wildlife Service, and, 

if construction or non-routine maintenance is proposed on Bureau of Land Management 

(BLM)-managed land, BLM. The licensee must include with each filed plan 

documentation of consultation, copies of comments and recommendations on the 

completed plan after it has been prepared and provided to the agencies, and specific 

descriptions of how the agencies’ comments are accommodated by each plan. The 

licensee must allow a minimum of 30 days for the agencies to comment before filing 

each plan with the Commission. If the licensee does not adopt a recommendation, the 

filing must include the licensee’s reasons, based on site-specific information.

The Commission reserves the right to require changes to each plan. Upon 

Commission approval, the licensee must implement each plan, including any changes 

required by the Commission.

Article 4XX. Ramping Rates. For all controllable flows above 200 cubic feet per 

second, the licensee must restrict the rate of change of releases from McSwain dam 

during any 1-hour period to not more than double the release from the reservoir at the 

start of the 1-hour period for upramping and not less than one-half the amount of 

controlled release from the reservoir at the start of the 1-hour period for downramping.

Article 4XX. Water Year Determination. Within 90 days of license issuance, the 

licensee must implement the process for determining water year type for instream flow 

allocations described in this license article. Water year determinations must be based on

the Hughes method, wherein the water year forecast of unregulated runoff in the Merced 

River below Merced Falls published near the beginning of each month from February 

through May in the California Department of Water Resources’ (California DWR) 

Bulletin 120, Report of Water Conditions in California. The water year types are defined 

as having the following numerical breakpoints (in thousands of acre-feet):

 Wet: ≥1,307 (75th percentile of record)

 Above normal: >919 (median) and <1,307

 Below normal: >546 (25th percentile) and ≤919

 Dry: >339 (5th percentile) and ≤546

 Critically dry: ≤339

California DWR’s forecast published in February, March, and April must apply 

from the 15th day of that month through the 14th day of the next month. From May 15th

through October 14th, the water year type must be based on California DWR’s forecast 

published in May.
A-9

From October 15th through February 14th of the following year, the water year 

type must be based on the sum of California DWR’s monthly unregulated flow for the 

full water year for the Merced River near Merced Falls as made available by California 

DWR on the California Data Exchange Center in the folder named FNF Sum, currently 

available at: http://cdec.water.ca.gov/cgi-progs/stages/FNFSUM. If the California 

Department of Fish and Wildlife (California DFW) does not make the unregulated flow 

for the full water year available until after October 14th, but prior to or on October 31st, 

from 3 days after the date the unregulated flow is made available until February 14th of 

the following year, the water year type must be based on the sum of California DWR’s 

monthly unregulated flow for the full water year as made available. If California DWR 

does not make available the final unregulated flow by October 31st, the water year type 

from November 1st through February 14th of the following year must be based on 

California DWR’s May Bulletin 120.

Article 4XX. Minimum Flow Releases from New Exchequer Dam. The licensee 

must maintain a minimum flow of 25 cubic feet per second at all times downstream of 

New Exchequer dam through the existing fixed orifice pipe used to deliver such flows in 

the past.

Article 4XX. Minimum Flow Releases from Crocker-Huffman Diversion Dam. 

The licensee must release flows from McSwain dam such that the minimum flows in the 

following table are maintained at the U.S. Geological Survey gage 11271290 at Shaffer 

Bridge.
A-10

Required minimum flows in cubic feet per second by water year type 

Wet Above Normal Below Normal Dry Critical Dry

January 1 through 15 175 175 150 150 140

January 16 through 

February 400 350 300 150 140

March 1 through 15 270 270 270 240 200

March 16 through 31 410 410 370 370 310

April 1 through 15 590 590 560 560 510

April 16 through 30 790 790 780 570 570

May 1 through 15 790a 790a 780a 570 a 570 a

May 16 through 31 790 a 790a 780a 570a 570a

June through July 200 b 200 b 200 b 200 b 200b

August 200 200 200 70 60

September 200 200 200 60 60

October 200 c 200 c 200 c 100 c 120

c

November 175d 175d 150d 150d 130

d

December 175 175 150 150 140

a Minimum flow up to the onset of the spring pulse flow required by article 4XX. 

b Minimum flow at the conclusion of the spring pulse flow required by article 4XX. 

c Minimum flow up to the onset of the fall pulse flow required by article 4XX. 

d Minimum flow at the conclusion of the fall pulse flow required by article 4XX.
A-11

Article 4XX. Fall Pulse Flow Releases. The licensee must provide for a fall 

pulse flow release of 1,000 cubic feet per second during October or November until a 

total volume of 12,500 acre-feet is released. This total volume must include the volume 

of water associated with the minimum flow specified in Article 4XX. The exact timing 

of the beginning of the release must be determined by the technical advisory committee

specified in California State Water Resources Control Board condition no. 1 and Bureau 

of Land Management condition no. 2. 

Article 4XX. Spring Pulse Flow Releases. The licensee must provide a spring 

pulse flow release of a total volume of 30,000 acre-feet during wet, above normal, and 

below normal water years, as determined in accordance with Article 4XX, and 10,000 

acre-feet during dry and critically dry water years. This total volume must include the 

volume of water associated with the minimum flow specified in Article 4XX. The 

releases during wet, above normal, and below normal water years must be configured to 

consist of flows above 1,000 cubic feet per second (cfs) for a total of 9 days, and peak 

flows holding for 2 or 3 days, with a gradually ascending and descending hydrograph. 

The time needed to reach the 1,000 cfs threshold at the beginning of the pulse flow and to 

downramp from 1,000 cfs to the required minimum flow must not be included in the 9 

days over 1,000 cfs. The total volume attributed to the pulse flow must take into account 

flows from the onset of upramping to the return to the designated minimum flow and 

must include the volume attributed to minimum flows that would have been in place in 

the absence of the pulse flow. The configuration of all releases (i.e., the targeted flows to 

be released on each day) and the exact timing of the beginning of the release must be 

determined by the technical advisory committee specified in California State Water 

Resources Control Board condition no. 1 and Bureau of Land Management condition 

no. 2

3

. The magnitude of the peak flows is purposely not specified to enable the technical 

advisory committee flexibility in adjusting the configuration of the releases to reflect 

monitoring results from past spring pulse flow releases. Compliance with this measure 

must be based on the verification of the number of days flows exceed 1,000 cfs (i.e., no 

less than 9) and the total volume of the pulse flow release (no less than 30,000 acre-feet).

After a minimum of two dry and critically dry water years, the licensee must

develop a report, in consultation with the technical advisory committee, that assesses 

whether the results of anadromous fish outmigration counts required by Article 4XX 

support a continuation or increase in the 10,000 acre-feet pulse flow to effectively trigger 

outmigration and makes specific recommendations to the Commission regarding future 

implementation of the dry and critically dry water year spring pulse flow release. The 

 

3 The technical advisory committee includes: the Bureau of Land Management, 

the California State Water Resources Control Board, U.S. Fish and Wildlife Service, the 

National Park Service, the National Marine Fisheries Service, the California Department 

of Fish and Wildlife, and the Conservation Groups.
A-12

licensee must include with the report documentation of consultation, copies of comments 

and recommendations on the completed report after it has been prepared and provided to 

the committee, and specific descriptions of how the committee’s comments are 

accommodated by the report. The licensee must allow a minimum of 30 days for the 

members of the committee to comment before filing the plan with the Commission. If 

the licensee does not adopt a recommendation, the filing must include the licensee’s 

reasons, based on site-specific information.

The Commission reserves the right to require changes to any recommendations 

that may be included in the report. The licensee must not implement any changes in the 

operating regime of the project not authorized by this license until authorized to do so by 

the Commission.

Article 4XX. Minimum Pool at Lake McClure. The licensee must maintain a 

minimum pool storage in Lake McClure of not less than 115,000 acre-feet, which 

corresponds to an elevation of 640 feet National Geodetic Vertical Datum of 1929, except 

for drawdowns necessary to maintain minimum streamflows specified in Article 4XX.

Article 4XX. Streamflow and Reservoir Elevation Monitoring and Reporting. 

The licensee must monitor the water surface elevation of Lake McClure on a daily basis 

at U.S. Geological Survey (USGS) gage 11269500 and convert the stage readings to acrefeet in its report to the Commission. The licensee must monitor McSwain powerhouse 

outflow on an hourly basis at USGS gage 11270610. The licensee must monitor hourly 

stage and flow at the gage described as “Merced River below Crocker-Huffman 

Diversion Dam” in table 4.5-1 of Exhibit B of the amended final license application, filed 

on April 23, 2014, and at USGS gage 11269500 at Shaffer Bridge.

The licensee must notify the Commission of the water year type of each year when 

it is initially determined in February and when any subsequent modifications of the water 

type are made pursuant to Article 4XX, Water Year Determination. The licensee must

make monitoring results at the four specified gages available in publicly-available and 

readily accessible formats and provide the data to USGS for inclusion in its annual 

hydrology summary reports. Within 6 months of the end of the water year (September 

30), the licensee must file a data report of the monitoring results with the Commission, 

allowing members of the technical advisory committee specified in California State 

Water Resources Control Board condition no. 1 and Bureau of Land Management 

condition no. 2 at least 30 days to comment on the draft data report. The report must also 

include in the report documentation of the water year type used for flow determinations 

in accordance with Article 4XX and the total volume and release configuration of fall and 

spring pulse flows required by Articles 4XX and 4XX. The licensee must include with 

the report documentation of consultation, copies of comments and recommendations on 

the completed report after it has been prepared and provided to the committee, and 

specific descriptions of how the committee’s comments are accommodated by the report. 
A-13

If the licensee does not adopt a recommendation, the filing must include the licensee’s 

reasons, based on site-specific information. In the first monitoring report filed with the 

Commission under the new license, the licensee must include a description of the 

discharge gage below Crocker-Huffman diversion dam, including the make and model of 

the gage, the effective discharge range of the gage, calibration procedures, and the 

stage/discharge relationship at the gage.

Article 4XX. Water Temperature Monitoring Plan. Within 6 months of license 

issuance, the licensee must develop the water temperature monitoring plan required by 

California State Water Resources Control Board (Water Board) condition no. 19. In 

addition to the plan components specified in condition no. 19, the plan submitted to the 

Commission for approval must include the justification for the placement of each 

monitoring station, including how each relates to project operations, and the coordinates 

and a map showing each station.

The licensee must prepare the plan in consultation with the technical advisory 

committee specified in Water Board condition no. 1 and Bureau of Land Management 

condition no. 2. The licensee must include with the plan documentation of consultation, 

copies of comments and recommendations on the completed plan after it has been 

prepared and provided to the members of the technical advisory committee, and specific 

descriptions of how the technical advisory committee members’ comments are 

accommodated by the plan. The licensee must allow a minimum of 30 days for the 

technical advisory committee members to comment before filing the plan with the 

Commission. If the licensee does not adopt a recommendation, the filing must include 

the licensee’s reasons, based on site-specific information.

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must implement the provisions of the plan, including 

any changes required by the Commission.

Article 4XX. General Drought Management Plan. The licensee must include in 

the drought plan required by California State Water Resources Control Board (Water 

Board) condition no. 9 the following elements: (1) the measures that would be 

considered to address droughts when they occur; (2) decision paths regarding how 

management options for a specific drought would be decided; and (3) a listing of any 

Commission license conditions, Bureau of Land Management 4(e) conditions, and water 

quality certification conditions that would require variances with each of the potential 

drought management measures identified in item (1).

The licensee must prepare the plan in consultation with the technical advisory 

committee specified in Water Board condition no. 1 and Bureau of Land Management 

condition no. 2. The licensee must include with the plan documentation of consultation, 

copies of comments and recommendations on the completed plan after it has been 
A-14

prepared and provided to the members of the technical advisory committee, and specific 

descriptions of how the technical advisory committee members’ comments are 

accommodated by the plan. The licensee must allow a minimum of 30 days for the 

technical advisory committee members to comment before filing the plan with the 

Commission. If the licensee does not adopt a recommendation, the filing must include 

the licensee’s reasons, based on site-specific information.

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must include in any drought-specific project 

operational plans developed under Article 4XX the provisions of the approved general 

plan, including any changes required by the Commission. 

Article 4XX. Drought Notifications and Modified Project Operational Plans. By 

March 10 of the second or subsequent dry and critically dry water year, the licensee must

notify the Bureau of Land Management (BLM), U.S. Fish and Wildlife Service (FWS), 

National Marine Fisheries Service (NMFS), California Department of Fish and Wildlife 

(California DFW), and the California State Water Resources Control Board (Water 

Board) of licensee’s drought concerns. By May 1 of these same years, the licensee must

consult with BLM, FWS, NMFS, California DFW, and the Water Board to discuss the 

licensee’s operational plans to manage the drought conditions. If the consulted parties 

agree on a drought management plan, the licensee must file the plan and documentation 

of the agreement with the Commission. If the consulted parties do not reach agreement 

on the plan, the licensee must file with the Commission for approval, a revised proposed 

operational drought plan that addresses as many of the consulted agencies concerns as 

possible, with any assenting and dissenting comments and the reasons why any dissenting 

comments cannot be accommodated by the plan. 

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must implement the provisions of the plan, including 

any changes required by the Commission.

Article 4XX. Flood Control Coordination. The licensee must operate the project 

as prescribed by the U.S. Army Corps of Engineers and approved by the Commission.

Article 4XX. Merced National Wildlife Refuge Water Delivery Plan. Within 2 

years of license issuance, the licensee must develop a Merced National Wildlife Refuge 

(Merced NWR) water delivery plan to ensure, to the extent reasonably practical, the 

delivery of 15,000 acre-feet to the refuge during times of the year when this would 

provide the most benefit to wildlife. Elements in the plan should include the following:

 Provisions to conduct a feasibility study for providing the recommended 

monthly volumes of water to the Merced NWR on a year-round basis, 

including an assessment of adverse and beneficial effects, estimated costs for 
A-15

any needed infrastructure changes, a schedule for conducting the study, and a 

report with a recommendation regarding proposed actions. 

 An assessment of whether an enhancement of water delivery to the Snobird 

Unit of the Merced NWR is needed to achieve the overall annual or monthly 

water delivery objectives.

 A clear statement regarding where water delivery to the Merced NWR would 

be measured and the means for measuring and reporting monthly deliveries to 

the agencies and the Commission.

 An evaluation of the environmental effects on the refuge if monthly deliveries 

are curtailed during dry or critically dry water years and make-up water is 

obtained via groundwater, and the ramifications if there are future restrictions 

on the use of groundwater in the Central Valley.

The licensee must prepare the plan in consultation with the U.S. Fish and Wildlife 

Service (FWS) and California Department of Fish and Wildlife (California DFW). The 

licensee must include with the plan documentation of consultation, copies of comments 

and recommendations on the completed plan after it has been prepared and provided to 

the agencies, and specific descriptions of how the agencies’ comments are accommodated 

by the plan. The licensee must allow a minimum of 30 days for the agencies to comment 

before filing the plan with the Commission. If the licensee does not adopt a 

recommendation, the filing must include the licensee’s reasons, based on site-specific 

information.

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must implement the provisions of the plan, including 

any changes required by the Commission.

The licensee must prepare the feasibility study report specified in the 

Commission-approved Merced NWR water delivery plan referenced in the first bullet 

above in consultation with FWS and California DFW. The licensee must include with 

the study report documentation of consultation, copies of comments and 

recommendations on the completed report after it has been prepared and provided to the 

agencies, and specific descriptions of how the agencies’ comments are accommodated by 

the study report. The licensee must allow a minimum of 30 days for the agencies to 

comment before filing the study report with the Commission. If the licensee does not 

adopt a recommendation, the filing must include the licensee’s reasons, based on sitespecific information.

The Commission reserves the right to require changes to the recommendations in 

the study report. Upon Commission approval, the licensee must implement the 

recommended actions in the study report, including any changes required by the 

Commission.
A-16

Article 4XX. Interim Delivery of Water to the Merced National Wildlife Refuge. 

Until the Commission approves any modifications to water deliveries that result from the 

plan and study report specified in Article 4XX, the licensee must, beginning the first full 

calendar year after license issuance, provide to the Merced National Wildlife Refuge 

15,000 acre-feet of water annually unless otherwise agreed to in advance by the U.S. Fish 

and Wildlife Service (FWS) and approved by the Commission. The water must be 

delivered to the refuge at a single delivery point in the northeast quarter of the southeast 

quarter of Section 36, Township 8S, Range 12E. On or before March 1 of each year, the 

licensee must notify FWS of the start date of the licensee’s irrigation season. Upon 

receiving such notification, FWS will provide the licensee with a preliminary schedule 

for delivery of 15,000 acre-feet of water, at a flow rate not to exceed 45 cubic feet per 

second, to the refuge during the irrigation season. The licensee must make deliveries in 

accordance with said preliminary schedule unless requested otherwise by FWS. 

The licensee must file a report with the Commission by January 30 of each year 

that documents the actual volume of water delivered to the refuge during the previous 

calendar year, how that volume was estimated, and, if 15,000 acre-feet is not delivered, 

the reasons why. 

Article 4XX. Large Woody Debris and Material Management Plan. The licensee 

must add the U.S. Army Corps of Engineers and California Department of Transportation 

to the consulted entities in the development of the large woody debris and material 

management plan required by Bureau of Land Management condition no. 6 and 

California State Water Resources Control Board condition no. 14. Implementation of this 

plan would benefit aquatic habitat in the lower Merced River.

The licensee must prepare the plan in consultation with the technical advisory 

committee specified in Water Board condition no. 1 and Bureau of Land Management 

condition no. 2 as well as the two agencies specified in the previous paragraph. The 

licensee must include with the plan documentation of consultation, copies of comments 

and recommendations on the completed plan after it has been prepared and provided to 

the consulted entities, and specific descriptions of how the consulted entities’ comments 

are accommodated by the plan. The licensee must allow a minimum of 30 days for the 

consulted entities to comment before filing the plan with the Commission. If the licensee 

does not adopt a recommendation, the filing must include the licensee’s reasons, based on 

site-specific information.

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must implement the provisions of the plan, including 

any changes required by the Commission. No large woody debris or material must be 

placed in the active channel until appropriate federal and state approvals have been 

obtained.
A-17

Article 4XX. Anadromous Fish Monitoring Plan. The licensee must develop, 

within 1 year of license issuance, the anadromous fish monitoring plan required by 

California State Water Resources Control Board (Water Board) condition no. 20. The 

plan must include provisions for monitoring downstream anadromous fish migration 

using a rotary screw trap from January 1 through May 31 at one location downstream of 

Crocker-Huffman diversion dam and monitoring upstream anadromous fish migration 

using one adult counting weir from October 1 through December 31. Data on 

downstream migrating anadromous fish must include, at a minimum, total number, and 

size, weight, and life stage of a representative sample. Data on upstream migrating 

anadromous fish must include, at a minimum, time and direction of migration, size, sex, 

and marks, such as adipose fin clips. In addition to the plan components required by 

Water Board condition no. 20, the plan must include: (1) a description of the proposed 

monitoring locations and the rationale for selecting these locations; (2) provisions for 

making recommendations for corrective actions if monitoring (including water 

temperature monitoring required by Article 4XX) shows the project is adversely affecting 

anadromous fish or their habitat, and reporting any such recommendations and associated 

costs to the Commission for approval; (3) identification of the process that would be used 

for identifying the licensee’s responsibilities during any anadromous fish rescue effort 

that is linked to project operations; and (4) provisions for posting monitoring results on a 

publicly available website on the Monday following the week of data collection.

The licensee must prepare the plan in consultation with the technical advisory 

committee specified in Water Board condition no. 1 and Bureau of Land Management 

condition no. 2. The licensee must include with the plan documentation of consultation, 

copies of comments and recommendations on the completed plan after it has been 

prepared and provided to the members of the technical advisory committee, and specific 

descriptions of how the technical advisory committee members’ comments are 

accommodated by the plan. The licensee must allow a minimum of 30 days for the 

technical advisory committee members to comment before filing the plan with the 

Commission. If the licensee does not adopt a recommendation, the filing must include 

the licensee’s reasons, based on site-specific information.

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must implement the provisions of the plan, including 

any changes required by the Commission.

The licensee must prepare an annual report, in consultation with the technical 

advisory committee, summarizing the monitoring results and making any 

recommendations for protocol modifications or other actions related to the monitoring 

results. If any such recommendation requires changes to the Commission-approved 

anadromous fish monitoring plan, the licensee must file the proposed changes with its 

annual report to the Commission. The licensee must include with the report 

documentation of consultation, copies of comments and recommendations on the 
A-18

completed report after it has been prepared and provided to the members of the technical 

advisory committee, and specific descriptions of how the technical advisory committee 

members’ comments are accommodated by the report. The licensee must allow a 

minimum of 30 days for the technical advisory committee members to comment before 

filing the report with the Commission. If the licensee does not adopt a recommendation, 

the filing must include the licensee’s reasons, based on site-specific information.

The Commission reserves the right to require changes to any recommended 

actions in the report. Upon Commission approval, the licensee must implement any 

recommended actions in the report and, as appropriate, the revised anadromous fish 

monitoring plan, including any changes required by the Commission.

Article 4XX. Gravel Augmentation Plan. Within 1 year of license issuance, the 

licensee must file with the Commission a gravel augmentation plan as required by 

California State Water Resources Control Board (Water Board) condition no. 4. This 

plan would enhance aquatic and riparian habitat in the lower Merced River. The licensee 

must develop the plan in consultation with the technical advisory committee specified in 

Water Board condition no. 1 and Bureau of Land Management condition no. 2. The plan 

must provide for the annual placement of 2,600 cubic yards of gravel in the lower Merced 

River and address, at a minimum, the following: (1) the range of particle sizes to be used 

for augmentation; (2) identification and mapping of potential gravel harvest sites adjacent 

to the lower Merced River on Merced Irrigation District, state, or federally owned land,

and the expected sequence of annual harvesting (i.e., which sites would be harvested first 

and why); (3) provisions for restoring riparian floodplains following gravel harvesting; 

(4) the protocol for selecting locations between Merced Falls dam and Shaffer Bridge for 

annual gravel augmentation based on consultation with the technical advisory committee; 

(5) provisions for monitoring and mapping augmented gravel after placement in the lower 

Merced River channel; and (6) provisions for annual reporting of the location of gravel 

harvesting and placement, and monitoring results. 

The licensee must include with the plan documentation of consultation with the 

technical advisory committee, copies of comments and recommendations on the 

completed plan after it has been prepared and provided to the members of the technical 

advisory committee, and specific descriptions of how the technical advisory committee 

members’ comments are accommodated by the plan. The licensee must allow a 

minimum of 30 days for the technical advisory committee members to comment before 

filing the plan with the Commission. If the licensee does not adopt a recommendation, 

the filing must include the licensee’s reasons, based on site-specific information.

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must implement the provisions of the plan, including 

any changes required by the Commission.
A-19

The licensee must prepare the annual report in consultation with the technical 

advisory committee and include any recommendations for protocol modifications or other 

actions related to the monitoring results. If any such recommendation requires changes to 

the Commission-approved gravel augmentation plan, the licensee must file the proposed 

changes with its annual report to the Commission. The licensee must include with the 

report documentation of consultation, copies of comments and recommendations on the 

completed report after it has been prepared and provided to the members of the technical 

advisory committee, and specific descriptions of how the technical advisory committee 

members’ comments are accommodated by the report. The licensee must allow a 

minimum of 30 days for the technical advisory committee members to comment before 

filing the report with the Commission. If the licensee does not adopt a recommendation, 

the filing must include the licensee’s reasons, based on site-specific information.

The Commission reserves the right to require changes to any recommended 

actions in the report. Upon Commission approval, the licensee must implement any 

recommended actions in the report, and, as appropriate, the revised gravel augmentation 

plan, including any changes required by the Commission.

Article 4XX. Aquatic Invasive Species Management Plan. The licensee must add 

to the Amended Aquatic Invasive Species Management Plan filed with the Commission 

on April 23, 2014, and supplemented on September 5, 2014, and required by Bureau of 

Land Management (BLM) condition no. 8 and California State Water Resources Control 

Board (Water Board) condition no. 17, provisions to monitor and document incidental 

observations of Brazilian elodea (Egeria densa) and, if found, consult with the California 

Department of Fish and Wildlife, the Water Board, U.S. Fish and Wildlife Service, and 

BLM regarding the need to take appropriate management actions. If monitoring results 

rise to the level of needing follow-up management actions, file a report with the 

Commission that documents the need for the actions and the specific management actions 

that are recommended and consulted agency comments on the proposed actions. 

The Commission reserves the right to require changes to any recommended 

actions in the report. Upon Commission approval, the licensee must implement any 

recommended actions in the report and, as appropriate, any revisions to the Aquatic 

Invasive Species Management Plan, including any changes required by the Commission.

Article 4XX. Federally Listed Plants Protection Plan. Within 6 months of 

license issuance, the licensee must file with the Commission for approval, a federally 

listed plants protection plan. The plan must include, at a minimum: (1) provisions to 

conduct surveys for federally listed plants and habitat areas that could support federally 

listed plants; (2) detailed survey methods; (3) protection and mitigation measures; (4) an 

implementation schedule; (5) reporting requirements; and (6) a provision for filing survey 

results and reports. 

The licensee must prepare the plan after consultation with the U.S. Fish and 
A-20

Wildlife Service, the Bureau of Land Management, the National Park Service, the 

California State Water Resources Control Board, and the California Department of Fish 

and Wildlife. The licensee must include with the plan documentation of consultation, 

copies of comments and recommendations on the completed plan after it has been 

prepared and provided to the agencies, and specific descriptions of how the agencies’ 

comments are accommodated by the plan. The licensee must allow a minimum of 30 

days for the agencies to comment and make recommendations before filing the plan with 

the Commission. If the licensee does not adopt a recommendation, the filing must

include the licensee’s reasons, based on project-specific information.

The Commission reserves the right to require changes to the plan. Land disturbing 

activities must not begin until the licensee is notified by the Commission that the plan is 

approved. Upon Commission approval, the licensee must implement the plan, including 

any changes required by the Commission.

Article 4XX. Vernal Pool Fairy Shrimp Protection Plan. Within 6 months of 

license issuance, the licensee must file with the Commission for approval, a vernal pool 

fairy shrimp protection plan. The plan must include, at a minimum: (1) provisions to 

conduct surveys for vernal pool fairy shrimp and habitat areas that could support vernal 

pool fairy shrimp; (2) detailed survey methods; (3) protection and mitigation measures; 

(4) an implementation schedule; (5) reporting requirements; and (6) a provision for filing 

survey results and reports. 

The licensee must prepare the plan after consultation with the U.S. Fish and 

Wildlife Service, the Bureau of Land Management, the National Park Service, the 

California State Water Resources Control Board, and the California Department of Fish 

and Wildlife. The licensee must include with the plan documentation of consultation, 

copies of comments and recommendations on the completed plan after it has been 

prepared and provided to the agencies, and specific descriptions of how the agencies’ 

comments are accommodated by the plan. The licensee must allow a minimum of 30 

days for the agencies to comment and make recommendations before filing the plan with 

the Commission. If the licensee does not adopt a recommendation, the filing must

include the licensee’s reasons, based on project-specific information.

The Commission reserves the right to require changes to the plan. Land disturbing 

activities must not begin until the licensee is notified by the Commission that the plan is 

approved. Upon Commission approval, the licensee must implement the plan, including 

any changes required by the Commission.
A-21

Article 4XX. San Joaquin Kit Fox Protection Plan. Within 6 months of license 

issuance, the licensee must file with the Commission for approval, a San Joaquin kit fox 

protection plan. The plan must include, at a minimum: (1) provisions to conduct surveys 

for San Joaquin kit fox; (2) detailed survey methods; (3) protection and mitigation 

measures; (4) an implementation schedule; (5) reporting requirements; and (6) a 

provision for filing survey results and reports. 

The licensee must prepare the plan after consultation with the U.S. Fish and 

Wildlife Service, the Bureau of Land Management, the National Park Service, the 

California State Water Resources Control Board, and the California Department of Fish 

and Wildlife. The licensee must include with the plan documentation of consultation, 

copies of comments and recommendations on the completed plan after it has been 

prepared and provided to the agencies, and specific descriptions of how the agencies’ 

comments are accommodated by the plan. The licensee must allow a minimum of 30 

days for the agencies to comment and make recommendations before filing the plan with 

the Commission. If the licensee does not adopt a recommendation, the filing must

include the licensee’s reasons, based on project-specific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities must not begin until the licensee is notified by the Commission that 

the plan is approved. Upon Commission approval, the licensee must implement the plan, 

including any changes required by the Commission.

Article 4XX. Western Pond Turtle Protection Plan. Within 6 months of license 

issuance, the licensee must file with the Commission for approval, a western pond turtle 

protection plan. The plan must include the following additional items, at minimum: (1) 

protocols to be followed when western pond turtles are observed; (2) detailed description 

of monitoring plans; and (3) reporting requirements. 

The licensee must prepare the plan after consultation with the U.S. Fish and 

Wildlife Service, the Bureau of Land Management, the California State Water Resources 

Control Board, and the California Department of Fish and Wildlife. The licensee must

include with the plan documentation of consultation, copies of comments and 

recommendations on the completed plan after it has been prepared and provided to the 

agencies, and specific descriptions of how the agencies’ comments are accommodated by 

the plan. The licensee must allow a minimum of 30 days for the agencies to comment 

and make recommendations before filing the plan with the Commission. If the licensee 

does not adopt a recommendation, the filing must include the licensee’s reasons, based on 

project-specific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities must not begin until the licensee is notified by the Commission that 

the plan is approved. Upon Commission approval, the licensee must implement the plan, 

including any changes required by the Commission.
A-22

Article 4XX. Bat Protection Plan. Within 6 months of license issuance, the 

licensee must file with the Commission for approval, a bat protection plan. The plan 

must include the following additional items, at minimum: (1) a list of special-status bats 

that will be protected by the measures contained in the plan; (2) methods of identifying 

bat roosts at project facilities; (3) detailed descriptions of the exclusion devices that will 

be installed at project facilities; (3) protocols that will be implemented if an exclusion 

device fails; (4) an implementation schedule; (5) reporting requirements; and (5) a 

schedule for filing reports.

The licensee must prepare the plan after consultation with the U.S. Fish and 

Wildlife Service, the Bureau of Land Management, the California State Water Resources 

Control Board, and the California Department of Fish and Wildlife. The licensee must

include with the plan documentation of consultation, copies of comments and 

recommendations on the completed plan after it has been prepared and provided to the 

agencies, and specific descriptions of how the agencies’ comments are accommodated by 

the plan. The licensee must allow a minimum of 30 days for the agencies to comment 

and make recommendations before filing the plan with the Commission. If the licensee 

does not adopt a recommendation, the filing must include the licensee’s reasons, based on 

project-specific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities must not begin until the licensee is notified by the Commission that 

the plan is approved. Upon Commission approval, the licensee must implement the plan, 

including any changes required by the Commission.

Article 4XX. Revised Bald Eagle Management Plan. Within 6 months of license 

issuance, the licensee must revise its Bald Eagle Management Plan filed on February 26, 

2012, and amended on September 22, 2014, and file the revised plan with the 

Commission for approval. The revised plan must include the following additional items: 

(1) Information about roost sites on public information boards; (2) descriptions of 

activities that would be considered emergencies with explanations of why these activities 

would supersede bald eagle protection; (3) measures to protect winter roost trees from 

vegetation management and future construction activities; (4) revised protocols and 

methodologies to be consistent with those recommended by the U.S. Fish and Wildlife 

Service (FWS); and (5) a schedule for filing reports. 
A-23

The licensee must prepare the plan after consultation with FWS, the Bureau of 

Land Management, the California State Water Resources Control Board, and the 

California Department of Fish and Wildlife. The licensee must include with the plan 

documentation of consultation, copies of comments and recommendations on the 

completed plan after it has been prepared and provided to the agencies, and specific 

descriptions of how the agencies’ comments are accommodated by the plan. The licensee 

must allow a minimum of 30 days for the agencies to comment and make 

recommendations before filing the plan with the Commission. If the licensee does not 

adopt a recommendation, the filing must include the licensee’s reasons, based on projectspecific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities must not begin until the licensee is notified by the Commission that 

the plan is approved. Upon Commission approval, the licensee must implement the plan, 

including any changes required by the Commission.

Article 4XX. Revised Invasive Species Management Plan. Within 6 months of 

license issuance, the licensee must revise its Invasive Species Management Plan on 

federal land, as filed with the final license application February 26, 2012, and amended 

on September 22, 2014, and file the revised plan with the Commission for approval. The 

revised plan must include the following additional items: (1) stipulations to apply the 

plan to all land within the project boundary, including treatment measures for the existing 

population of perennial pepperweed on Merced Irrigation District’s land; (2) details about 

specific best management practices to be implemented as part of the plan; (3) a 

component on pest management and pesticide use notification that requires prior 

notification to agencies of pesticide use; (4) descriptions of unexpected outbreaks that 

would not require notification prior to use; and (5) a schedule for filing reports. 

The licensee must prepare the plan after consultation with the U.S. Fish and 

Wildlife Service, the Bureau of Land Management, the California State Water Resources 

Control Board, and the California Department of Fish and Wildlife. The licensee must

include with the plan documentation of consultation, copies of comments and 

recommendations on the completed plan after it has been prepared and provided to the 

agencies, and specific descriptions of how the agencies’ comments are accommodated by 

the plan. The licensee must allow a minimum of 30 days for the agencies to comment 

and make recommendations before filing the plan with the Commission. If the licensee 

does not adopt a recommendation, the filing must include the licensee’s reasons, based on 

project-specific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities must not begin until the licensee is notified by the Commission that 

the plan is approved. Upon Commission approval, the licensee must implement the plan, 

including any changes required by the Commission.
A-24

Article 4XX. Revised Vegetation Management Plan. Within 6 months of license 

issuance, the licensee must revise its Vegetation Management Plan on federal land, as 

filed with the final license application on February 26, 2012, and amended on September 

22, 2014, and file the revised plan with the Commission for approval. The revised plan 

must include the following additional items: (1) provide details about specific best 

management practices that would be implemented as part of the plan; (2) include maps in 

section 3.0 to show locations of elderberry plants and identify which plants show signs of 

occupancy by the valley elderberry longhorn beetle; (3) include provisions for

consultation with the Bureau of Land Management (BLM), the California Department of 

Fish and Wildlife (California DFW), the California State Water Resources Control Board

(Water Board), and the U.S. Fish and Wildlife Service (FWS) during the planning phases 

for any new disturbance to identify the need for pre-disturbance surveys; and (4) develop 

protection measures for any sensitive species in the disturbance area.

The licensee must prepare the plan after consultation with FWS, BLM, the Water 

Board, and California DFW. The licensee must include with the plan documentation of 

consultation, copies of comments and recommendations on the completed plan after it 

has been prepared and provided to the agencies, and specific descriptions of how the 

agencies’ comments are accommodated by the plan. The licensee must allow a minimum 

of 30 days for the agencies to comment and make recommendations before filing the plan 

with the Commission. If the licensee does not adopt a recommendation, the filing must

include the licensee’s reasons, based on project-specific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities must not begin until the licensee is notified by the Commission that 

the plan is approved. Upon Commission approval, the licensee must implement the plan, 

including any changes required by the Commission.

Article 4XX. Revised Limestone Salamanders Sensitive Areas Management Plan. 

Within 6 months of license issuance, the licensee must revise its Limestone Salamanders 

Sensitive Areas Management Plan, as filed with the final license application on February 

26, 2012, and amended on September 22, 2014, and file the revised plan with the 

Commission for approval. The revised plan must include the following additional items: 

(1) details about the specific best management practices that would be implemented as 

part of the plan; (2) provisions to site new hiking trails or modifications to existing hiking 

trails outside limestone salamander sensitive habitat; and (3) a schedule for filing reports. 

The licensee must prepare the plan after consultation with the U.S. Fish and 

Wildlife Service, the Bureau of Land Management, the California State Water Resources 

Control Board, and the California Department of Fish and Wildlife. The licensee must

include with the plan documentation of consultation, copies of comments and 

recommendations on the completed plan after it has been prepared and provided to the 

agencies, and specific descriptions of how the agencies’ comments are accommodated by 

the plan. The licensee must allow a minimum of 30 days for the agencies to comment 
A-25

and make recommendations before filing the plan with the Commission. If the licensee 

does not adopt a recommendation, the filing must include the licensee’s reasons, based on 

project-specific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities must not begin until the licensee is notified by the Commission that 

the plan is approved. Upon Commission approval, the licensee must implement the plan, 

including any changes required by the Commission.

Article 4XX. Recreation Facilities Plan. Within 1 year of license issuance, the 

license must file, for Commission approval, a revised Recreation Facilities Plan. The 

plan, filed August 21, 2014, and required by Bureau of Land Management condition no. 

22, must include the following modifications to:

(1) extend the paved bicycle lane along the entire length of Lake McClure Road 

(7.8 miles) between County Road J16 and the proposed parking area from the 

McSwain shoreline trailhead;

(2) identify the location of the project’s three floating restrooms provided on Lake 

McClure, and include an operation and maintenance schedule and 

construction and rehabilitation measures (if needed) for each restroom; and

(3) revise the implementation schedule to: to begin construction no earlier than

Labor Day and no later than Memorial Day to avoid the primary recreation 

season; begin construction at the project’s Bagby recreation area within 2 

years of license issuance; begin construction of the project’s non-motorized 

trails at the project’s Horseshoe Bend recreation area, McSwain reservoir 

shoreline, and the new Mack Island recreation area within 3 years of license 

issuance; begin rehabilitation planning at each project campground within 3 

years of license issuance (to be completed within 6 years of license issuance);

and include a mid-license term rehabilitation assessment in the 

implementation schedule that would identify any project facilities and/or 

water systems in need of rehabilitation.

The Commission reserves the right to require changes to the revised plan. 

Implementation of the revised plan must not begin until the licensee is notified by the 

Commission that the plan is approved. Upon Commission approval, the licensee must 

implement the revised plan, including any changes required by the Commission.

Article 4XX. Recreation Streamflow Information. Within 1 year of license 

issuance, the licensee must provide real-time recreation streamflow information to the 

public via its webpage or on the California Data Exchange Center’s webpage for: (1) 

Merced River below Merced Falls, Dry Creek near the city of Snelling, Merced River 

near the cities of Snelling, Cressy, and Stevinson, and Merced River at Shaffer Bridge 
A-26

(U.S. Geological Survey gage no. 11271290); and (2) elevations for Lake McClure and 

McSwain reservoir.

Article 4XX. Fish Stocking Plan. Within 1 year of license issuance, the licensee

must file, for Commission approval, a fish stocking plan. The plan must include, 

consistent with California State Water Resources Control Board condition no. 16, at 

minimum, the species, size, and number of fish to be stocked in Lake McClure and 

McSwain reservoir for the first 3 years following license issuance and a consultation 

schedule to address fish stocking over the term of the license. 

The Commission reserves the right to require changes to the revised plan. 

Implementation of the revised plan must not begin until the licensee is notified by the 

Commission that the plan is approved. Upon Commission approval, the licensee must 

implement the revised plan, including any changes required by the Commission.

Article 4XX. Visual Resources Plan. The licensee must implement the Visual 

Resources Plan, filed September 22, 2014, and required by Bureau of Land Management 

condition no. 26, for all project lands. 

The Commission reserves the right to require changes to the revised plan. 

Implementation of the revised plan must not begin until the licensee is notified by the 

Commission that the plan is approved. Upon Commission approval, the licensee must 

implement the revised plan, including any changes required by the Commission.

Article 4XX. Programmatic Agreement and Historic Properties Management 

Plan. The licensee must implement the "Programmatic Agreement Between the Federal 

Energy Regulatory Commission and the California State Historic Preservation Officer for 

Managing Historic Properties that may be Affected by a License to Merced Irrigation 

District for the Continued Operation of the Merced River Hydroelectric Project, in 

Merced and Mariposa County, California (FERC No. 2179-043),” executed on ____,

including but not limited to the Historic Properties Management Plan (HPMP) for the 

project. In the event that the Programmatic Agreement is terminated, the licensee must

continue to implement the provisions of its approved HPMP. The Commission reserves 

the authority to require changes to the HPMP at any time during the term of the license.
APPENDIX B

Draft License Articles for the Merced Falls Hydroelectric Project
This page intentionally left blank.
B-1

DRAFT LICENSE ARTICLES

I. ADMINISTRATIVE ARTICLES

Article 2XX. Administrative Annual Charges. The licensee must pay the United 

States annual charges, effective the first day of the month in which the license is issued, 

and as determined in accordance with provisions of the Commission’s regulations in 

effect from time to time, for the purposes of: 

(a) reimbursing the United States for the cost of administration of Part I of the Federal 

Power Act. The authorized installed capacity for that purpose is 3.4 megawatts. 

(b) recompensing the United States for the use, occupancy, and enjoyment of 1.0 acre of 

its lands (other than for transmission line right-of-way).

Article 2XX. Exhibit Drawings. Within 45 days of the date of issuance of this 

license, as directed below, the licensee must file two sets of the approved exhibit 

drawings, form FERC-587, and GIS data in electronic file format on compact disks with 

the Secretary of the Commission, ATTN: OEP/DHAC.

(1) Digital images of the approved exhibit drawings must be prepared in 

electronic format. Prior to preparing each digital image, the FERC Project-Drawing 

Number (i.e., P-2467-1001 through P-2467-###) must be shown in the margin below the 

title block of the approved drawing. Exhibit F drawings must be segregated from other 

project exhibits, and identified as (CEII) material under 18 CFR §388.113(c). Each 

drawing must be a separate electronic file, and the file name must include: FERC 

Project-Drawing Number, FERC Exhibit, Drawing Title, date of this license, and file 

extension in the following format [P-2467-####, G-1, Project Boundary, MM-DDYYYY.TIF]. 

Each Exhibit G drawing that includes the project boundary must contain a 

minimum of three known reference points (i.e., latitude and longitude coordinates, or 

state plane coordinates). The points must be arranged in a triangular format for GIS 

georeferencing the project boundary drawing to the polygon data, and must be based on a 

standard map coordinate system. The spatial reference for the drawing (i.e., map 

projection, map datum, and units of measurement) must be identified on the drawing and 

each reference point must be labeled. In addition, each project boundary drawing must 

be stamped by a registered land surveyor. All digital images of the exhibit drawings must 

meet the following format specification:
B-2

IMAGERY - black & white raster file 

FILE TYPE – Tagged Image File Format (TIFF), CCITT Group 4 

(also known as T.6 coding scheme)

RESOLUTION – 300 dpi desired, (200 dpi min)

DRAWING SIZE FORMAT – 22” x 34” (min), 24” x 36” (max)

FILE SIZE – less than 1 MB desired

A third set (Exhibit G only) and a copy of Form FERC-587 must be filed with the Bureau 

of Land Management office at the following address:

Bureau of Land Management

Branch of Adjudication and Records (CA-943.5)

2800 COTTAGE WAY SUITE W1623

SACRAMENTO CA 95825-1886

ATTN: FERC Withdrawal Recordation

Form FERC-587 is available through the Commission’s website at the following URL: 

http://www.ferc.gov/docs-filing/forms/form-587/form-587.pdf. Although instruction no. 

3 requires microfilm copies of the project boundary maps in aperture card format, 

electronic copies that meet the digital specifications in this ordering paragraph should be 

substituted. 

If the FERC-587 cannot be downloaded from the Internet, a hard copy may be obtained 

by mailing a request to the Secretary of the Commission.

(2) Project boundary GIS data must be in a georeferenced electronic file format 

(such as ArcView shape files, GeoMedia files, MapInfo files, or a similar GIS format). 

The filing must include both polygon data and all reference points shown on the 

individual project boundary drawings. An electronic boundary polygon data file(s) is 

required for each project development. Depending on the electronic file format, the 

polygon and point data can be included in single files with multiple layers. The 

georeferenced electronic boundary data file must be positionally accurate to ±40 feet in 

order to comply with National Map Accuracy Standards for maps at a 1:24,000 scale. 

The file name(s) must include: FERC Project Number, data description, date of this 

license, and file extension in the following format [P-2467 boundary polygon/or point 

data, MM-DD-YYYY.SHP]. The filing must be accompanied by a separate text file 

describing the spatial reference for the georeferenced data: map projection used (i.e., 

UTM, State Plane, Decimal Degrees, etc.), the map datum (i.e., North American 27, 

North American 83, etc.), and the units of measurement (i.e., feet, meters, miles, etc.). 

The text file name must include: FERC Project Number, data description, date of this 

license, and file extension in the following format [P-2467, project boundary metadata, 

MM-DD-YYYY.TXT].
B-3

In addition, for those projects that occupy federal lands, a separate georeferenced 

polygon file(s) is required that identifies transmission line acreage and non-transmission 

line acreage affecting federal lands for the purpose of meeting the requirements of 18 

CFR §11.2. The file(s) must also identify each federal owner (e.g., Bureau of Land 

Management, Forest Service, U.S. Army Corps of Engineers, etc.), land identification 

(e.g., forest name, Section 24 lands, national park name, etc.), and federal acreage 

affected by the project boundary. Depending on the georeferenced electronic file format, 

the polygon, point, and federal lands data can be included in a single file with multiple 

layers.

Article 2XX. Amortization Reserve. Pursuant to section 10(d) of the Federal 

Power Act, a specified reasonable rate of return upon the net investment in the project 

must be used for determining surplus earnings of the project for the establishment and

maintenance of amortization reserves. The licensee must set aside in a project 

amortization reserve account at the end of each fiscal year one half of the project surplus 

earnings, if any, in excess of the specified rate of return per annum on the net investment. 

To the extent that there is a deficiency of project earnings below the specified rate of 

return per annum for any fiscal year, the licensee must deduct the amount of that 

deficiency from the amount of any surplus earnings subsequently accumulated, until 

absorbed. The licensee must set aside one-half of the remaining surplus earnings, if any, 

cumulatively computed, in the project amortization reserve account. The licensee must 

maintain the amounts established in the project amortization reserve account until further 

order of the Commission.

The specified reasonable rate of return used in computing amortization reserves 

must be calculated annually based on current capital ratios developed from an average of 

13 monthly balances of amounts properly included in the licensee’s long-term debt and 

proprietary capital accounts as listed in the Commission’s Uniform System of Accounts. 

The cost rate for such ratios must be the weighted average cost of long-term debt and 

preferred stock for the year, and the cost of common equity must be the interest rate on 

10-year government bonds (reported as the Treasury Department’s 10-year constant 

maturity series) computed on the monthly average for the year in question plus four 

percentage points (400 basis points).

Article 2XX. Headwater Benefits. If the licensee’s project was directly benefited 

by the construction work of another licensee, a permittee, or the United States on a 

storage reservoir or other headwater improvement during the term of the original license 

(including extensions of that term by annual licenses), and if those headwater benefits 

were not previously assessed and reimbursed to the owner of the headwater 

improvement, the licensee must reimburse the owner of the headwater improvement for 

those benefits, at such time as they are assessed, in the same manner as for benefits 

received during the term of this new license. The benefits will be assessed in accordance 

with Part 11, Subpart B, of the Commission’s regulations.
B-4

II. ENGINEERING ARTICLES

Article 3XX. Project Modification Resulting from Environmental 

Requirements. If environmental requirements under this license require modification that 

may affect the project works or operations, the licensee must consult with the 

Commission’s Division of Dam Safety and Inspections—San Francisco Regional 

Engineer. Consultation must allow sufficient review time for the Commission to ensure 

that the proposed work does not adversely affect the project works, dam safety, or project 

operation.

III. MANDATORY CONDITIONS 

On July 22, 2014, the California State Water Resources Control Board (Water 

Board) filed 36 preliminary water quality certification conditions (appendix E). These 

conditions are described in section 2.2.2.5 of the environmental impact statement (EIS). 

We consider 27 (1, and 10 through 36) of the Water Board preliminary conditions to be 

administrative or legal in nature and not specific environmental measures. Of the 8 

conditions we consider to be environmental measures applicable to the Merced River 

Project, we include 5

1 of these conditions in the staff alternative as specified by the Water 

Board.

We recognize, however, that the Commission is required to include water quality 

certification conditions in any license issued for the project. As such, each of the 

measures that staff recommend be modified in the staff alternative (as discussed in 

section 5.1.2, Comprehensive Development and Recommended Alternative) would not be 

included in any license issued by the Commission. Instead, those conditions would be 

replaced with the Water Board’s corresponding conditions, as filed with the Commission.

IV. ADDITIONAL LICENSE ARTICLES RECOMMENDED BY 

COMMISSION STAFF

We recommend including the following license articles in any license issued for 

the project in addition to the mandatory conditions.

 

1 As explained in section 5 of the draft EIS, we recommend modifying the 

following condition specified by the Water Board: condition no. 8. We do not 

recommend the following conditions: (1) gravel augmentation in the Merced Falls reach; 

(2) a fish passage plan; and (3) annual consultation to review the project status and plans, 

results of studies, necessary modifications to plans, and protection measures for newly 

listed species.
B-5

Article 4xx. Requirement to File Amendment Applications

Certain California State Water Resources Control Board preliminary water quality 

certification conditions appear to contemplate requiring unspecified long-term changes to 

project operations or facilities based on new information or results of monitoring but do 

not appear to require Commission approval for such changes (e.g., water quality 

monitoring, climate change). Such changes may not be implemented without prior 

Commission authorization granted after the filing of an application to amend the license.

Article 4XX. Reservation of Authority to Prescribe Fishways. Authority is 

reserved to the Commission to require the licensee to construct, operate, and maintain, or 

to provide for the construction, operation, and maintenance of such fishways as may be 

prescribed by the Secretaries of the Interior and/or Commerce pursuant to section 18 of 

the Federal Power Act.

Article 4XX. Coordinated Operations Plan. Within 120 days of license issuance, 

the licensee must file the plan in conjunction with Merced Irrigation District and in 

consultation with the California State Water Resources Control Board, the Bureau of 

Land Management, the U.S. Fish and Wildlife Service, the California Department of Fish 

and Wildlife, the National Marine Fisheries Service, and the National Park Service. The 

licensee must include with the plan filed with the Commission documentation of 

consultation, copies of comments and recommendations on the completed plan after it 

has been prepared and provided to the consulted entities, and specific descriptions of how 

the consulted entities’ comments are accommodated by the plan. The licensee must 

allow a minimum of 30 days for the consulted entities to comment before filing the plan 

with the Commission. If the licensee does not adopt a recommendation, the filing must 

include the licensee’s reasons, based on site-specific information.

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must implement the plan, including any changes 

required by the Commission.

Article 4XX. Water Quality Monitoring Plan. Within 120 days of license 

issuance, the licensee must file, in consultation with the technical advisory committee

specified in Merced Irrigation District’s Merced River Project California State Water 

Resources Control Board condition no. 1, a long-term water quality monitoring program 

for periodic (10-year intervals) assessment of water temperature and dissolved oxygen in 

the reach of the Merced River downstream of the project dam and upstream of CrockerHuffman diversion dam. The licensee must include with the plan filed with the 

Commission documentation of consultation, copies of comments and recommendations 

on the completed plan after it has been prepared and provided to the consulted entities, 

and specific descriptions of how the consulted entities’ comments are accommodated by 

the plan. The licensee must allow a minimum of 30 days for the consulted entities to 

comment before filing the plan with the Commission. If the licensee does not adopt a 
B-6

recommendation, the filing must include the licensee’s reasons, based on site-specific 

information.

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must implement the plan, including any changes 

required by the Commission.

Article 4XX. Fish Monitoring Plan. Within 90 days of license issuance, the 

licensee must prepare a plan to monitor Oncorhynchus mykiss abundance and distribution

in the reach of the Merced River downstream of the project dam and upstream of 

Crocker-Huffman diversion dam. The licensee should prepare the plan, including the 

necessity of monitoring additional species or metrics, in consultation with the technical 

advisory committee specified in Merced Irrigation District’s Merced River Project

California State Water Resources Control Board condition no. 1. The licensee must 

include with the plan filed with the Commission documentation of consultation, copies of 

comments and recommendations on the completed plan after it has been prepared and 

provided to the consulted entities, and specific descriptions of how the consulted entities’ 

comments are accommodated by the plan. The licensee must allow a minimum of 30 

days for the consulted entities to comment before filing the plan with the Commission. If 

the licensee does not adopt a recommendation, the filing must include the licensee’s 

reasons, based on site-specific information 

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must implement the provisions of the plan, including 

any changes required by the Commission.

Article 4XX. Large Woody Debris and Material Management Plan. Within 1 

year of license issuance, the licensee must prepare the plan in consultation with the 

technical advisory committee specified in Merced Irrigation District’s Merced River 

Project California State Water Resources Control Board condition no. 1. The licensee 

must include with the plan filed with the Commission documentation of consultation, 

copies of comments and recommendations on the completed plan after it has been 

prepared and provided to the consulted entities, and specific descriptions of how the 

consulted entities’ comments are accommodated by the plan. The licensee must allow a 

minimum of 30 days for the consulted entities to comment before filing the plan with the 

Commission. If the licensee does not adopt a recommendation, the filing must include 

the licensee’s reasons, based on site-specific information.

The Commission reserves the right to require changes to the plan. Upon 

Commission approval, the licensee must implement the provisions of the plan, including 

any changes required by the Commission. No large woody debris or material must be 

placed in the active channel until appropriate federal and state approvals have been 

obtained.
B-7

Article 4XX. Bald Eagle Management Plan. Within 6 months of license 

issuance, the licensee must file with the Commission for approval, a bald eagle 

management plan. The plan must include the following items, at a minimum: (1) 

educational information about roost sites on public information boards; (2) descriptions 

of activities that would be considered emergencies with explanations of why these 

activities would supersede bald eagle protection; (3) protocols and methodologies to be 

consistent with those recommended by the U.S. Fish and Wildlife Service (FWS); and (4) 

a schedule for filing reports. 

The licensee must prepare the plan after consultation with FWS, the Bureau of 

Land Management, the California State Water Resources Control Board, and the

California Department of Fish and Wildlife. The licensee must include with the plan 

documentation of consultation, copies of comments and recommendations on the 

completed plan after it has been prepared and provided to the agencies, and specific 

descriptions of how the agencies’ comments are accommodated by the plan. The licensee 

must allow a minimum of 30 days for the agencies to comment and to make 

recommendations before filing the plan with the Commission. If the licensee does not 

adopt a recommendation, the filing must include the licensee’s reasons, based on projectspecific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities, including use of construction staging areas, must not begin until the 

licensee is notified by the Commission that the plan is approved. Upon Commission 

approval, the licensee must implement the plan, including any changes required by the 

Commission.

Article 4XX. Noxious Weeds and Invasive Plants and Pesticide Use and 

Notification Plan. Within 6 months of license issuance, the licensee must file with the 

Commission for approval, a noxious weeds and invasive plants and pesticide use and 

notification plan. The plan must include, at a minimum: (1) details about methods to 

control noxious weeds and invasive plants; (2) a map showing locations of noxious 

weeds and invasive plants that would be controlled; (3) an implementation schedule,

including the frequency and timing of the control methods; (4) any best management 

practices that would be implemented as part of the plan; (5) specifications for pesticide 

use on project lands to be consistent with state and federal laws; (6) provisions requiring 

notification of pesticide use on project lands; and (7) reporting requirements.

The licensee must prepare the plan after consultation with the U.S. Fish and 

Wildlife Service, the Bureau of Land Management, the California State Water Resources 

Control Board, and the California Department of Fish and Wildlife. The licensee must

include with the plan documentation of consultation, copies of comments and 

recommendations on the completed plan after it has been prepared and provided to the 

agencies, and specific descriptions of how the agencies’ comments are accommodated by 

the plan. The licensee must allow a minimum of 30 days for the agencies to comment 
B-8

and to make recommendations before filing the plan with the Commission. If the 

licensee does not adopt a recommendation, the filing must include the licensee’s reasons, 

based on project-specific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities must not begin until the licensee is notified by the Commission that 

the plan is approved. Upon Commission approval, the licensee must implement the plan, 

including any changes required by the Commission.

Article 4XX. Valley Elderberry Longhorn Beetle Protection Plan. Within 6 

months of license issuance, the licensee must file with the Commission for approval, a 

valley elderberry longhorn beetle protection plan. The plan must include, at a minimum: 

(1) maps showing locations of any elderberry plants in the project area; (2) identification 

of any elderberry plants showing signs of occupancy by the valley elderberry longhorn 

beetle; (3) the development of protection measures; (4) implementation schedule; and (5) 

reporting requirements.

The licensee must prepare the plan after consultation with the U.S. Fish and 

Wildlife Service, the Bureau of Land Management, the California State Water Resources 

Control Board, and the California Department of Fish and Wildlife. The licensee must

include with the plan documentation of consultation, copies of comments and 

recommendations on the completed plan after it has been prepared and provided to the 

agencies, and specific descriptions of how the agencies’ comments are accommodated by 

the plan. The licensee must allow a minimum of 30 days for the agencies to comment 

and to make recommendations before filing the plan with the Commission. If the 

licensee does not adopt a recommendation, the filing must include the licensee’s reasons, 

based on project-specific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities, including use of construction staging areas, must not begin until the 

licensee is notified by the Commission that the plan is approved. Upon Commission 

approval, the licensee must implement the plan, including any changes required by the 

Commission.

Article 4XX. San Joaquin Kit Fox Protection Plan. Within 6 months of license 

issuance, the licensee must file with the Commission for approval, a San Joaquin kit fox 

protection plan. The plan must include, at a minimum: (1) provisions to conduct surveys 

for San Joaquin kit fox; (2) detailed survey methods; (3) protection and mitigation 

measures; (4) an implementation schedule; (5) reporting requirements; and (6) a 

provision for filing survey results and reports. 

The licensee must prepare the plan after consultation with the U.S. Fish and 

Wildlife Service, the Bureau of Land Management, the National Park Service, the 

California State Water Resources Control Board, and the California Department of Fish 
B-9

and Wildlife. The licensee must include with the plan documentation of consultation, 

copies of comments and recommendations on the completed plan after it has been 

prepared and provided to the agencies, and specific descriptions of how the agencies’ 

comments are accommodated by the plan. The licensee must allow a minimum of 30 

days for the agencies to comment and to make recommendations before filing the plan 

with the Commission. If the licensee does not adopt a recommendation, the filing must

include the licensee’s reasons, based on project-specific information.

The Commission reserves the right to require changes to the plan. Landdisturbing activities must not begin until the licensee is notified by the Commission that 

the plan is approved. Upon Commission approval, the licensee must implement the plan, 

including any changes required by the Commission.

Article 4XX. Fish Stocking Plan. Within 1 year of license issuance, the license 

must file, for Commission approval, a plan to stock 11,000 adult-sized rainbow trout in 

the Merced Falls impoundment for the first two years following license issuance and a 

plan for stocking (species, number, and stocking schedule) for the remainder of the 

license term. 

The fish stocking plan must be developed after consultation with the California 

Department of Fish and Wildlife (California DFW). The licensee must include with the 

plan an implementation schedule, documentation of consultation, copies of 

recommendations on the complete plan after it has been prepared and provided to 

California DFW, and specific descriptions of how California DFW’s comments are 

accommodated by the plan. The licensee must allow a minimum of 30 days for 

California DFW to comment and to make recommendations before filing the plan with 

the Commission. If the licensee does not adopt a recommendation, the filing must 

include the licensee’s reasons, based on project-specific information.

The Commission reserves the right to require changes to the revised plan. 

Implementation of the revised plan must not begin until the licensee is notified by the 

Commission that the plan is approved. Upon Commission approval, the licensee must 

implement the revised plan, including any changes required by the Commission.

Article 4XX. Recreation Operations. The licensee must operate and maintain all 

project recreation facilities, which includes all facilities at the Merced Falls Fishing 

Access area (signage, restroom, parking area, and car-top boat launch), the informal 

angler trail located along the northern shoreline, the two informal parking areas on either 

side of Hornitos County Bridge, and the informal canoe portage trail located at the south 

end of Merced Falls dam.

Article 4XX. Programmatic Agreement and Historic Properties Management 

Plan. The licensee must implement the “Programmatic Agreement Between the Federal 

Energy Regulatory Commission and the California State Historic Preservation Officer for 
B-10

Managing Historic Properties that may be Affected by a License to Pacific Gas and 

Electric Company for the Continued Operation of the Merced Falls Hydroelectric Project, 

in Merced and Mariposa counties, California (FERC No. 2467-020),” executed on 

______, including but not limited to the Historic Properties Management Plan (HPMP) 

for the project. In the event that the Programmatic Agreement is terminated, the licensee 

must continue to implement the provisions of its approved HPMP. The Commission 

reserves the authority to require changes to the HPMP at any time during the term of the 

license.
APPENDIX C

Entities that filed Letters

in Response to the

Notice of Application Accepted for Filing, Soliciting Motions to Intervene and 

Protests, Ready for Environmental Analysis, and Soliciting Comments, 

Recommendations, Preliminary Terms and Conditions, and Preliminary Fishway 

Prescriptions for the Merced River Hydroelectric Project
This page intentionally left blank.
C-1

The following entities filed letters in response to the notice of application accepted 

for filing, soliciting motions to intervene and protests, ready for environmental analysis, 

and soliciting comments, recommendations, preliminary terms and conditions, and 

preliminary fishway prescriptions for the Merced River Hydroelectric Project issued on 

March 28, 2014. 

Commenting Entity Filing Date

Daniel Chavez July 21, 2014

Judie Arthur July 21, 2014

Micheal Ohki July 21, 2014

Thomas McHatton July 21, 2014

Irene M. Roberts July 21, 2014

Suzanne Hultgren July 21, 2014

Ezio A. Samsoni July 21, 2014

Rory Randol July 21, 2014

Stan Callan July 21, 2014

Individual July 21, 2014

Martin DeJaquer July 21, 2014

Antonio Rednger July 21, 2014

Ray Thomas July 21, 2014

Thomas F. Valenito July 21, 2014

Arlene Engel July 21, 2014

Chelley Dallara July 21, 2014

Judie Arthur July 21, 2014

Willie Raheed July 21, 2014

Individual July 21, 2014

Joe Zester July 21, 2014

Individual July 21, 2014

Bill and Pam Ferrari July 21, 2014

Douglas Guesling July 21, 2014

Conde Burnett July 21, 2014

Individual July 21, 2014

Pamela Brewer July 21, 2014

Thomas G. Innerbichler July 21, 2014

Individual July 21, 2014

Ray Marino July 21, 2014

Individual July 21, 2014

Individual July 21, 2014

James Cepalinario July 21, 2014

James Packso July 21, 2014

Joseph Brown July 21, 2014

Bruce Edwards July 21, 2014
C

-2

Commenting Entity Filing Date

Chris Sumpter July 21, 2014

Gary Tessin July 21, 2014

Patrick Spielman July 21, 2014

Charles D. July 21, 2014

Leo and Eva Andrews July 21, 2014

Anne Cooper July 21, 2014

Individual July 21, 2014

Yuki Nishihama July 21, 2014

Francisco J. Gonzalez July 21, 2014

Chris Sehler July 21, 2014

Individual July 21, 2014

Vicki and Henry Spencer July 21, 2014

Viani Farms July 21, 2014

Shirley Granes July 21, 2014

Alice Souza July 21, 2014

Stu and Nancy McElwain July 21, 2014

Doris Crafts July 21, 2014

John Gun July 21, 2014

Mary and Micthell Reynolds July 21, 2014

Joe Baker July 21, 2014

Mike Mackinzie July 21, 2014

Individual July 21, 2014

Scott Wickstrom July 21, 2014

Pat Murphy July 21, 2014

Bob Majors July 21, 2014

Tom and Diane Gannon July 21, 2014

Emanuel and Sonia Belo July 21, 2014

Augif Scond July 21, 2014

Robert and Geraldine Hiser July 21, 2014

Sanford Wickum July 21, 2014

Ray and Loretta Fernandes July 21, 2014

Jean, Philippe, and Kathryn Favier July 21, 2014

Joseph M. Fagundes July 21, 2014

Henry Soares July 21, 2014

Braden Farms July 21, 2014

Manuel E. Vieira July 21, 2014

Mark F. Dent July 21, 2014

Joe Zester July 21, 2014

Shirley Young July 21, 2014

Michael Hoyt July 21, 2014
C

-3

Commenting Entity Filing Date

Daryl Hofman July 21, 2014

June A. Tonery July 21, 2014

Georgia Johnson July 21, 2014

Mark Dent July 21, 2014

Michael Vander Dussen July 21, 2014

Diulinda Daley July 21, 2014

Randy Lafollette July 21, 2014

Suzanne Langley Sabatino July 21, 2014

John P. Lourenco July 21, 2014

John Ferrari July 21, 2014

Randy Pimental July 21, 2014

John and Edyne Hultgren July 21, 2014

Joe Scoto July 21, 2014

Pete Bandoni July 21, 2014

David Silveira July 21, 2014

Karen Miller July 21, 2014

Hulbert E. Edrington July 21, 2014

Robert Crawford July 22, 2014

Individual July 22, 2014

Irene Schmidt July 22, 2014

Aron Schmidt July 22, 2014

Joe Connelly July 22, 2014

Lea Van Domever July 22, 2014

Thomas G. Innerbichler July 22, 2014

Wilder M. Thornhulk July 22, 2014

Individual July 22, 2014

Lang H. Montgomery July 22, 2014

Individual July 22, 2014

John Larson July 22, 2014

Larry Jones July 22, 2014

Bob Giampaoli July 22, 2014

Vann M. and Lynne J. Smith July 22, 2014

Ken Braden July 22, 2014

Carol Boesch July 22, 2014

Henry Soares July 22, 2014

Joseph M. Fagundes July 22, 2014

Ray and Loretta Fernandes July 22, 2014

Hulbert Edington July 22, 2014

Frank V Mumatore July 22, 2014

Betty Mooney Raw July 22, 2014
C

-4

Commenting Entity Filing Date

Joel Vicker July 22, 2014

Bromley A. Null July 22, 2014

Individual July 22, 2014

M. and M. Bairos July 22, 2014

Robert and Patricia Gamble July 22, 2014

Lola F. Sutra July 22, 2014

Barry and Helen Daughdrill July 23, 2014

Baltazar and Maurilia Cabellero July 23, 2014

Maria and Jose Duran July 23, 2014

Mitsue Jakahaski July 23, 2014

Lloyd an Etta Weaver July 23, 2014

Donald and Edna Mason July 23, 2014

Individual July 23, 2014

Individual July 23, 2014

Grove and Norma May July 23, 2014

Alice Zeran July 23, 2014

Farm Management, Inc. July 23, 2014

Karen Miller July 23, 2014

Gerald L. and Marcia J. Mincer July 23, 2014

Douglas Beames July 23, 2014

Clay Harmon July 23, 2014

Mike Brown July 23, 2014

Ray and Maria Glampaoli July 23, 2014

Vernon Boyd July 23, 2014

Individual July 23, 2014

Individual July 23, 2014

Donald H. Rogers July 23, 2014

Victor Mormles July 23, 2014

Individual July 23, 2014

Bill Adams July 24, 2014

Meridan O'Bara July 24, 2014

G. Weststeyz July 24, 2014

Daryl W. Wood July 24, 2014

Ezio A. Samisoni July 24, 2014

Charlene R. Dew July 24, 2014

F. D. Thompson July 24, 2014

Dennis Wittchow July 24, 2014

Glenn Arnold July 24, 2014

Bob Giampaoli July 24, 2014

Merton G. Dodge July 24, 2014
C

-5

Commenting Entity Filing Date

Gilbert M. Limera July 24, 2014

Bartica and Baxter Johnston July 24, 2014

Wesley N. Jantz July 24, 2014

Anna Kuniyski July 24, 2014

Gerardo Money July 24, 2014

John M. Mackermen July 24, 2014

Henry G. Kelsey July 24, 2014

Miguel Vega July 25, 2014

Randy Fritus July 28, 2014

Mike Pellicano July 28, 2014

Steve Whitaker July 28, 2014

James L. Glams July 28, 2014

Individual July 28, 2014

Individual July 28, 2014

Russell Peason and Custon Haying July 28, 2014

Individual July 28, 2014

Bonnie Nuemann-Bramell July 28, 2014

Robin Koda July 28, 2014

Ross Koda July 28, 2014

Linda Jordan July 28, 2014

Bruce Barnes July 28, 2014

Michelle Clark July 28, 2014

Betty Walker July 28, 2014

Individual July 28, 2014

Takako T. Endo July 28, 2014

Jeff Chance July 28, 2014

E. King July 28, 2014

Individual July 28, 2014

K Chevalier July 28, 2014

Tabir Yasub July 28, 2014

Individual July 28, 2014

Julie Ferrario July 28, 2014

David Long July 28, 2014

Robert Chad July 29, 2014

Thomas R. Barnell July 29, 2014

Penny D. Gatch July 29, 2014

Gino Pedretti, III July 29, 2014

Diulinda Daley July 29, 2014

Individual July 29, 2014

Gino Pedretti July 29, 2014
C

-6

Commenting Entity Filing Date

S. Jackson July 29, 2014

Roger Wood July 29, 2014

Philip Crites July 30, 2014

Gina Crites July 30, 2014

Nancy Deavours July 30, 2014

Nathan McDowell July 30, 2014

Ethan McDowell July 30, 2014

Individual July 30, 2014

Robert Alvernaz July 30, 2014

William Vander Helen July 30, 2014

Bettencourt Family Property July 30, 2014

Bettencourt Family Property July 30, 2014

Mike Dragovich July 30, 2014

Travis Costa July 30, 2014

Sharon B. Dragovich July 30, 2014

Bettencourt Family Property July 30, 2014

Bettencourt Family Property July 30, 2014

Molly Bettencourt Mullen July 30, 2014

Leanne Lopez July 30, 2014

Richard Lopez July 30, 2014

Pat Ferrigno July 30, 2014

Seth McDowell July 30, 2014

Lorrie McDowell July 30, 2014

Marilyn Landlino July 30, 2014

Lisa Mari Tsuchiya July 30, 2014

Jack Deavours July 30, 2014

Merced Union High School District July 30, 2014

Gina D. Bettencourt July 30, 2014

Mandy Ballenger July 30, 2014

Steven Mullen July 30, 2014

Gene Beach July 30, 2014

Alice Moschitto July 30, 2014

Aldo Assali July 30, 2014

Marchini and Marchini LP July 31, 2014

Bella Verde LLC July 31, 2014

Bona Vista Orchards July 31, 2014

Pieretti and Eyraud LLC July 31, 2014

J and J Marchini Enterprise July 31, 2014

Big Crops LLC July 31, 2014

JJ and R Ranches July 31, 2014
C-7

Commenting Entity Filing Date

Kevin L. Malone August 5, 2014

Jimmy Frazier August 5, 2014

Individual August 5, 2014

Individual August 6, 2014

Individual August 6, 2014

Individual August 6, 2014

City of Merced, CA September 3, 2014

Individual September 30, 2014
C-8

This page intentionally left blank.
APPENDIX D

Bureau of Land Management Preliminary Conditions
This page intentionally left blank.
D-1

PRELIMINARY RECOMMENDATIONS, TERMS AND CONDITIONS FOR 

THE MERCED RIVER HYDROELECTRIC PROJECT

The BLM through its preliminary recommendations, terms and conditions and 

prescriptions seeks to ensure appropriate levels of resource protection are incorporated in 

any new license. The BLM recommends that the FERC include in any new license issued 

for the Merced River Hydroelectric Project the following BLM preliminary 

recommendations, terms and conditions. The BLM believes that the resource measures 

presented in this section adequately address impacts to the ecological and cultural 

resources impacted by the Merced River Hydroelectric Project. 

PRELIMINARY LICENSE ARTICLES FOR THE MERCED RIVER 

HYDROELECTRIC PROJECT, FERC NO. 2179

These Preliminary License Articles are submitted to FERC as 4(e) Conditions 

(both specific and general/administrative) and 10(a) Recommendations.

Preliminary 4(e) Conditions 

Condition No. 1 – Consultation

Licensee shall annually consult with BLM regarding license implementation. The date of 

the consultation meeting will be mutually agreed to by Licensee and BLM, but in general 

should be held by April 15. At least 30 days in advance of the meeting, Licensee shall 

notify BLM and other interested stakeholders (interested stakeholders are defined as 

anyone who sends a letter to the licensee requesting to be a part of the consultation group. 

Any organized group will select an individual to represent them and will notify the 

licensee who their representative will be when they are attending these meetings), 

confirming the meeting location, time and agenda. At the same time, Licensee shall also 

provide notice to the: United States Fish and Wildlife Service (USFWS); National Park 

Service (NPS); National Oceanic and Atmospheric Administration’s National Marine 

Fishery Service (NMFS); California State Department of Fish and Wildlife (CDFW); and 

the State Water Resources Control Board (SWRCB) who may choose to participate in the 

meeting. 

Two weeks prior to the meeting, the Licensee shall make available to BLM, interested 

stakeholders, and the agencies listed above an operations and maintenance plan for the 

forthcoming year in which the meeting occurs. The goals of the meetings are to: discuss 

the past and current year implementation of the license conditions affecting BLM lands. 

Discussions about forthcoming year’s operations and maintenance plan; to have the 

Licensee present results from the past/current year monitoring of noxious weeds and 

special status species, as well as any additional information that has been compiled for 

the Project area including progress reports on any other issues related to preserving and 

protecting ecological values affected by the Project; to share information on mutually 

agreed upon planned maintenance activities; identify concerns that BLM may have 

regarding project operations/activities and their potential effects on sensitive resources, 
D-2

any measures required to avoid or mitigate those potential effects; and review and discuss 

the results of implementing the streamflow and reservoir-related conditions. 

Consultation shall include, but is not be limited to:

 A status report regarding implementation of license conditions.

 Discussion on any conditions that were not implemented.

 Results of any monitoring studies performed over the previous year in 

formats agreed to by BLM and the Licensee during development of 

implementation plans.

 Review of any non-routine maintenance.

 Discussion of any foreseeable changes to Project facilities or features.

 Discussion of any necessary revisions or modifications to resource 

implementation plans approved as part of this license.

 Discussion of needed protection measures for species newly listed as 

threatened, endangered, or sensitive, or changes to existing management 

plans that may no longer be warranted due to de-listing of species or, to 

incorporate new knowledge about a species requiring protection.

 Discussion of needed protection measures for newly discovered cultural 

resource sites.

 Discussion of elements of current year maintenance plans, e.g. road and 

trail maintenance.

 Discussion of any planned pesticide use.

 Discussion of BLM identified concerns regarding project 

operations/activities and their potential effects on sensitive resources, and 

any measures required to avoid or mitigate those potential effects.

 Discussion of information on mutually agreed upon planned maintenance 

activities.

A record of the meeting shall be kept by the Licensee and shall include any 

recommendations made by BLM for the protection of BLM land and resources. The 

Licensee shall file the meeting record, if requested, with FERC no later than 60 days 

following the meeting.

A copy of the reports/records for the previous water year regarding streamflow, study 

reports, and other pertinent records shall be provided to BLM, CDFW, USFWS, NPS, 

NMFS, and SWRCB by Licensee at least 60 days prior to the meeting date, unless 

otherwise agreed. 
D-3

Copies of other reports including, but not limited to, monitoring reports, non-compliance 

reports filed by Licensee, geologic or seismic reports, and structural safety reports for 

facilities affecting to BLM land shall be submitted to BLM concurrently with submittal to 

the FERC, with the goal of providing the material to BLM no later than 90 days in 

advance of the annual meeting. 

During the first several years of license implementation, it is likely that more consultation 

than just one annual meeting will be required, given the complexity of the project. 

Condition No. 2 - Consultation Group Specific to the Merced Hydroelectric Project

The Licensee shall, within 3 months of license issuance, establish a Consultation Group 

under the following contexts:

Purpose:

The primary purpose of Consultation Group is to provide a forum for the Licensee to 

consult with resource agencies and other interested parties on the following:

 To the extent topics covered in Condition No. 1 affect project-affected 

areas outside BLM jurisdiction, consultation with appropriate resource 

agencies on those same topics will occur at the Annual Meeting, other 

Consultation Group meetings, or as otherwise agreed with the Licensee and 

appropriate resource agencies. Licensee shall provide copies of the meeting 

materials to those who request it.

 Plans that are developed as required by the new license and plans that 

require specific consultation processes during implementation.

 Proposed temporary or permanent modifications to license conditions.

Licensee shall also provide notification of license compliance deviations to the current 

members of the Consultation Group.

Decision Making:

The Consultation Group will make recommendations to BLM. The BLM shall be 

responsible for final decisions within BLM jurisdiction. Licensee shall also ensure that 

consultation, permitting, and any necessary approvals within the jurisdiction of other 

agencies are completed. Licensee shall implement license conditions as approved and 

directed by FERC.

Participation:

In addition to the Licensee, BLM, SWRCB, USFWS, NPS, NMFS, and CDFW, 

Consultation Group meetings shall be open to any organization or individual that notifies

the Licensee in writing of interest in participating in the Annual Meeting or Consultation
D-4

Group meetings. The Consultation Group should establish mutually agreeable process

guidelines for conducting effective and efficient meetings no later than 1 year after 

license issuance. Each organization or individual shall be responsible for providing 

notification information to the Licensee and shall be responsible for keeping current a 

single point of contact for purposes of notification related to the Consultation Group. If a 

participant is interested in a particular meeting or topic, the participant is responsible for 

ensuring they are represented.

Meetings:

Separate from the Annual Meeting, the Licensee shall organize four Consultation Group

meetings per year. Additional meetings may be scheduled if the Consultation Group

decides additional meetings are necessary. Fewer meetings shall also be scheduled if the

Consultation Group decides that four meetings per year are not necessary. 

Condition No. 3 – Annual Employee Training

Licensee shall, beginning in the first full calendar year after license issuance, annually 

perform employee awareness training, and shall also perform such training when a staff 

member is first assigned to the Project. The goal of the training shall be to familiarize 

Licensee's operations and maintenance (O&M) staff with special-status species, nonnative invasive plants, and sensitive areas (e.g. special-status plant populations and nonnative invasive plant locations) that are known to occur within or adjacent to the FERC 

Project Boundary. Licensee shall provide to each O&M staff a confidential map showing 

these sensitive areas including GPS coordinates, as well as pictures and other guides to 

assist staff in recognizing special-status species, non-native invasive plants, and sensitive 

areas. It is not the intent of this measure that Licensee’s O&M staff performs surveys or 

become specialists in the identification of special-status species or noxious weeds. 

Licensee shall direct its O&M staff to avoid disturbance to sensitive areas, and to advise 

all Licensee contractors to avoid sensitive areas. If Licensee determines that disturbance 

of a sensitive area is unavoidable, License shall consult with BLM to minimize adverse 

effects to sensitive resources. This measure applies to employee training that is not 

otherwise covered by a specific plan.

Condition No. 4 - Coordinated Operations Plan

Licensee shall, within 90 days after issuance of new licenses for the Merced River

Hydroelectric Project (2179) or Merced Falls Hydroelectric Project (2467), whichever is

later, file with FERC for approval a Coordinated Operations Plan. Licensee shall develop

the Plan in consultation with the licensee for the Merced Falls Hydroelectric Project No.

2467 to assure implementation of flow-related measures in the two project licenses, and

with, BLM, F&WS, CDFW, NPS, NMFS, and SWRCB as interested parties of the 

Project flow-related measures. The purpose of the Plan shall be to provide for 
D-5

coordination between the Merced River Hydroelectric Project and Merced Falls 

Hydroelectric Project to assure implementation of flow–related measures in the two 

project licenses. Licensee shall file the Plan with the Commission, with copies provided 

to the above listed state and federal agencies. Licensee shall implement those portions of 

the Plan approved by the Commission. 

Condition No. 5 – Erosion Control and Restoration Plan

Licensee shall develop an Erosion Control and Restoration Plan with BLM approval for

erosion and/or restoration actions to be carried out by Licensee on or affecting BLM 

lands that are within or adjacent to the Project boundary. Licensee must acquire BLM 

approval before submitting this plan for Commission approval. Licensee shall file the 

approved plan with the Commission at least 90-days in advance of initiating construction 

of recreation or other Project facilities. 

Condition No. 6 – Large Woody Debris Material Management Plan

Licensee shall, within one year after license issuance prepares a large Woody Material

Management Plan after consultation with, and approval from, CDFW, BLM, USFWS,

SWRCB, and NFMS. The plan shall: (1) address the location of LWM collection in 

Lakes McClure and McSwain; (2) describe potential options for moving the LWM 

collected in Lake McClure and Lake McSwain and depositing it downstream of CrockerHuffman Diversion Dam; and (3) identify suitable locations in the Merced River 

downstream of Crocker-Huffman Diversion Dam where LWM can be placed within the 

active channel and be passively mobilized by 2-5 year high flow events, or where it 

would be appropriate to anchor LWM in the active channel and floodplain. BLM will not 

allow LWM to be stock piled on BLM land, especially in the Piney Creek Red legged 

Frog Core Area. BLM prefers the Licensee to pass through LWM past the dams over any 

other approach. Licensee must acquire CDFW, BLM, USFWS, SWRCB, and NFMS 

approval before submitting this plan for Commission approval. Licensee shall file the 

approved plan with the Commission Licensee will implement the plan within 90 days of 

its approval by the Commission. 

Condition No. 7 – Modifications of 4(e) Conditions in the Event of Anadromous Fish 

Re-introduction

BLM exercises its 4(e) authority by reserving that authority to modify these conditions to

respond to any reintroduction of Chinook salmon or steelhead trout, listed under the

Endangered Species Act, to stream reaches through BLM lands where the flow is 

controlled by the Merced River Hydroelectric Project. 
D-6

Condition No. 8 –Aquatic Invasive Species Management and Monitoring Plan

Within one year of license issuance, Licensee shall develop an Aquatic Invasive Species

(AIS) Plan that meets applicable State and Federal laws and regulations. The plan shall 

be subject to review and approval by BLM after Licensee consultation with CDFW, 

USFWS, and SWRCB. The applicable State and Federal resource agencies shall be 

responsible for making the determination as to whether the AIS Plan complies with the 

State and/or Federal regulations under the purview of the respective agencies. Once 

approved, Licensee will file the plan with FERC. 

The AIS Plan shall initially address the following AIS: dreissenid mussels (Dreissena

bugensis and Dreissena polymorpha); New Zealand mudsnail (Potamopyrgus

antipodarum); Eurasian milfoil (Myriophyllum spicatum); Hydrilla (Hydrilla 

verticillata); didymo (Didymosphenia reminata), and Asian clam (Corbicula fluminea). 

However, other AIS may be identified through monitoring. 

The AIS Plan shall include the following elements:

Public Education Program

The AIS Plan shall include a public education program, including appropriate signage 

and information pamphlets at designated public boat access sites on Lake McClure which

include information about:

 Draining water from boat, motor, bilge, live well and bait containers before 

leaving a water access site. • Removing visible plants, animals and mud 

from boat before leaving water body.

 Cleaning and drying boats and fishing equipment using California 

Department of Fish and Wildlife (CDFW) accepted protocols for the 

prevention of all AIS before entering any water body area.

 Disposing of unwanted bait in trash, including earthworms.

 Avoiding the release of plants and animals into a water body unless they 

originally came from that water body. 

AIS information shall be included on Project websites that provide public information on

Project facilities. The public information website will also include information on the

amphibian chytrid fungus. 

Best Management Practices

The AIS Plan shall specify that Licensee is responsible for developing BMPs for 

individual Project O&M activities, performed by MERCED-ID and/or its contractors 

which have the potential to introduce AIS into a Project reservoir, that prevent the spread 

of AIS. Licensee shall submit them to BLM, SWRCB, USFWS, and CDFW for review at 

the Annual Consultation Meeting (Condition 1) required in the FERC license. 
D-7

Development of BMPs for Project activities shall include, but are not be limited to, the

following:

 List of AIS with potential to be introduced.

 Control or preventive measures for AIS.

 Identification of critical control points in the Project activity sequence at 

which to prevent the introduction of AIS.

 Any necessary implementation monitoring for potential AIS to ensure 

BMPs are followed.

 Actions that will be taken if an introduction of AIS is found.

If invasive aquatic species are detected within any reservoir, Licensee will consult with 

the appropriate agencies and institute an appropriate plan of action. 

Monitoring and Reporting

The AIS Plan shall include a specific monitoring program that addresses Lake McClure

reservoir and that follows State and/or Federal laws, regulations, and policies. The

following initial monitoring methods shall be discussed in the monitoring section of the 

AIS Plan:

 Zebra and Quagga Mussel Surface Surveys

 Zebra and Quagga Mussel Veliger Sampling

 Zebra and Quagga Mussel Artificial Substrate Monitoring 

Incidental Observations Monitoring

The AIS plan shall include Incidental Observations Monitoring requirements as follows:

During AIS and other license-related aquatic monitoring in project reservoirs and project

affected stream reaches (e.g., monitoring for fish, foothill yellow-legged frogs (Rana

boylii), riparian habitat, and geomorphology), Licensee shall record incidental 

observations of the following species: Quagga or Zebra Mussel, New Zealand Mudsnail, 

Asian clam, Eurasian milfoil, Hydrilla, Didyomosphenia geminate, and American 

bullfrog (Lithobates catesbeianus). This initial list may be revised if other potential AIS 

are identified in project-affected reservoirs and stream reaches. The following practices 

will be implemented:

 Field personnel performing the license-related aquatic monitoring will be 

trained in the identification of the species listed above.

 Field crews working in aquatic environments (reservoirs, creeks, or rivers) 

conducting other biological monitoring will complete a checklist data form 

at the end of each day indicating the presence/absence (detect/non-detect) 

and location of the species listed above. It is recommended that at least one 
D-8

field crew member make a full pass of the survey area each day focusing 

exclusively on the species on the checklist.

Mapping and monitoring results shall be provided to BLM, CDFW, and SWRCB. 

Plan Revisions

Licensee, in consultation with BLM, CDFW, USFWS, and SWRCB shall review, update,

and/or revise the AIS Plan, as determined necessary by BLM in consultation with 

CDFW, USFWS, and SWRCB, when substantial changes in the existing conditions 

occur. Additional monitoring may be part of any plan revisions. Changes or revisions to 

the Plan would be expected if AIS conditions change as a result of unforeseen 

circumstances, either from new or existing Project-related activities, the potential for new 

AIS to occur, from natural events, or if other regulatory or legal requirements are 

established. Changes in the existing conditions could include such things as new methods 

for the treatment of Didymosphenia geminiata. Licensee shall file with FERC any revised 

plan and include all relevant documentation of coordination/consultation with the BLM, 

CDFW, and SWRCB. 

Condition No. 9 – Terrestrial Protection Measures

Vegetation and Non-Native Invasive Plant Management Plan

Upon the Commission approval, Licensee shall implement the Integrated Vegetation

Management Plan.

Resource Objectives:

The following resource objectives are drawn from the BLM Sierra Resource 

Management Plan (RMP) and other relevant BLM regulations and documents (see 

References section). 

Invasive Plant Objectives:

 Control invasive species using early detection, rapid response and 

prevention measures (USDI BLM 2008, Sierra RMP and ROD).

 Prevent, eliminate, and/or control undesired non-native vegetation or other 

invasive species using an Integrated Pest Management approach that 

combines biological, cultural, physical and chemical tools to minimize 

economic, health and environmental risks (USDI BLM 2008, Sierra RMP 

and ROD).

 Implement and meet national BLM policies consistent with the Partners 

against Weeds Initiative and Executive Order 13112 (USDI BLM 2008, 

Sierra RMP and ROD).
D-9

 The Carlson-Foley Act of 1968 and the Plant Protection Act of 2000 

authorize and direct the BLM to manage noxious weeds and to coordinate 

with other Federal and state agencies in activities to eradicate, suppress, 

control, prevent, or retard the spread of any noxious weeds on Federal 

lands.

 The Federal Noxious Weed Act of 1974 established and funded an 

undesirable plant management program, implemented cooperative 

agreements with state agencies, and established integrated management 

systems to control undesirable plant species.

 Executive Order 13112, Invasive Species, directs Federal agencies to 

prevent the introduction of invasive species and provide for their control, 

and to minimize the economic, ecological, and human health impacts that 

invasive species cause.

 The BLM has also produced national-level strategies for invasive species 

prevention and management. These include Partners Against Weeds (USDI 

BLM 1996), which outlines the actions BLM will take to develop and 

implement a comprehensive integrated weed management program; and 

Pulling Together: National Strategy for Invasive Plant Management (USDI 

BLM 1998), which illustrates the goals and objectives of a National 

invasive plant management plan (prevention, control and eradication).

 The Federal Interagency Committee for the Management of Noxious and 

Exotic Weeds is leading a national effort to develop and implement a 

National Early Detection and Rapid Response System for Invasive Plants in 

the United States (FICMNEW 2003). The primary long-term goals of the 

proposed system are to detect, report, and identify suspected new species of 

invasive plants in the United States. 

General Vegetation Management Objectives:

 Conserve and restore oak woodland, conifer forest, chaparral, riparian, 

meadow, Central Valley wetland and grassland habitats to support longterm viability of native species, sensitive species and the associated natural 

diversity of these habitats (USDI BLM 2008, Sierra RMP and ROD).

 Vegetation management is implemented to ensure safe and effective 

operation of the Licensee’s facilities by maintaining safe access to Project 

facilities including recreation facilities, protecting worker and public health 

and safety, and reducing fire hazards. It is BLM policy to reduce hazardous 

fuels to prevent catastrophic wildlife (USDI BLM 2008, Sierra RMP and 

ROD).
D-10

 The Federal Land Policy and Management Act of 1976 (FLPMA) directs 

the BLM to manage public lands “in a manner that will protect the quality 

of scientific, scenic, historical, ecological, environmental, air and 

atmospheric, water resources, and archeological values.”

Condition No. 10 – Bald Eagle Management Plan

Licensee must acquire CDFW, BLM, USFWS, and SWRCB, approval before submitting

this plan for Commission approval. Upon Commission approval, Licensee shall 

implement the Bald Eagle Management Plan, filed separately with the Commission.

Condition No. 11– Annual Review of Special-Status Species Lists and

Assessment of New Species on Federal Land

Licensee shall consult with BLM within 3 months, after license issuance, and annually

thereafter during the annual consultation meeting, to review the current list of specialstatus plant and wildlife species (species that are Federally Endangered or Threatened, 

Proposed Threatened or Endangered, BLM Sensitive, State Threatened or Endangered,

State Species of Special Concern, and CDFW Fully Protected) that might occur on public 

land administered by BLM in the Project area that may be directly or indirectly affected 

by Project operations. When a species is added to one or more of the lists, BLM shall

determine if the species, or un-surveyed suitable habitat for the species, is likely to occur 

on public land administered by BLM in or around the Project area. For any such newly 

added species, if BLM determines that the species is likely present on public land 

administered by BLM that may be directly or indirectly affected by the Project, Licensee 

shall develop and implement a study plan in consultation with BLM, and other 

appropriate agencies, to reasonably assess the effects of the Project on the species. 

Licensee shall prepare a report on the study, including objectives, methods, results, 

recommended resource measures where appropriate, and a schedule of implementation, 

and shall provide a draft of the final report to BLM and other appropriate agencies for 

review and approval. Licensee shall file the report, including evidence of consultation, 

with the Commission and shall implement those resource management measures required 

by the Commission.

If new occurrences of BLM special status plant or wildlife species as defined above are

detected prior to or during ongoing construction, operation, or maintenance of the 

Project, Licensee shall immediately notify BLM. If BLM determines that the Projectrelated activities are adversely affecting BLM sensitive or watch list species, Licensee 

shall, in consultation with BLM, develop and implement appropriate protection measures.

If new occurrences of state or federally listed or proposed threatened or endangered 

species are detected prior to or during ongoing construction, operation, or maintenance of 

the Project, Licensee shall immediately notify BLM, FERC, and the relevant agency 
D-11

(United States Fish and Wildlife Service or National Marine Fisheries Service) for 

consultation or conference in accordance with the Endangered Species Act. If state listed 

or fully protected species are affected, CDFW shall be notified.

The following resource objectives are drawn from the BLM Sierra Resource 

Management Plan (RMP) and other relevant BLM regulations and documents (see

References section).

Threatened, Endangered, and Sensitive Plant Species Objectives:

 Ensure that proposed license conditions and recommended measures 

provide for well distributed, viable populations of special status species 

including threatened, endangered and BLM sensitive species, and are 

consistent with any applicable biological opinion issued under the federal 

or state Endangered Species Act (ESA). Ensure that proposed license 

conditions and recommended measures comply with BLM plans and 

policy.

 Ensure that actions authorized on BLM administered lands do not 

contribute to the need to list any sensitive plant species under the provisions 

of the ESA and to initiate proactive conservation measures that reduce or 

eliminate threats to BLM sensitive plant species to minimize their need for 

listing under ESA (USDI BLM 2012, Special Status Plant Management 

Manual).

 Conserve ESA-listed species and the ecosystems on which they depend and 

to the extent possible recover these species so that ESA protection is no 

longer needed (USDI BLM 2012, Special Status Plant Management 

Manual).

 Ensure that BLM activities affecting the habitat of federally listed plant 

species and BLM sensitive plant species are carried out in a manner 

consistent with the objectives for managing those species (USDI BLM 

2012, Special Status Plant Management Manual).

 Monitor populations and habitats of federally listed and BLM sensitive 

plant species to determine whether management objectives are being met 

(USDI BLM 2012, Special Status Plant Management Manual).

 Develop site-specific management objectives for each occurrence of listed 

threatened and endangered plant species and BLM sensitive plant species 

on BLM lands that will be affected by BLM actions (USDI BLM 2012, 

Special Status Plant Management Manual).
D-12

 Modify proposed actions, to the extent possible, to avoid adverse impacts to 

special status plant species; where avoidance is not possible, develop 

measures to mitigate impacts to these species (USDI BLM 2012, Special 

Status Plant Management Manual).

 Conduct inventories to determine the occurrence and status of all special 

status plant species on lands managed by BLM or affected by BLM actions 

to ensure compliance with NEPA and the ESA by having sufficient 

information to adequately assess the effects of proposed actions on special 

status plants. Inventories are to be conducted at the time of year when such 

plant species can be found and positively identified (USDI BLM 2012, 

Special Status Plant Management Manual).

Condition No. 12 – Bat Management

In the first full calendar year after license issuance, Licensee shall inspect and document 

all known bat roosts within Project buildings (e.g., powerhouses, storage buildings, valve

houses), dams, or other structures that may be used as a roosting structure. The results of

the inspection will be provided to CDFW and BLM if the facility is located on BLM 

lands, at least 90 days prior to the Annual Consultation Meeting (described in Condition 

No. 1) that follows collection of the information. If bats or signs of roosting are present 

where staff have a routine presence (i.e., at least daily or weekly), Licensee will attempt, 

where feasible, and in the calendar year following the Annual Consultation Meeting 

described above, to place humane exclusion devices to prevent occupation of the 

structure by bats. Humane exclusion devices will be placed when bats are absent from the 

facility, generally between November 1 and February 28. Prior to installation of the 

exclusion devices, Licensee shall perform an inspection of the facility to ensure that 

overwintering bats are not trapped. If overwintering bats are present during the 

inspection, installation of exclusion devices shall be delayed. Licensee shall notify 

CDFW and BLM of the overwintering bats. Licensee shall consult with the CDFW and 

BLM during the Annual Consultation Meeting to identify future dates that would be 

suitable for installation of humane exclusion devices. All exclusion devices will be 

inspected on an annual basis and the facility will be reevaluated for roosting bats every 3 

years after the initial exclusion devices are installed to insure that no new roosts or entry 

points have been established.

Bat Objectives:

 Ensure all management activities and BLM authorizations are consistent 

with the conservation needs for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 Maintain or improve habitat for special status species (USDI BLM 2008, 

Sierra RMP and ROD).
D-13

 Maintain, improve, or enhance native fish and wildlife populations and the 

ecosystems upon which they depend (USDI BLM 2008, Sierra RMP and 

ROD).

 Ensure all management activities and BLM authorizations are consistent 

with the conservation needs for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 Promote the recovery of listed species and improve the status of candidate 

and special status species to eliminate the need to officially list these 

species (USDI BLM 2008, Sierra RMP and ROD).

 During FERC relicensing maintain and improve meadow and wetland 

habitat, riparian, and aquatic habitat for all life stages of native fish, 

macroinvertebrates, other aquatic species, and special status species (USDI 

BLM 2008, Sierra RMP and ROD).

 To initiate proactive conservation measures that reduces or eliminates 

threats to Bureau sensitive species to minimize the likelihood of and need 

for listing of these species under the ESA (USDI BLM 2008, Special Status 

Species Management Manual).

 Because of the wide‐spread decrease in bat numbers and increasing loss of 

habitat, BLM Folsom management approach will be an effort to protect all 

species of bats and their habitats. Conservation of bat roosting and foraging 

habitats is important to consider when conserving bats on BLM land. 

Habitats include specific roost and foraging requirements which vary by 

species, as well as by season and reproductive status.

 To sustain and manage viable populations of these bat species by managing 

factors affecting the distribution, abundance and quality of habitat for these 

species, and by minimizing adverse impacts to these species.

Condition No. 13 - Red Legged Frog Management Plan for Piney Creek Core 

Area.

Licensee must acquire CDFW, BLM, USFWS, and SWRCB, approval before submitting

this plan for Commission approval. Upon Commission approval, Licensee shall 

implement the Red Legged Frog Management Plan for Piney Creek Core Area.

California Red-legged Frog Objectives:

 Ensure all management activities and BLM authorizations are consistent 

with the conservation needs for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 Maintain or improve habitat for special status species (USDI BLM 2008, 

Sierra RMP and ROD).
D-14

 Maintain, improve, or enhance native fish and wildlife populations and the 

ecosystems upon which they depend (USDI BLM 2008, Sierra RMP and 

ROD).

 Maintain or improve numbers of native fish, macroinvertebrates and other 

aquatic species (USDI BLM 2008, Sierra RMP and ROD).

 Prevent and control infestations of non-native species that negatively 

impact native and game species (USDI BLM 2008, Sierra RMP and ROD).

 Ensure all management activities and BLM authorizations are consistent 

with the conservation needs for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 Manage special status species habitat to assist in the recovery of listed 

species (USDI BLM 2008, Sierra RMP and ROD).

 Restore and maintain the ecological health of watersheds and aquatic 

ecosystems on BLM lands and, to the extent possible, partner with other 

landowners and stakeholders to coordinate restoration efforts across 

watersheds (USDI BLM 2008, Sierra RMP and ROD).

 Promote the recovery of listed species and improve the status of candidate 

and special status species to eliminate the need to officially list these 

species (USDI BLM 2008, Sierra RMP and ROD).

 Restore disturbed or altered habitat for all life stages of native wildlife 

species, aquatic species, macroinvertebrates, special status species, and 

native fish species, including spawning fish passage habitat (USDI BLM 

2008, Sierra RMP and ROD).

 During FERC relicensing maintain and improve meadow and wetland 

habitat, riparian, and aquatic habitat for all life stages of native fish, 

macroinvertebrates, other aquatic species, and special status species (USDI 

BLM 2008, Sierra RMP and ROD).

 To conserve listed species and the ecosystems on which they depend (USDI 

BLM 2008, Special Status Species Management Manual).

 Determine, to the extent practicable, the occurrence, distribution, 

population dynamics and habitat condition of all listed species on lands 

administered by BLM, and evaluate the significance of lands administered 

by BLM in the conservation of those species (USDI BLM 2008, Special 

Status Species Management Manual).

 Develop and implement management plans and programs that will conserve 

listed species and their habitats (USDI BLM 2008, Special Status Species 

Management Manual).
D-15

 Ensure that all activities affecting the populations and habitats of listed 

species are designed to be consistent with recovery needs and objectives 

(USDI BLM 2008, Special Status Species Management Manual).

 To sustain and manage viable populations of the California red‐legged frog 

and foothill yellow‐legged frog in the planning area. Stabilize and manage 

the California redlegged frog population at Spivey Pond. Repatriate the 

California red‐legged frog to suitable habitat on BLM lands (USDI BLM 

2008, Sierra RMP and ROD).

Prioritized Goal(s) for above objective (Partial list as related to California redlegged frog and potentially applicable to this relicensing) (USDI BLM 2008, Sierra 

RMP and ROD).

 Identify sites where deleterious non‐native predators are present. Prioritize 

where control efforts should take place.

 For all known occurrences of the California red‐legged frog on BLM land,

control/eliminate deleterious non‐native species/predators (plants, 

vertebrates) using methods that are determined to be the most effective.

 Within watersheds, identify suitable habitat that includes a mosaic of 

breeding habitat interspersed with a matrix of barrier free dispersal habitat. 

For the California red‐legged frog, this is optimally in the form of pond 

complexes.

Condition No.14 - Foothill Yellow-Legged Frog Management Plan

Licensee must acquire CDFW, BLM, USFWS, and SWRCB, approval before submitting

this plan for Commission approval. Upon Commission approval, Licensee shall 

implement the Foothill Yellow-legged Frog Management Plan within 3 years of license 

issuance. At a minimum, the temperature plan shall include the following locations:

Located at the confluence of Sherlock Creek and the Merced River Frequency: Once in 

each water year type for first 10 years. Once every 5 years after the first ten years.

Foothill Yellow-Legged Frog Objectives:

 Ensure all management activities and BLM authorizations are consistent 

with the conservation needs for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 Maintain or improve habitat for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 Maintain, improve, or enhance native fish and wildlife populations and the 

ecosystems upon which they depend (USDI BLM 2008, Sierra RMP and 

ROD).
D-16

 Restore disturbed or altered habitat for all life stages of native wildlife 

species, aquatic species, macroinvertebrates, special status species, and 

native fish species, including spawning fish passage habitat (USDI BLM 

2008, Sierra RMP and ROD).

 Maintain or improve numbers of native fish, macroinvertebrates and other 

aquatic species (USDI BLM 2008, Sierra RMP and ROD).

 Restore and maintain the ecological health of watersheds and aquatic 

ecosystems on BLM lands and, to the extent possible, partner with other 

landowners and stakeholders to coordinate restoration efforts across 

watersheds (USDI BLM 2008, Sierra RMP and ROD).

 Ensure all management activities and BLM authorizations are consistent 

with the conservation needs for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 Promote the recovery of listed species and improve the status of candidate 

and special status species to eliminate the need to officially list these 

species (USDI BLM 2008, Sierra RMP and ROD).

 During FERC relicensing maintain and improve meadow and wetland 

habitat, riparian, and aquatic habitat for all life stages of native fish, 

macroinvertebrates, other aquatic species, and special status species (USDI 

BLM 2008, Sierra RMP and ROD).

 To initiate proactive conservation measures that reduces or eliminates 

threats to Bureau sensitive species to minimize the likelihood of and need 

for listing of these species under the ESA (USDI BLM 2008, Special Status 

Species Management Manual).

 To sustain and manage viable populations of the California red‐legged frog 

and foothill yellow‐legged frog in the planning area. Stabilize and manage 

the California redlegged frog population at Spivey Pond. Repatriate the 

California red‐legged frog to suitable habitat on BLM lands (USDI BLM 

2008, Sierra RMP and ROD).

Condition No. 15 - Limestone Salamander Sensitive Areas Management Plan 

and Studies:

Licensee must acquire BLM approval before submitting this plan for Commission 

approval. Upon Commission approval, Licensee shall implement the Limestone 

Salamander Sensitive Areas Management Plan and studies. Licensee shall perform 

limestone salamander studies to determine if the population is on the increase or in 

decline once every seven years beginning in year one of license issuance will conduct this 

study once every 7 years beginning in year one of license issuance.
D-17

Limestone Salamander Sensitive Areas Management Plan and Studies Objectives:

 Ensure all management activities and BLM authorizations are consistent 

with the conservation needs for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 Maintain or improve habitat for special status species (USDI BLM 2008, 

Sierra RMP and ROD). • Maintain, improve, or enhance native fish and 

wildlife populations and the ecosystems upon which they depend (USDI 

BLM 2008, Sierra RMP and ROD).

 Provide opportunities for research and education (USDI BLM 2008, Sierra 

RMP and ROD).

 Maintain or improve habitat for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 Promote the recovery of listed species and improve the status of candidate 

and special status species to eliminate the need to officially list these 

species (USDI BLM 2008, Sierra RMP and ROD).

 To initiate proactive conservation measures that reduces or eliminates 

threats to Bureau sensitive species to minimize the likelihood of and need 

for listing of these species under the ESA (USDI BLM 2008, Special Status 

Species Management Manual).

 Prevent all surface‐disturbing activities which would alter or degrade 

confirmed or potential limestone salamander habitat on BLM lands (USDI 

BLM 2008, Sierra RMP and ROD).

 Maintain vegetative cover in the Area of Critical Environmental Concern 

(ACEC) within specification outlined in the Management Plan for the 

Limestone Salamander Area of Critical Environmental Concern (ACEC 

Management Plan) (Lehman 1989). (USDI BLM 2008, Sierra RMP and 

ROD).

 Identify additional limestone salamander occurrences and consolidate BLM 

holdings within the species’ range. Adjust ACEC boundaries as necessary 

to increase habitat protection (USDI BLM 2008, Sierra RMP and ROD).

 Promote public use of the Limestone Salamander ACEC which is 

compatible with general wildland management goals and which does not 

conflict with the limestone salamander’s habitat needs. Integrate 

management of the ACEC with other BLM programs in the Merced River 

corridor to meet this objective (USDI BLM 2008, Sierra RMP and ROD).

Prioritized Goal(s) for above objective (Partial list as related to limestone salamander and

potentially applicable to this relicensing) (USDI BLM 2008, Sierra RMP and ROD).
D-18

Inventory all suitable but unconfirmed habitats on BLM lands for the presence of 

limestone salamanders.

Condition No.16-Western Pond Turtle Incidental Observations Monitoring

Licensee shall perform incidental observations for Western Pond Turtle as follows:

 Crews need to be trained on identification of Western Pond Turtle.

 Record any incidental sightings of Western Pond Turtles during all 

monitoring field work in rivers and lakes/reservoirs.

 Data shall include location, GPS if available, or location shown on USGS 

map.

 A written report (including location data) shall be compiled annually and 

provided at Annual Consultation meeting.

 The report shall be filed with FERC.

Western Pond Turtle Objectives:

 Ensure all management activities and BLM authorizations are consistent 

with the conservation needs for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 Maintain or improve habitat for special status species (USDI BLM 2008, 

Sierra RMP and ROD).

 To initiate proactive conservation measures that reduces or eliminates 

threats to Bureau sensitive species to minimize the likelihood of and need 

for listing of these species under the ESA (USDI BLM 2001, Special Status 

Species Management Manual).

Condition No. 17 - Riparian Vegetation Monitoring Plan

Licensee must acquire BLM, CDFW, USFWS, and SWRCB, approval before submitting

this plan for Commission approval. Upon Commission approval, Licensee shall 

implement the Riparian Vegetation Monitoring Plan.

Riparian Vegetation Objectives:

 Conserve and restore oak woodland, conifer forest, chaparral, riparian, 

meadow, Central Valley wetland, and grassland habitats to support long‐

term viability of native bird species, sensitive species, and the associated 

natural diversity of these habitats.

 BLM’s objectives during FERC relicensing include maintenance or 

improvement of the following (relevant RMP sections containing greater 

detail are in parentheses): Meadow and wetland habitat (2.4); riparian and 
D-19

aquatic habitat for all life stages of native fish, macroinvertebrates, other 

aquatic species, and special status species (2.5).

 Ensure riparian/wetland vegetation and structure and associated stream 

channels and floodplains are functioning properly, achieving an advanced 

ecological status, or making significant progress toward these conditions.

Condition No. 18 – Licensee Contacts

The Licensee shall designate an individual as its liaison with BLM, whenever planning or

construction of recreation facilities, other major Project improvements, or Project-related

maintenance activities are taking place on BLM lands. The Licensee agrees to coordinate

with BLM through this individual in contract review and work inspection.

Condition No. 19 – Annual Recreation Coordination Meeting

Each year during the term of the license, Licensee will arrange to meet with interested

resource agencies – BLM at a minimum) for an Annual Recreation Coordination Meeting 

to discuss the measures needed to ensure use and management, public safety, and 

protection and utilization of the recreation facilities and resources. The date of the 

meeting will be mutually agreed to by Licensee and the resource agencies but in general 

will be held within the first 90 days of each calendar year. A detailed agenda will be 

provided to the resource agencies when the meeting date is proposed to assure that the 

appropriate parties are present.

The following will be discussed, at a minimum:

 Need for garbage collection based on the results of visitor surveys, 

evidence that wildlife is becoming habituated, and the status of garbage and 

litter left on site by users.

 Need for toilet facilities where dispersed camping is occurring will be 

discussed at least every 6 years (following submittal of Monitoring Report 

from the Recreation Facilities plan), and more frequently if warranted.

 Report on significant changes in sanitation issues and number and size of 

user created dispersed camping areas.

 Other O&M issues identified by BLM or Licensee.

 Schedule and invite BLM to the recreation resource impact field 

evaluations and facility condition assessment to be conducted on BLM 

lands.

 Significant issues raised by the public.
D-20

 Any Licensee proposal for new or increases in recreation fees on BLM 

lands to help cover the costs of recreation facility construction, operation, 

and maintenance, as allowed by FERC regulations, will be discussed for 

consideration and approval by BLM.

 Recreation use data that is available from Licensee or the BLM, which 

includes summary data, at a minimum; and, upon request, raw data.

 Licensee will provide BLM a copy of all documentation associated with 

FERC inspections of Project recreation facilities and use on BLM lands, 

including follow-up action taken by the Licensee.

 Status of recreation projects from the previous year, including rehabilitation 

of existing recreation facilities, the establishment of new recreation 

facilities, and any other recreation measures or programs that were 

implemented.

 Recreational use data that is available.

 List of the recreation facilities scheduled for rehabilitation and any other 

Plan measures or programs to be implemented, including

Logistical and coordination planning.

Implementation schedule

Coordination needs.

Permitting requirement.

Key resources that will need to be protected from potential impacts 

associated with the implementation of the scheduled recreation projects.

Potential adjustments in schedule.

 Licensee and the agencies will identify any coordination needed with other 

projects being implemented in the area. Permitting requirements, additional 

required environmental documentation and key resources that will need to 

be protected from potential impacts associated with the implementation of 

the scheduled recreation projects will be addressed. BLM must approve any 

revisions to the Project’s Recreation Facilities Plan schedule when BLM 

land is involved, and the revised schedule will be submitted to FERC. 

Within 60 days following the meeting, Licensee will file with FERC 

evidence of the meeting, which will summarize comments made by the 

agencies, and Plan revisions or other agreements that were reached by 

Licensee and the agencies. The Annual Recreation Coordination Meeting is 

a minimum requirement and it is anticipated that meetings may occur 

throughout each year as needed to implement the Recreation Facilities 

Plans.
D-21

Any adjustments in specific actions or schedules shall be approved by BLM and filed 

with FERC.

Condition No. 20 – Merced River Trail Conceptual Plans and Implementation

Licensee shall, within 18 months of license issuance and in conjunction with BLM, 

develop and file with the Commission an agreed upon Conceptual Plan for the Merced 

River Trail from McSwain Dam to Bagby Recreation Area. The overall planning goal 

will be to align the Merced River Trail to follow the shoreline of Lake McClure and 

McSwain Reservoirs where it is possible to do so. The Merced River Trail Conceptual 

Plan shall include the following:

 Introduction

 Table of Contents

 Table of Tables/Figures (Photos and maps)

 Executive Summary

 Vision Statement

 Purpose and Need

 Setting

 Discussion By Trail Alternative

 Implementation - The Merced River Trail Conceptual Plan will contain 

three levels of recommendations for trail segments – ‘priority,’ ‘potential,’ 

and ‘conceptual.’ Priority trail segments are those that have primary 

importance and a great deal of support and are relatively ‘ready’ to 

implement. Potential trail segments need a little more work before they 

could be taken to the implementation level. Conceptual trail segments are 

mostly placeholders – ideas that need further research before they are

considered in planning processes.

Conclusion:

 The plan shall identify on Geographic Information System (GIS) maps 

using BLM approved GIS protocols at least three corridors, each 

approximately 100 feet wide, in which a pedestrian trail may be sited. 

Topographic mapping, satellite imagery and other planning tools that are 

available will be used in showing the locations of the three trail alternative 

routes and any features or issues relating to these proposed segments.
D-22

 For the purpose of the plan, Licensee shall assume the trail is 4-8 feet wide, 

made up of natural-surface material, has a maximum grade of 10%, with an 

understanding that in most areas the standard threshold of 5% or less will 

be the goal that Licensee will try to adhere to in designing the trail route 

alternatives. The Merced River Trail alignment does not need to be located 

within the existing FERC Project Boundary.

 The GIS maps shall show for each corridor: land ownership, elevation 

along the corridor centerline to approximately 2 foot horizontal resolution, 

streams, roads, key results from Licensee’s relicensing studies (e.g., 

sensitive areas due to special-status plants and wildlife resources), and 

other pertinent features and information. Known cultural and ESA-listed 

resources will be included in the evaluation but will not be specifically 

identified on the GIS maps.

 Licensee shall include in the plan, for each alternative trail corridor, 

concept-level drawings for trailhead access points, typical trail sections, and 

any associated trail facilities (e.g., campsites, picnic areas, foot bridges, 

causeways and signs). The plan shall include, for each alternative trail 

corridor, a discussion of agency permitting/approval requirements and a 

conceptual level cost by major cost areas for completion of the entire trail. 

The plan will also evaluate soils, erosion issues, brush removal, trail 

clearing by machines, hand crews, etc...for each alternative.

 Licensee shall develop an operations and maintenance section for each 

proposed alternative trail corridor. Included in this section will be projected 

costs to maintain the trails, and facilities.

 Licensee will hold a public meeting annually for the first five years after the 

Plan is Approved by FERC, and again as needed to discuss trail related 

issues with stakeholders, BLM, and other agencies.

Licensee will develop an MOU with BLM to address issues related to the Merced River

Trail that are outside the Project Boundary, including how to proceed in producing a 

Final Merced River Conceptual Trail Plan and producing a NEPA//CEQA document, 

funding and implementation.

Following the Merced Trail Conceptual Plan, Licensee shall provide a trail 

implementation proposal, which shall include Licensee’s and BLM’s agreed upon 

proposed alternative trail corridor, to BLM and interested parties for 90-day review and 

comment. BLM will allow Licensee 60 days to respond to its review. Licensee will file 

the agreed upon Final Merced Trail Conceptual Plan with the Commission. If agreement 

has not been reached by the licensee and BLM on a preferred route, Licensee will keep 

the Commission informed biannually of the current status. Once agreement has been 

reached, Licensee will file the agreed upon plan with the Commission.
D-23

 Funding for implementing the Merced River Trail Conceptual Plan will be 

the responsibility of both parties, the Licensee for their lands and federal 

lands within the FERC project boundary and for BLM on their lands 

outside of the FERC project boundary. Responsibilities for each party 

include the cost of permitting, design, construction, and maintenance for 

their respective lands and land management responsibilities. It is expected 

that most if not all of the funding will come from outside sources where 

both agencies and their partners are able to secure grant funding sources.

Condition No. 21 – Operation, Maintenance, and Administration Agreement

Beginning 90 days after license issuance, the licensee shall enter into an Operation and

Maintenance Agreement to provide annual funding in a contributed funds account set up 

by BLM. The cost basis for these payments shall originate from the first year of payment. 

The cost shall be escalated annually based on the U.S. Gross Domestic Product – Implicit 

Price Deflator (GDP-IDP).

Condition No. 22 – Recreation Facilities Plan

Licensee must acquire BLM approval before submitting this plan for Commission 

approval. Upon Commission approval, Licensee shall implement the Recreation Facilities 

Plan.

Condition No. 23 – Close Off Illegal Off Road Vehicle Access at Piney Creek 

Within one year of license issuance Licensee will: 

 Identify and map where ORV roads are and where they enter public land. 

 Determine if physical closure of these access roads is feasible 

 Require physical closure of ORV roads where it is determined to be 

feasible 

 If physical closure is not a viable solution, post signage that indicates that 

the area is closed to ORV use 

 Provide law enforcement assistance in enforcing the closure Rationale for 

Closing off illegal Off Road Vehicle Access at Piney Creek is to prevent 

illegal ORV use on the project lands. 

Condition No. 24– Historic Properties Management Plan 

Licensee must acquire BLM approval before submitting this plan for Commission 

approval. Upon Commission approval, Licensee shall implement the Historic Properties 

Management Plan. 
D-24

Condition No. 25 – Fire Prevention and Response Plan 

Licensee must acquire approval before submitting this plan for Commission approval. 

Upon Commission approval, Licensee shall implement the Fire Management and 

Response Plan. 

Condition No. 26 – Visual Resource Plan 

Licensee must acquire BLM approval before submitting this plan for Commission 

approval. Upon Commission approval, Licensee shall implement the Visual Resource 

Plan. Although the Merced ID did address visual resource mitigation issues, Merced ID 

did not write a plan for this measure. BLM expects that a visual resource plan will need 

to written to address the procedures Merced ID will go through when they are addressing 

visual resource impacts, from project proposals. In numerous other relicensing’s 

Licensees are required to develop a Visual Resource Plan. In order to meet the Visual 

Resource Management (VRM) goals outlined in BLM’s Sierra Resource Management 

Plant BLM will require a plan be develop that discusses the process and protocols and 

mitigating measures to be implemented to reduce visual resource impacts. BLM will 

work with Merced ID to complete this plan. 

Preliminary 4(e) Administrative Conditions 

The following Section 4(e) Conditions include requirements that serve to address the 

statutory and administrative rights and responsibilities of the BLM pursuant to Federal, 

State, and local laws. 

Condition No. 27 – Approval of Changes 

Notwithstanding any license authorization to make changes to the Project, when such 

changes directly affect BLM lands the Licensee shall obtain written approval from BLM 

prior to making any changes in any constructed Project features or facilities, or in the 

uses of Project lands and waters or any departure from the requirements of any approved 

exhibits filed with the Commission. Following receipt of such approval from BLM, and a 

minimum of 60 days prior to initiating any such changes, the Licensee shall file a report 

with the Commission describing the changes, the reasons for the changes, and showing 

the approval of BLM for such changes. The Licensee shall file an exact copy of this 

report with BLM at the same time it is filed with the Commission. This condition does 

not relieve the Licensee from the amendment or other requirements of Article 2 or Article 

3 of this license. 
D-25

Condition No. 28 – Maintenance of Improvements on or Affecting Bureau of 

Land Management Lands 

The Licensee shall maintain all its improvements and premises on BLM lands to 

standards of repair, orderliness, neatness, sanitation, and safety acceptable to BLM. 

Disposal of all materials will be at an approved existing location, except as otherwise 

agreed to by BLM. 

Condition No. 29 – Existing Claims 

The license shall be subject to all valid claims and existing rights of third parties. The 

United States is not liable to the Licensee for the exercise of any such right or claim. 

Condition No. 30 – Compliance with Regulations 

The Licensee shall comply with the regulations of the Department of the Interior on BLM 

lands for activities on BLM lands, and all applicable Federal, State, county, and 

municipal laws, ordinances, or regulations in regards to the area or operations on or 

directly affecting BLM lands, to the extent those laws, ordinances or regulations are not 

preempted by federal law. 

Condition No. 31– Surrender of License or Transfer of Ownership 

Prior to any surrender of this license, the Licensee shall provide assurance acceptable to 

BLM that Licensee shall restore any Project area directly affecting BLM lands to a 

condition satisfactory to BLM upon or after surrender of the license, as appropriate. To 

the extent restoration is required, Licensee shall prepare a restoration plan which shall 

identify the measures to be taken to restore such BLM lands and shall include or identify 

adequate financial mechanisms to ensure performance of the restoration measures. In the 

event of any transfer of the license or sale of the Project, the Licensee shall assure that, in 

a manner satisfactory to BLM, the Licensee or transferee will provide for the costs of 

surrender and restoration. If deemed necessary by BLM to assist it in evaluating the 

Licensee's proposal, the Licensee shall conduct an analysis, using experts approved by 

BLM, to estimate the potential costs associated with surrender and restoration of any 

Project area directly affecting BLM lands to BLM specifications. In addition, BLM may 

require the Licensee to pay for an independent audit of the transferee to assist BLM in 

determining whether the transferee has the financial ability to fund the surrender and 

restoration work specified in the analysis. 

Condition No. 32 – Protection of United States Property 

The Licensee, including any agents or employees of the Licensee acting within the scope 

of their employment, shall exercise diligence in protecting from damage the land and 

property of the United States covered by and used in connection with this license. 
D-26

Condition No. 33 - Indemnification 

The Licensee shall indemnify, defend, and hold the United States harmless for: 

 any violations incurred under any laws and regulations applicable to, or 

 judgments, claims, penalties, fees, or demands assessed against the United 

States caused by, or 

 costs, damages, and expenses incurred by the United States caused by, or 

 the releases or threatened release of any solid waste, hazardous substances, 

pollutant, contaminant, or oil in any form in the environment related to the 

construction, maintenance, or operation of the Project works or of the 

works appurtenant or accessory thereto under the license. 

The Licensee’s indemnification of the United States shall include any loss by personal 

injury, loss of life or damage to property caused by the construction, maintenance, or 

operation of the Project works or of the works appurtenant or accessory thereto under the 

license. Indemnification shall include, but is not limited to, the value of resources 

damaged or destroyed; the costs of restoration, cleanup, or other mitigation; fire 

suppression or other types of abatement costs; third party claims and judgments; and all 

administrative, interest, and other legal costs. Upon surrender, transfer, or termination of 

the license, the Licensee’s obligation to indemnify and hold harmless the United States 

shall survive for all valid claims for actions that occurred prior to such surrender, transfer 

or termination. 

Condition No. 34 – Damage to Land, Property, and Interests of the United 

States 

The Licensee has an affirmative duty to protect the land, property, and interests of the 

United States from damage arising from the Licensee's construction, maintenance, or 

operation of the Project works or the works appurtenant or accessory thereto under the 

license. The Licensee's liability for fire and other damages to BLM lands shall be 

determined in accordance with the Federal Power Act and standard Form L-1 Articles 22 

and 24. 

Condition No. 35 – Risks and Hazards on Bureau of Land Management Lands 

As part of the occupancy and use of the Project area, the Licensee has a continuing 

responsibility to reasonably identify and report all known or observed hazardous 

conditions on or directly affecting BLM lands within the Project boundary that would 

affect the improvements, resources, or pose a risk of injury to individuals. Licensee will 

abate those conditions, except those caused by third parties or not related to the 

occupancy and use authorized by the License. Any non-emergency actions to abate such 
D-27

hazards on BLM lands shall be performed after consultation with BLM. In emergency 

situations, the Licensee shall notify BLM of its actions as soon as possible, but not more 

than 48 hours, after such actions have been taken. Whether or not BLM is notified or 

provides consultation, the Licensee shall remain solely responsible for all abatement 

measures performed. Other hazards should be reported to the appropriate agency as soon 

as possible. 

Condition No. 36 – Protection of Bureau of Land Management Special Status 

Species 

Before taking actions to construct new Project features on BLM lands that was not 

addressed in the Commission’s NEPA processes for relicensing that may affect BLM 

threatened and endangered species or BLM special status species or their critical habitat, 

the Licensee shall prepare and submit a biological evaluation (BE) for BLM approval. 

The BE shall evaluate the potential impact of the action on the species or its habitat. In 

coordination with the Commission, BLM may require mitigation measures for the 

protection of the affected species. The biological evaluation shall: 

 Include procedures to minimize adverse effects to threatened and 

endangered species and special status species and their critical habitat. 

 Include information on the current status of the special-status species within 

the project area, a full description of the Project and potential effects, if 

BLM determines that existing information is out of date.

 Ensure project-related activities shall meet restrictions included in site 

management plans for threatened and endangered species and special-status 

species and their habitat. 

 Develop implementation and effectiveness monitoring of measures taken or 

employed to reduce effects to special status species. 

Condition No. 37 – Access 

Subject to the limitations set forth under the heading of “Access By The United States” in 

Condition No.44 hereof, BLM reserves the right to use or permit others to use any part of 

the licensed area on BLM lands for any purpose, provided such use does not interfere 

with the rights and privileges authorized by this license or the Federal Power Act 

Condition No. 38 – Crossings 

The Licensee shall maintain suitable crossings as required by BLM for all roads and trails 

that intersect the right-of-way occupied by linear Project facilities (powerline, penstock, 

ditch, and pipeline). 
D-28

Condition No. 39 – Surveys, Land Corners 

The Licensee shall avoid disturbance to all public land survey monuments, private 

property corners, and forest boundary markers. In the event that any such land markers or 

monuments on BLM lands are destroyed by an act or omission of the Licensee, in 

connection with the use and/or occupancy authorized by this license, depending on the 

type of monument destroyed, the Licensee shall reestablish or reference same in 

accordance with (1) the procedures outlined in the "Manual of Instructions for the Survey 

of the Public Land of the United States," (2) the specifications of the County Surveyor, or 

(3) the specifications of BLM. Further, the Licensee shall ensure that any such official 

survey records affected are amended as provided by law. 

Condition No. 40 – Pesticide-Use Restrictions on Bureau of Land 

Management Lands 

Pesticides may not be used on BLM lands or in areas affecting BLM lands to control 

undesirable woody and herbaceous vegetation, aquatic plants, insects, rodents, non-native 

fish, etc., without the prior written approval of BLM. During the Annual Consultation 

Meeting described in Condition No. 1, the Licensee shall submit a request for approval of 

planned uses of pesticides for the upcoming year. The Licensee shall provide at a 

minimum the following information essential for review: 

 whether pesticide applications are essential for use on BLM lands; 

 specific locations of use; 

 specific herbicides proposed for use; 

 application rates; 

 dose and exposure rates; and 

 safety risk and timeframes for application. 

Exceptions to this schedule may be allowed only when unexpected outbreaks of pests 

require control measures that were not anticipated at the time the report was submitted. In 

such an instance, an emergency request and approval may be made. Any pesticide use 

that is deemed necessary to use on BLM lands within 500 feet of known locations of 

Western Pond Turtles, Sierra Nevada Yellow-Legged Frog, Foothill Yellow Legged 

Frog, or known locations of BLM Special Status or culturally significant plant 

populations will be designed to avoid adverse effects to individuals and their habitats. 

Application of pesticides must be consistent with BLM riparian conservation objectives. 

On BLM lands, the Licensee shall only use those materials registered by the U.S. 

Environmental Protection Agency and consistent with those applied by BLM and 

approved through BLM review for the specific purpose planned. The Licensee must 
D-29

strictly follow label instructions in the preparation and application of pesticides and 

disposal of excess materials and containers. The Licensee may also submit Pesticide Use 

Proposal(s) with accompanying risk assessment and other BLM required documents to 

use pesticides on a regular basis for the term of the license as addressed further in 

Condition No.10 – Terrestrial Protection Measures. Submission of this plan will not 

relieve the Licensee of the responsibility of annual notification and review. 

Condition No. 41 – Modifications of 4(e) Conditions after Biological Opinion 

or Water Quality Certification 

BLM exercises its 4(e) authority by reserving that authority to modify these conditions, if 

necessary, to respond to any Final Biological Opinion issued for this Project by the 

National Marine Fisheries Service, United States Fish and Wildlife Service; or any 

Certification issued for this Project by the State Water Resources Control Board. 

Condition No. 42– Signs 

The Licensee shall consult with BLM prior to erecting signs related to safety issues on 

BLM lands covered by the license. Prior to the Licensee erecting any other signs or 

advertising devices on BLM lands covered by the license, the Licensee must obtain the 

approval of BLM as to location, design, size, color, and message. The Licensee shall be 

responsible for maintaining all Licensee-erected signs to neat and presentable standards. 

Condition No. 43 – Ground Disturbing Activities

If the Licensee proposes ground-disturbing activities on or directly affecting BLM lands 

that were not specifically addressed in the Commission’s NEPA processes, the Licensee, 

in consultation with BLM, shall determine the scope of work and potential for Projectrelated effects, and whether additional information is required to proceed with the 

planned activity. Upon BLM request, the Licensee shall enter into an agreement with 

BLM under which the Licensee shall fund a reasonable portion of BLM staff time and 

expenses for staff activities related to the proposed activities time and expenses for staff 

activities related to the proposed activities. 

Condition No. 44 – Use of Bureau of Land Management Roads for Project 

Access 

The Licensee shall obtain suitable authorization for all project access roads and BLM 

roads needed for Project access. The term of the permit shall be the same as the term of 

the license. The authorization shall require road maintenance and cost sharing in 

reconstruction commensurate with the Licensee’s use and project-related use. The 

authorization shall specify road maintenance and management standards that provide for 

traffic safety, minimize erosion, and damage to natural resources and that are acceptable 
D-30

to BLM as appropriate. The Licensee shall pay BLM for its share of maintenance cost or 

perform maintenance or other agreed to services, as determined by BLM for all use of 

roads related to project operations, project-related public recreation, or related activities. 

The maintenance obligation of the Licensee shall be proportionate to total use and 

commensurate with its use. Any maintenance to be performed by the Licensee shall be 

authorized by and shall be performed in accordance with an approved maintenance plan 

and applicable BMPs. In the event a road requires maintenance, restoration, or 

reconstruction work to accommodate the Licensee's needs, the Licensee shall perform 

such work at its own expense after securing BLM authorization. The Licensee shall 

complete a condition survey and a proposed maintenance plan subject to BLM review 

and approval as appropriate once each year. The plan may take the format of a road 

maintenance agreement provided all the above conditions are met as well as the 

conditions set forth in the proposed agreement. In addition, all BLM roads used as Project 

Access roads (PAR) and Right-of-Way access roads (ROW) shall have: 

 Current condition survey. 

 Be mapped at a scale to allow identification of specific routes or segments. 

 BLM assigned road numbers are used for reference on the maps, tables, and

in the field. 

 GIS compatible files of GPS alignments of all roads used for Project access 

are provided to BLM. 

 Adequate signage is installed and maintained by the Licensee at each road 

or route, identifying the road by BLM road number. 

Condition No. 45 – Access by the United States 

The United States shall have unrestricted use of any road over which the Licensee has 

control within the project area for all purposes deemed necessary and desirable in 

connection with the protection, administration, management, and utilization of Federal 

lands or resources. When needed for the protection, administration, and management of 

Federal lands or resources the United States shall have the right to extend rights and 

privileges for use of the right-of-way and road thereon to States and local subdivisions 

thereof, as well as to other users. The United States shall control such use so as not to 

unreasonably interfere with the safety or security uses, or cause the Licensee to bear a 

share of costs disproportionate to the Licensee’s use in comparison to the use of the road 

by others. 

Condition No. 46 – Road Use 

The Licensee shall confine all vehicles being used for project purposes, including but not 

limited to administrative and transportation vehicles and construction and inspection 
D-31

equipment, to roads or specifically designed access routes, as identified in the 

Transportation System Management Plan (Condition No.23). BLM, as appropriate, 

reserves the right to close any and all such routes where damage is occurring to the soil or 

vegetation, or, if requested by Licensee, to require construction/construction by the 

Licensee to the extent needed to accommodate the Licensee’s use. BLM agrees to 

provide notice to the Licensee and the Commission prior to road closures, except in an 

emergency, in which case notice will be provided as soon as practicable. 

Condition No. 47 – Bureau of Land Management Approval of Final Design 

Before any new construction of the Project occurs on Bureau of Land Management lands, 

the Licensee shall obtain prior written approval of BLM for all final design plans for 

Project components, which BLM deems as affecting or potentially affecting Bureau of 

Land Management lands within the Project boundary. The Licensee shall follow the 

schedules and procedures for design review and approval specified in the conditions 

herein. As part of such written approval, BLM may require adjustments to the final plans 

and facility locations to preclude or mitigate impacts and to insure that the Project is 

either compatible with on-the-ground conditions or approved by BLM based on agreed 

upon compensation or mitigation measures to address compatibility issues. Should such

necessary adjustments be deemed by BLM, FERC, or the Licensee to be a substantial 

change, the Licensee shall follow the procedures of FERC Standard Article 2 of the 

license. Any changes to the license made for any reason pursuant to FERC Standard 

Article 2 or Article 3 shall be made subject to any new terms and conditions of the 

Secretary of Interior made pursuant to Section 4(e) of the Federal Power Act to address 

Project effects within the Project boundary. 

Condition No. 48 – Unattended Construction Equipment 

The Licensee shall not place construction equipment on BLM lands prior to actual use or 

allow it to remain on BLM lands subsequent to actual use, except for a reasonable 

mobilization and demobilization period agreed to by BLM. 

Condition No. 49 – Maintenance of Improvements 

The Licensee shall maintain the improvements and premises on BLM lands within the 

Project boundary and Licensee adjoining property to standards of repair, orderliness, 

neatness, sanitation, and safety. For example, trash, debris, and unusable machinery will 

be disposed of separately; other materials will be stacked, stored neatly, or placed within 

buildings. Disposal will be at an approved existing location, except as otherwise agreed 

to by BLM. 
D-32

Condition No. 50 - Construction Inspections 

Within 60 days of planned ground-disturbing activity on or affecting BLM lands, 

Licensee shall file with the Commission a Safety during Construction Plan that identifies 

potential hazard areas and measures necessary to address public safety. Areas to consider 

include construction activities near public roads, trails, and recreation areas and facilities. 

Licensee shall perform daily (or on a schedule otherwise agreed to by BLM in writing) 

inspections of Licensee's construction operations on BLM lands and Licensee adjoining 

property while construction is in progress. Licensee shall document these inspections 

(informal writing sufficient) and shall deliver such documentation to BLM on a schedule 

agreed to by BLM. The inspections must specifically include fire plan compliance, public 

safety, and environmental protection. Licensee shall act immediately to correct any items 

found to need correction. A registered professional engineer or other qualified employee 

of the appropriate specialty shall regularly conduct construction inspections of structural 

improvements on a schedule approved by BLM. 
APPENDIX E

Preliminary Water Quality Certification Conditions for the 

Merced River Hydroelectric Project
This page intentionally left blank.
E-1

1. Merced River Anadromous Fish Committee:

Within 3 months of license issuance, Merced Irrigation District (MID or Licensee) 

shall organize and host a meeting and all future meetings with the Merced River 

Anadromous Fish Committee (Committee). The Committee shall be comprised of 

one representative from MID, Pacific Gas and Electric Company (PG&E), 

National Marine Fisheries Service (NMFS), US Fish and Wildlife Service 

(USFWS), California Department of Fish and Wildlife (CDRN), State Water 

Board, and a non-governmental organization. Committee members shall be 

selected by the organizations represented.

2. Minimum Instream Flow

State Water Board staff reserve the right to condition the Project with minimum 

instream flows in light of the whole record. The whole record includes but is not 

limited to the FERC record (i.e., recommendation by the resource agencies) the 

final NEPA document, and the final CEQA document.

3. Consultation Regarding New Ground Disturbing Activities

For any activity not addressed in the National Environmental Policy Act (NEPA) 

or California Environmental Quality Act (CEQA) or water quality certification 

documents, that may adversely affect water quality, the Licensee shall consult 

with the relevant resource agencies to determine if supplemental NEPA or CEQA 

documents are required and/or a water quality certification amendment.

4. Gravel Augmentation Plan

Within one year of license issuance, MID shall submit the Gravel Augmentation 

Plan to the Deputy Director. MID shall create the Gravel Augmentation Plan in 

consultation with the Committee. The amount of gravel augmented shall be 

consistent with annual gravel amount trapped behind New Exchequer and 

McSwain. 

5. Bald and Golden Eagle Plan

Within one year of license issuance MID shall submit the Bald and Golden Eagle 

Monitoring Plan (Eagle Plan) to the Deputy Director. The Eagle Plans shall that 

include protective measures when nesting is identified. MID shall create the Eagle 

Plan in consultation with USFWS, and CDFW.

The Eagle Plan shall:

A. Be consistent with the most current USFWS National Bald Eagle Management

Guidelines;

B. Include a statement of the goals and objectives;

C. Include a description of the proposed monitoring protocol(s);

D. Include specific, measureable criteria that will be used in combination with 

monitoring data and the comprehensive list of factors to objectively evaluate if 
E-2

the goals and objectives of the Eagle Plan are being met or the Project may be 

adversely affecting eagles and/or eagle nests;

E. Include a detailed monitoring and reporting schedule;

F. Include a plan for the development of corrective measures and a timetable for 

action in cases when the Eagle Plan's goals and objectives are not being 

achieved or data indicate the Project may be impacting eagles and/or eagle 

nests;

and

At a minimum monitoring shall include:

G. One breeding and one wintering survey every three years beginning within 

three years of license issuance;

H. Monitoring surveys within 30 days prior to any activity in the Project area 

listed or similar to the listed activities in the USFWS National Bald Eagle 

Management Guidelines; and

I. Include documentation of any eagle or eagle nest discovered during monitoring

as well as any incidental eagle or eagle nest observations.

Within 60 days of the conclusion of the monitoring, MID shall submit the results 

of the monitoring data with a description of location of eagle(s) or nest(s), date(s) 

of discovery, timeframe(s) of monitoring and protective measure implementation. 

Monitoring reports shall also include recommendations for more frequent 

monitoring based on increased use of the Project area by eagles, changes in Project 

operation and management activities, information derived from other resource 

studies or the state or federal resource agencies, and updates to be consistent with 

updates to the USFWS National Bald Eagle Management Guidelines.

If monitoring or incidental (other) reports confirm the presence of an eagle(s) or 

eagle nest(s) in the Project area, protective measures must be implement prior to 

any Project-associated activity.

6. Vernal Pool Fairy Shrimp and Conservation Fairy Shrimp Monitoring and 

Conservation Plan (Shrimp Plan)

Within one year of license issuance, MID shall submit a Shrimp Monitoring and 

Conservation Plan (Shrimp Plan) to the Deputy Director. MID shall create the 

Shrimp Plan in consultation with the Committee. The Shrimp Plan shall include 

monitoring Vernal Pool Fairy Shrimp and Conservation fairy Shrimp and their 

habitat on the Merced River, Deadman Slough, and associated tributaries. 

Monitoring shall be conducted for the first four consecutive years.

After the fourth year, MID shall monitor every three years and prior to 

construction, or any ground disturbing maintenance or exploration activity. The 

Shrimp Plan shall include monitoring so that pesticides (pesticides, as defined by 
E-3

the Water Quality Control Plan for the Sacramento River and San Joaquin River 

Basins (Basin Plan)) will not be applied where the pesticide may reach shrimp or 

their habitat.

The Shrimp Plan shall include, at a minimum:

A. A statement of goals and objectives;

B. A description of proposed monitoring protocols;

C. A comprehensive description of factors that may adversely affect Vernal Pool 

or Conservation Fairy Shrimp. This description shall also identify whether the 

factors are associated with the Project’s operation;

D. A detailed monitoring and reporting schedule;

E. Protective measures; and 

F. A Plan for corrective measures and a timetable for implementation if data 

indicate that the Project may be impacting Vernal Pool and/or Conservation 

Fairy Shrimp or their habitat.

7. Tiger Salamander Monitoring and Conservation Plan

Pesticide use and recreation construction may adversely impact Tiger Salamander.

Monitoring, documentation, and avoidance of Tiger Salamanders and their habitat 

are crucial to avoid adversely impacting Tiger Salamanders. Within one year after 

license issuance, MID shall submit the Tiger Salamander Monitoring and 

Conservation Plan (Tiger Plan) to the Deputy Director. MID shall create the Tiger 

Plan in consultation with the Committee.

The Tiger Plan shall include, at a minimum:

A. A statement of goats and objectives;

B. A description of proposed monitoring protocols;

C. A comprehensive description of factors that may adversely affect Tiger

Salamanders. This description shall also identify whether the factors are

associated with the Project’s operation;

D. A detailed monitoring and reporting schedule;

E. Protective measures; and 

F. A Plan for corrective measures and a timetable for implementation if data 

indicate that the Project may be impacting Tiger Salamanders or their habitat.

8. Fish Passage or Habitat Restoration Plan

Within one year after license issuance, MID shall submit the Fish Passage or 

Habitat Restoration Plan to the Deputy Director. MID shall evaluate, develop, and 

implement a fish passage or habitat restoration plan that will result in passage over 

Crocker-Huffman, McSwain Dam, and New Exchequer or decreasing 
E-4

temperatures in and downstream of the Project. The Fish Passage or Habitat 

Restoration Plan shall be created in consultation with the Committee. MID shall 

submit the Fish Passage or Habitat Restoration Plan to the Deputy Director within 

one year of License issuance. Within three years of license issuance, MID shall 

implement Fish passage or Habitat Restoration Plan.

9. Drought Plan

Within one year after license issuance, MID shall submit the Drought Plan to the 

Deputy Director. Drought Plan shall provide overarching guidance for operations 

during an emergency drought and/or multiple critically dry years and shall be 

created in consultation with the Committee. The Drought Plan shall include FERC 

License or water quality certification (WQC) variances that MID may request.

10. California Red-legged Frog (CRLF), Foothill Yellow-legged Frog (FYLF), 

and Western Spadefoot Monitoring and Conservation Plan (Frog Plan)

Within one year of license issuance, MID shall file a Frog Plan with the Deputy 

Director. MID shall create the Frog Plan in consultation with the Committee. The 

Frog Plan shall include monitoring CRLF, FYLF, and Western Spadefoot egg 

masses, tadpoles and adults on the Merced River, Deadman Slough (if 

appropriate), and associated tributaries. Monitoring shall be conducted no later 

than the first spring following approval of the Frog plan by the Deputy Director. 

Monitoring egg masses, tadpoles, and adults will be required for the first three

consecutive years. After the fourth year, MID shall monitor every three years:

The Frog Plan shall include, at a minimum:

A. A statement of goals and objectives;

B. A description of proposed monitoring protocols;

C. A comprehensive description of factors that may adversely affect CRLF, 

FYLF, and Western Spadefoot. This description shall also identify whether the

factors are associated with the Project’s operation:

D. Monitoring water temperature where eggs and tad poles are found; 

E. A detailed monitoring and reporting schedule; 

F. Protective measures; and

G. A Plan for corrective measures and a timetable for implementation if data

indicate that the Project may be impacting CRLF, FYLF, or Western

Spadefoot.

11. Valley Elderberry Longhorn Beetle Monitoring and Conservation Plan

Within one year of license issuance, MID shall submit the Shrimp Flan with the 

Deputy Director. MID shall create the Valley Elderberry Longhorn Beetle (VELB) 

Plan in consultation with the Committee. The VELB Plan shall include monitoring 
E-5

of VELB and their habitat on the Merced River, Deadman Slough (if appropriate), 

and associated tributaries. Monitoring shall be conducted prior to construction and 

every three years.

The VELB Plan, shall at a minimum include:

A. A statement of goals and objectives;

B. A description of proposed monitoring protocols;

C. A comprehensive description of factors that may adversely affect VELB. This

description shall also identify whether the factors are associated with the

Project’s operation.

D. A detailed monitoring and reporting schedule;

E. A Plan for corrective measures and a timetable for implementation if data 

indicate that the Project may be impacting VELB or their habitat; and

F. Protective measures.

12. Annual Consultation

MID shall annually consult with BLM, the Committee, and the Park Service, 

regarding measures needed to ensure protections. The date of the Annual 

Consultation shall be mutually agreed to by BLM, Park Service, and the 

Committee. MID shall still provide notice to tribes and interested parties.

At the Annual consult meeting, MID shall at a minimum present the following:

A. A status report regarding implementation of license conditions;

B. Results of any studies performed over the previous year in formats agreed to

by MID and agencies consulted with during the development of the study plan;

C. Review of any non-routine maintenance;

D. Discussion of any necessary revisions or modifications to resource plans 

included in the license;

E. Discussion of needed protection measures for species newly listed as 

threatened, endangered, or special-status or, changes to existing management 

plans that may no longer be warranted due to de-listing of species or, to 

incorporate new knowledge about a species requiring protections; and

F. Discussion of elements of current year operations and maintenance plans in the

Project Area.

A record of the meeting shall be kept by MID and shall include any 

recommendations made by BLM and the Committee.

13. Annual Review of Endangered Species Act Lists and Special Status Species 

Lists, and Assessment of New Species
E-6

MID shall consult with BLM, the Park Service, and the Committee within 3 

months after license issuance, and annually every for the term of the license and 

any annual extension. At the annual meeting, participants will review the current 

list of threatened and endangered species and special status plant and wildlife 

species that may be adversely impacted by the Project. When a species is added to 

one or more of the lists, MID, in consultation with BLM, Park Service, and the 

Committee shall determine if the species may be adversely affected by the Project. 

If it is determined that the species may be adversely affected by the Project, MID

shall develop and implement a new species specific study plan. The study plan 

shall be created in consultation with BLM and other appropriate agencies to assess 

the effects of the Project on the species.

Each species specific study plans, shall at a minimum include:

A. A statement of goals and objectives;

B. A description of proposed monitoring protocols;

C. A comprehensive description of factors that may adversely affect VELB. This

description shall also identify whether the factors are associated with the 

Project’s operation.

D. A detailed monitoring and reporting schedule;

E. A Plan for corrective measures and a timetable for implementation if data 

indicate that the Project may be impacting the newly listed specific species or 

their habitat; and

F. Protective measures.

MID shall implement and prepare a report on the study including objectives, 

methods, results, recommended measures where appropriate, and a schedule of 

implementation.

14. Large Woody Materials Plan

Within one year after license issuance, shall submit the Large Woody Materials 

Management Plan (LWM Plan) to the Deputy Director. MID shall create the 

LWM Plan in consultation with the Committee.

15. Lake McClure Minimum Pool

Minimum instream flow increases will correspond to decreased water 

temperatures downstream of Lake McClure; as such an increase to the minimum 

pool requirement of Lake McClure may also be needed to achieve decreased water 

temperatures. State Water Board staff reserves the right to require a new value for 

the minimum pool requirement in Lake McClure in light of the whole record. The 

whole record includes but is not limited to the FERC record (i.e., recommendation 

by the resource agencies), the final NEPA document, and the final CEQA 

document.
E-7

16. Lake McClure and McSwain Reservoir Fish Stocking

Within 3 months of license issuance MID shall submit the Lake McClure and 

McSwain Reservoir Fish Stocking Plan (Fish Stocking Plan). MID shall create the 

Fish Stocking Plan in consultation with the Committee. Beginning the first year 

after license issuance MID shall annually stock fish in Lake McClure and 

McSwain Reservoir with a minimum of: 

Lake McClure

1) 32,000 to 70,000 of catchable sized fish; and 2) 39,000 to 95,000 fingerings.

McSwain Reservoir

1) 1,000 to 2,000 catchable-sized rainbow trout

Fish stocked shall only be native cold water species. MID shall only stock fish 

from facilities free of invasive species and that provide documentation of 

monitoring and testing that fish source facility and equipment is free of invasive 

species.

17. Aquatic Invasive Species Management Plan

Within one year of license issuance, MID shall submit the Aquatic Invasive 

Species Management Plan to the Deputy Director. MID shall create the Aquatic 

Invasive Species Plan in consultation with CDFW. MID shall include monitoring 

and corrective action steps as part of the Aquatic Invasive Species Management 

Plan.

The Aquatic Invasive Species Management Plan shall at a minimum include:

A. A statement of goals and objectives;

B. A description of proposed monitoring protocols;

C. A detailed monitoring and reporting schedule;

D. A Plan for corrective measures and a timetable for implementation if data

indicate presence of aquatic invasive species; and

E. Protective measures that will prevent introduction of aquatic invasive species 

in the project area.

18. Pesticide Use Plan

Within six months of license issuance, MID shall submit the Pesticide Use Plan to 

the Deputy Director. MID shall create the Pesticide Use Plan in consultation with 

BLM and the Committee. The Pesticide Use Plan shall include provisions that 

restrict application of pesticides (pesticides, as defined by the Basin Plan) so 

pesticides will not reach ESA, CSA species or their habitat in or downstream of 

the Project area. Pesticides shall only be applied by an individual with a current 

and valid Qualified Applicator License issued by the California Department of 
E-8

Pesticide Regulation or under the direct visual supervision of an individual with a 

current and valid Qualified Applicator License issued by the California

Department of Pesticide Regulation. MID shall include dates or timeframes when 

pesticides will be applied and a map that includes: topography, waterways, scale, 

areas that pesticides will be applied, roads, locations of ESA and CESA listed 

species. In case of an emergency, MID shall seek approval from BLM and the 

Committee.

19. Water Temperature Monitoring Plan

Within six months of license issuance, MID shall submit the Water Temperature 

Monitoring Plan to the Deputy Director. MID shall create the Water Temperature 

Monitoring Plan in consultation with the Committee. MID shall install and operate 

4 to 8 water temperature monitoring devices within 1.5years of license issuance.

The Water Temperature Monitoring Plan shall at a minimum include:

A. A statement of goals and objectives;

B. A description of proposed monitoring protocols;

C. A comprehensive description of factors that may affect water temperature. This

description shall also identify whether the factors are associated with the 

Project’s operation.

D. A detailed monitoring and reporting schedule; and

E. A Plan for corrective measures and a timetable for implementation if data 

indicate that the Project may be increasing water temperature and/or adversely 

effecting water quality.

Locations shall be suitable to the Committee. Monitoring stations shall be realtime or downloaded weekly and publically available within 1 week from

download.

20. Anadromous Fish Monitoring Plan

Within one year of license issuance, MID shall submit Anadromous Fish 

Monitoring Plan (Anadromous Fish Plan) to the Deputy Director. The 

Anadromous Fish Plan shall include monitoring of CESA and ESA listed 

Anadromous Fish. MID shall create the Anadromous Fish Plan in consultation 

with the Committee.

The Anadromous Fish Plan shall at a minimum include:

A. A statement of goals and objectives;

B. A description of proposed monitoring protocols;

C. A comprehensive description of factors that may adversely affect CESA and 

ESA listed anadromous fish. This description shall also identify whether the 

factors are associated with the Project’s operation;
E-9

D. A detailed monitoring and reporting schedule;

E. A Plan for corrective measures and a timetable for implementation if data 

indicate that the Project may be impacting anadromous fish or their habitat; 

and

F. Protective measures.

If passage at Crocker-Huffman is scheduled to resume, one year prior to passage, 

MID shall submit a revised Anadromous Fish Plan to the Deputy Director. MID 

shall create the revised Anadromous Fish Plan in consultation with the Committee. 

The revised Anadromous Fish Plan shall contain provisions that geographically 

expand anadromous fish monitoring locations.

21. Transportation Management Plan

Within one year of license issuance, MID shall submit the Transportation 

Management Plan to the Deputy. Director.

The Transportation Management Plans shall include:

A. Map/Inventory. MID shall map and inventory roads associated with the 

Project, as follows:

I. Develop a clear and legible map with a scale and topography using a

geographic information system (GIS) that includes all roads associated with the 

project, appurtenant facilities (e.g., gates, closures, associated infrastructure, 

etc.), and locations of drainage structures, locations of streams, surface water 

bodies, ephemeral and intermittent waters, wetlands, and equipment storage 

and service areas for equipment; and

II. Develop a road inventory that includes: addressing uses (e.g., recreation, 

facility access, etc.) or non-use of the roads; condition surveys; associated 

facilities (e.g., culverts, gates, etc.); improvement needs; road closures; and 

safety, jurisdiction, and maintenance responsibilities. 

B. Road Monitoring and Maintenance. MID shall perform at least annual 

monitoring and inspection of Project road conditions, as well as inspection of 

drainage structures and runoff patterns after major storm events. Annual 

monitoring and maintenance reports shall be submitted to the Deputy Director 

and shall identify any roads or drainage structures not meeting stipulated 

maintenance levels. Proposed measures to improve performance comparable to 

the most current United States Department of Agriculture, Forest Service 

National BMP’s Road Management Activities shall be identified and a

schedule for repair.

22. General Preliminary Condition

This condition applies to daft Conditions 1 through 21, as well as all plans or 

changes to plans required by the water quality certification or related to water 
E-10

quality shall be developed in consultation with relevant state and federal agencies.

MID shall provide the relevant state and federal agencies with a minimum 30-day 

comment period on the plans and draft report, if applicable. The final plans and 

final reports shall include documentation of consultation with the relevant state 

and federal agencies, all comments made by the relevant state and federal

agencies, and a description of how the final plan and/or final report incorporates or 

addresses the comments made by the relevant state and federal agencies. The 

Licensee shall implement the plans and draft the report(s). Licensee shall file the 

final report and final plan with the Deputy Director for revision or approval. Upon 

Deputy Director approval, the Licensee shall file the approved final plan and 

approved final report with FERC.

The following conditions also apply to this Project in order to protect water 

quality and beneficial uses over the term of the Project’s license and any annual 

extensions.

23. Control measures for erosion, excessive sedimentation and turbidity shall be 

implemented and in place at the commencement of and throughout any ground 

clearing activities, excavation, or any other Project activities that could result in 

erosion or sediment discharges to surface waters. Erosion control blankets, liners 

with berms, and/or other erosion control measures shall be used for any stockpile 

of excavated material to control runoff resulting from precipitation, and prevent 

material from contacting or entering surface water.

24. Waters shall be free of changes in turbidity (due to Project activities) that 

cause nuisance or adversely affect beneficial uses. Increases in turbidity 

attributable to Project controllable water quality factors shall not exceed the 

following limits as defined in the Central Valley Basin Plan:

a. Where natural turbidity is less than 1 nephelometric turbidity unit (NTU), 

controllable factors shall not cause downstream turbidity to exceed 2 NTUs.

b. Where natural turbidity is between 1 and 5 NTUs, increases in turbidity shall 

not exceed 1 NTU.

c. Where natural turbidity is between 5 and 50 NTUs, increases in turbidity shall 

not exceed 20 percent.

d. where natural turbidity is between 50 and 100 NTUs, increases in turbidity 

shall not exceed 10 NTUs.

e. Where natural turbidity is greater than 100 NTUs, increases in turbidity shall 

not exceed 10 percent.

25. All imported riprap, rocks, and gravels used for construction within or adjacent 

to any watercourses shall be pre-washed. Wash water generated on-site shall not 

contact or enter surface waters. Wash water shall be contained and disposed of in 

compliance with state and local laws, ordinances, and regulations.
E-11

26. Construction material, debris, spoils, soil, silt, sand, bark, slash, sawdust, 

rubbish, steel, or other inorganic, organic, or earthen material, and any other 

substances from any Project related activity shall be prevented from entering: 

surface waters. All construction debris and trash shall be contained and regularly 

removed from the work area to the staging area during construction activities. 

Upon completion, all Project-generated debris, building materials, excess material, 

waste, and trash shall be removed from all the Project sites for disposal at an 

authorized landfill or other disposal site in compliance with State and local laws,

ordinances, and regulations.

27. No unset cement, concrete, grout, damaged concrete, concrete spells, or wash 

water used to clean concrete surfaces shall contact or enter surface waters. Any 

area containing wet concrete shall be completely bermed and isolated. The berm 

shall be constructed of sandbags or soil and shall be lined with plastic to prevent 

seepage. No leachate from truck or grout mixer cleaning stations shall percolate 

into Project area soils. Cleaning of concrete trucks or grout mixers shall be 

performed in such a manner that wash water and associated debris is captured, 

contained and disposed of in compliance with State and local laws, ordinances and 

regulations. Washout areas shall be of sufficient size to completely contain all 

liquid and waste concrete or grout generated during washout procedures. 

Hardened concrete or grout shall be disposed at an authorized landfill, in 

compliance with State and local laws, ordinances and regulations.

28. All equipment must be washed prior to transport to the Project site and must be 

free of sediment, debris, and foreign matter. Any equipment used in direct contact 

with surface water shall be steam cleaned prior to use. All equipment using gas,

oil, hydraulic fluid, or other petroleum products shall be inspected for leaks prior 

to use and shall be monitored for leakage. Stationary equipment (e.g., motors, 

pumps, generator, etc.) shall be positioned over drip pans or other types of 

containment. Spill and containment equipment (e.g., oil spill booms, sorbent pads, 

etc.) shall be maintained onsite at all locations where such equipment is used or 

staged.

29. Onsite containment for storage of chemicals classified as hazardous shall be 

away from watercourses and include secondary containment and appropriate 

management as specified in California Code of Regulations, title 27, section 

20320.

30. Unless otherwise specified in this WQC or, at the request of the Deputy 

Director, data and/or reports must be submitted electronically in a format accepted 

by the State Water Board to facilitate the incorporation of this information into 

public reports and the State Water Board’s water quality database systems in 

compliance with California Water Code section 13167.

31. The State Water Board’s approval authority includes the authority to withhold

approval or to require modification of a proposal or plan prior to approval. The 
E-12

State Water Board may take enforcement action if the Licensee fails to provide or 

implement a required plan in a timely manner.

32. The State Water Board reserves the authority to add to or modify the

conditions of this WQC to incorporate load allocations developed in a total 

maximum daily load developed by the State Water Board or the Central Valley 

Water Board.

33.The State Water Board reserves the authority to add to or modify the conditions 

of this WQC: (1) if monitoring results indicate that continued operation of the 

project could violate water quality objectives or impair the beneficial uses of the 

Merced River or Deadman Slough or tributaries to either waterway; (2) to 

coordinate the operations of this Project and other hydrologically connected water 

development projects, where coordination of operations is reasonably necessary to 

achieve water quality standards or protect beneficial uses of water; or (3) to 

implement any new or revised water quality standards and implementation plans

adopted or approved pursuant to section 303 of the CWA.

34. Future changes in climate projected to occur during the license term may 

significantly alter the baseline assumptions used to develop the conditions of this 

certification. The State Water Board reserves authority to add to or modify the 

conditions in this certification to require additional monitoring and/or other 

measures, as needed, to verify that Project operations meet water quality 

objectives and protect the beneficial uses assigned to the Project-affected stream 

reaches.

35. The Licensee shall comply with all applicable requirements of the SR/SJR 

Basin Plan. Licensee must notify the Deputy Director and Executive Office within 

24 hours of any unauthorized discharge to surface waters.

36. Notwithstanding any more specific conditions in this WQC, the Project shall 

be operated in a manner consistent with all water quality standards and 

implementation plans adopted or approved pursuant to section 303 of the CWA. 

The Licensee must take all reasonable measures to protect the beneficial uses of 

waters of the Merced River and Deadman Slough as well as tributaries to both 

waterways.

37. This WQC does not authorize any act which results in the taking of a 

threatened, endangered or candidate species or any act, which is now prohibited, 

or becomes prohibited in the future, under either the California ESA (Fish & 

Game Code 5 §§ 2050 2097) or the federal ESA (16 U.S.C. §§ 1531 - 1544). If a 

“take” will result from any act authorized under this WQC or water rights held by 

the Licensee, the Licensee must obtain authorization for the take prior to any 

construction or operation of the portion of the Project that may result in a take. 

The Licensee is responsible for meeting all requirements of the applicable ESAs 

for the Project authorized under this WQC.
E-13

38. In the event of any violation or threatened violation of the conditions of this 

WQC, the violation or threatened violation is subject to all remedies, penalties,

processes, or sanctions as provided for under applicable state or federal law. For 

the purposes of section 401(d) of the CWA, the applicability of any state law 

authorizing remedies, penalties, process, or sanctions for the violation or 

threatened violation constitutes a limitation necessary to ensure compliance with 

the water quality standards and other pertinent requirements incorporated into this 

WQC.

39. In response to a suspected violation of any condition of this WQC, the Deputy 

Director or the Executive Officer may require the holder of any federal permit or 

license subject to this WQC to furnish, under penalty of perjury, any technical or 

monitoring reports the Deputy Director or the Executive Officer deems 

appropriate, provided that the burden, including costs, of the reports shall bear a 

reasonable relationship to the need for the reports and the benefits to be obtained 

from the reports. (Wat. Code, §§ 1051, 13185, 13267 & 13383). The State Water

Board may add to or modify the conditions of this WQC as appropriate to ensure 

compliance.

40. No construction shall commence until all necessary federal, state, and local 

approvals are obtained.

41. Any requirement in this WQC that refers to an agency whose authorities and 

responsibilities are transferred to or subsumed by another state or federal agency 

will apply equally to the successor agency.

42. The Licensee must submit any change to the Project, including changes in 

Project operation, technology, upgrades, or monitoring, that could have a 

significant or material effect on the findings, conclusions, or conditions of this 

WQC, to the State Water Board for prior review and written approval. The State 

Water Board shall determine significance and may require consultation with state 

or federal agencies. If the State Water Board is not notified of a potentially 

significant change to the Project, it will be considered a violation of this WQC. If

such a change would also require submission to FERC, the change must first be 

submitted and approved by the State Water Board, unless otherwise noted in this 

certification.

43. The Deputy Director and the Executive Officer shall be notified one week 

prior to the commencement of ground disturbing activities. Upon request, a 

construction schedule shall be provided to agency staff in order for staff to be 

present onsite to answer any public inquiries during construction and to document 

compliance with this WQC. The Licensee must provide State Water Board and 

Central Valley Water Board staff reasonable access to Project sites to document 

compliance with this WQC.
E-14

44. This WQC is subject to modification or revocation upon administrative or 

judicial review, including review and amendment pursuant to California Water 

Code section 13330 and California Code of Regulations, title 23, division 3, 

chapter 28, article 6 (commencing with section 3867).

45. The State Water Board shall provide notice and an opportunity to be heard in 

exercising its authority to add to or modify the conditions of this WQC.

46. Activities associated with operation and maintenance of the Project that 

threaten or potentially threaten water quality shall be subject to further review by 

the Deputy Director and Executive Officer.

47. Nothing in this certification shall be construed as State Water Board approval 

of the validity of any water rights, including pre-1914 claims. The State Water 

Board has separate authority under the Water Code to investigate and take 

enforcement action if necessary to prevent any unauthorized or threatened 

unauthorized diversions of water.

48. This WQC is not intended and shall not be construed to apply to any activity 

involving a hydroelectric facility and requiring a FERC license or an amendment 

to a FERC license unless the pertinent certification application was filed pursuant 

to California Code of Regulations, title 23, section 3855, subdivision (b) and that 

application specifically identified that a FERC license or amendment to a FERC 

license for a hydroelectric facility was being sought.

49. This WQC is conditioned upon total payment of any fee required under 

California Code of Regulations, title 26, division 3 chapter 28.
APPENDIX F

Preliminary Water Quality Certification Conditions for the 

Merced Falls Hydroelectric Project
This page intentionally left blank.
F-1

PRELIMINARY CONDITIONS FOR THE MERCED 

FALLS HYDROELECTRIC PROJECT

In accordance with Item 2 under the Post-Application Filing Activities under

the Integrated Licensing Process section of the memorandum of understanding

executed between the Federal Energy Regulatory Commission (FERC) and the State

Water Resources Control Board (State Water Board) on November 19, 2013, and to

the extent that information is available, State Water Board staff is providing 

preliminary terms and conditions in response to the notice of Ready for

Environmental Analysis (REA) by FERC for the Merced Falls Hydroelectric Project 

(Project), FERC Project No. 2467.

1. General Preliminary Condition

This condition applies to daft Conditions 2-9 below, as well as all plans or

changes to plans required by the water quality certification or related to water

quality shall be developed in consultation with relevant state and federal

agencies. Pacific Gas and Electric Company (Licensee) shall provide the

relevant state and federal agencies with a minimum 30-day comment period on

the plans and final report, if applicable. The plans and final reports shall 

include documentation of consultation with the relevant state and federal 

agencies, all comments made by the relevant state and federal agencies, and a

description of how the final plan and/or final report incorporates or addresses 

the comments made by the relevant state and federal agencies. Licensee shall

file the final report and final plan with the Deputy

Director for the Division of Water Rights (Deputy Director) for revision or 

approval. Upon Deputy Director approval, the Licensee shall fill the approved 

final plan and approved final report with the FERC.

2. Pesticide Use Plan

Within six months of license issuance, the licensee shall submit the Pesticide Use 

Plan to the Deputy Director. The Licensee shall create the Pesticide Use Plan in 

consultation with the Bureau of Land Management, California Department of Fish 

and Wildlife (CDFW), US Fish and Wildlife Service (USFWS), National Marine 

Fisheries Agency (NMFS), and the State Water Board. The Pesticide Use Plan 

shall include provisions that restrict application of pesticides (as defined by the 

Water Quality Control Plan for the Sacramento River and San Joaquin River 

Basins (Basin Plan)) so pesticides will not reach Endangered Species Act (ESA), 

California Endangered Species Act (CESA) listed species or their habitat in or 

downstream of the Project area. Pesticides shall only be applied by an individual 

with a current and valid Qualified Applicator License issued by the California 

Department of Pesticide Regulation or under the direct visual supervision of an 

individual with a current and valid Qualified Applicator License issued by the 

California Department of Pesticide Regulation.
F-2

3. Gravel Augmentation Plan

Within one year of license issuance, the Licensee shall submit the Gravel 

Augmentation Plan to the Deputy Director. The Licensee shall create the Gravel 

Augmentation Plan in consultation with CDFW, USFWS, and NMFS. The amount 

of gravel augmented shall be consistent with annual gravel amount trapped behind 

Merced Falls Dam.

4. Fish Passage Plan

If fish passage resumes at Crocker-Huffman Diversion Dam, the Licensee shall 

consult with NMFS, CDFW, and USFWS. If during the consultation it is 

recommended that passage resume at Merced Falls the licensee shall submit a Fish 

Passage Plan to the Deputy Director. The Licensee shall create the Fish Passage 

Plan in consultation with the NMFS, CDFW, and USFWS.

5. Eagle Monitoring and Conservation Plan

Within one year of license issuance, the Licensee shall submit the Bald and 

Golden Eagle Monitoring Plan (Eagle Plan) to the Deputy Director. The Licensee 

shall create the Eagle Plan in consultation with USFWS, CDFW, and BLM. The 

Eagle Plan shall include monitoring and protective measures when nesting is 

identified. This is necessary to protect the wildlife beneficial use.

The Eagle Plan shall:

A. Be consistent with the most current USFWS National Bald Eagle

Management Guidelines;

B. Include a statement of the goals and objectives;

C. Include a description of the proposed monitoring protocol(s);

D. Include specific, measureable criteria that will be used in combination with 

monitoring data and the comprehensive list of drivers to objectively evaluate if 

the goals and objectives of the Eagle Plan are being met or the Project may be 

adversely affecting eagles and/or eagle nests;

E. Include a detailed monitoring and reporting schedule;

F. Include a plan for the development of corrective measures and a timetable for 

action in cases when the Eagle Plan's goals and objectives are not being 

achieved or data indicate the Project may be impacting eagles and/or eagle 

nests; and

At a minimum monitoring shall include:

G. One breeding and one wintering survey every five years after license issuance;

H. Monitoring surveys within 30 days prior to any activity in the Project area 

listed or similar to the listed activities in the USFWS National Bald Eagle 

Management Guidelines; and
F-3

I. Include documentation of any eagle or eagle nests discovered during 

monitoring as well as any incidental eagle or eagle nest observations.

Within 60 days of the conclusion of the monitoring cycle, the Licensee shall 

submit the results of the monitoring data with a description of location of eagle(s) 

or nest(s), date(s) of discovery, timeframe(s) of monitoring and protective measure 

implementation. Monitoring reports shall also include recommendations for more 

frequent monitoring based on increased use of the Project area by eagles, changes 

in Project operation and management activities, information derived from other 

resource studies or the state or federal resource agencies, and updates to be 

consistent with updates to the USFWS National Bald Eagle Management 

Guidelines.

If monitoring or incidental (other) reports confirm the presence of eagle(s) or eagle 

nest(s) in the Project area, protective measures must be implement prior to any 

Project-associated activity.

6. Valley Elderberry Longhorn Beetle Monitoring and Conservation Plan

Within 6 months of license issuance, the Licensee shall submit the Valley 

Elderberry Longhorn Beetle Monitoring and Conservation Plan (VELB Plan) to 

the Deputy Director. The Licensee shall create the VELB Plan in consultation with 

USFWS, CDFW, and BLM. The VELB Plan shall include monitoring of Valley 

Elderberry Longhorn Beatles and their habitat in the Project area, and associated 

tributaries. Monitoring shall be conducted prior to construction and every 5 years 

after license issuance.

The VELB Plan, shall at a minimum include: 

A. A statement of goals and objectives;

B. A description of proposed monitoring protocols;

C. A comprehensive description of factors that may adversely affect VELB. This

description shall also identify whether the factors are associated with the 

Project's operation.

D. A detailed monitoring and reporting schedule;

E. Plan for corrective measures and a timetable for implementation if data 

indicate that the Project may be impacting VELB or their habitat; and

F. Protective measures.

7. Review of Endangered Species Act Lists and Special-Status Species Lists, and

Assessment of New Species in the Project Area

The Licensee shall consult with the USFWS, CDFG, and NMFS within 6 months

of license issuance and at the Pentennial Meeting (see below) for the term of the 

license and any extension. At the meetings, participants will review the current list 

of threatened and endangered species and special-status plant and wildlife species 
F-4

that may be adversely impacted by the Project. When a species is added to one or 

more of the lists, the Licensee, in consultation with the CDFW, USFWS, NMFS, 

and the State Water Board shall determine if the species may be adversely affected 

by the Project. If it is determined that the species may be adversely affected by the 

Project, the Licensee shall develop and implement a new species specific study 

plan. The study plan shall be created in consultation with the appropriate state or 

federal resource agencies to assess the effects of the Project on the species.

Each species specific study plans, shall at a minimum include: 

A. A statement of goals and objectives;

B. A description of proposed monitoring protocols;

C. A comprehensive description of factors that may adversely affect VELB. This 

description shall also identify whether the factors are associated with the 

Project's operation.

D. A detailed monitoring and reporting schedule;

E. A Plan for corrective measures and a timetable for implementation if data 

indicate that the Project may be impacting the newly listed specific species or 

their habitat; and

F. Protective measures.

The Licensee shall implement and prepare a report on the study including 

objectives, methods, results, recommended measures where appropriate, and a 

schedule of implementation.

8. Pentennial Meeting with Resource Agencies

Beginning one year after license issuance, the Licensee shall hold a Pentennial 

Meeting with the resource agencies. Resource agencies include but are not limited 

to State Water Board, USFWS, CDFG, and NMFS. The date of the Annual 

Consultation shall be mutually agreed to by the Licensee, State Water Board, 

USFWS, CDFG, and NMFS. The meeting shall be open to the public and the 

Licensee shall also provide notice to tribes and interested parties.

The Licensee shall provide 1) an update of all a monitoring and data required by 

the new license and water quality certification; and 2) a map that clearly depicts 

locations that pesticides were applied in the previous five year cycle, CESA and 

ESA listed species, and topography.

A record of the meeting shall be kept by Licensee and shall include any 

recommendations made by State Water Board, USFWS, CDFG, and NMFS for the 

protection of resources effected by the Project. Licensee shall include a description 

of how the Licensee incorporated recommendations made by State Water Board, 

USFWS, CDFG, and NMFS at the meeting.
F-5

9. Frog Monitoring Plan

The Licensee shall monitor and identify the locations of California Red-legged 

Frog (CRLF), Foothill Yellow-legged Frog (FYLF), and Western Spadefoot. 

Within one year of license issuance, the Licensee shall file a Frog Monitoring Plan 

(Frog Plan) with the Deputy Director for approval. The Licensee shall create the 

Frog Plan in consultation with BLM, USFWS, and CDFW. The Frog Plan shall 

include monitoring CRLF, YLF, and Western Spadefoot egg masses, tadpoles and 

adults in the Project area and associated tributaries influenced by the Project. 

Monitoring of egg masses, tadpoles, and adults shall be required every five years 

from license issuance.

The Frog Plan shall include, at a minimum: 

A. A statement of goals and objectives;

B. A description of proposed monitoring protocols;

C. A comprehensive description of factors that may adversely affect CRLF, FYLF 

and Western Spadefoot. This description shall also identify whether the factors 

are associated with the Project's operation.

D. Monitoring water temperature where eggs and tadpoles are found; 

E. A detailed monitoring and reporting schedule;

F. Protective measures; and

G. A Plan for corrective measures and a timetable for implementation if data 

indicate that the Project may be impacting CRLF, FYLF, or Western 

Spadefoot.

The following conditions also apply to this Project in order to protect water

quality and beneficial uses over the term of the Project's license and any annual

extensions.

10. Control measures for erosion, excessive sedimentation and turbidity shall be 

implemented and in place at the commencement of and throughout any ground 

clearing activities, excavation, or any other Project activities that could result in 

erosion or sediment discharges to surface waters. Erosion control blankets, liners 

with berms, and/or other erosion control measures shall be used for any stockpile 

of excavated material to control runoff resulting from precipitation, and prevent 

material from contacting or entering surface waters.

11. Waters shall be free of changes in turbidity (due to Project activities) that 

cause nuisance or adversely affect beneficial uses. Increases in turbidity 

attributable to Project controllable water quality factors shall not exceed the 

following limits as defined in the Central Valley Basin Plan:

a. Where natural turbidity is less than 1 nephelometric turbidity unit (NTU), 

controllable factors shall not cause downstream turbidity to exceed 2 NTUs.
F-6

b. Where natural turbidity is between 1 and 5 NTUs, increases in turbidity shall 

not exceed 1 NTU.

c. Where natural turbidity is between 5 and 50 NTUs, increases in turbidity shall 

not exceed 20 percent.

d. Where natural turbidity is between 50 and 100 NTUs, increases in turbidity 

shall not exceed 10 NTUs.

e. Where natural turbidity is greater than 100 NTUs, increases in turbidity shall 

not exceed 10 percent.

12. All imported riprap, rocks, and gravels used for construction within or adjacent 

to any watercourses shall be pre-washed. Wash water generated on-site shall not 

contact or enter surface waters. Wash water shall be contained and disposed of in 

compliance with state and local laws, ordinances, and regulations.

13. Construction material, debris, spoils, soil, silt, sand, bark, slash, sawdust, 

rubbish, steel, or other inorganic, organic, or earthen material, and any other 

substances from any Project- related activity shall be prevented from entering 

surface waters. All construction debris and trash shall be contained and regularly 

removed from the work area to the staging area during construction activities. 

Upon completion, all Project-generated debris, building materials, excess material, 

waste, and trash shall be removed from all the Project sites for disposal at an 

authorized landfill or other disposal site in compliance with State and local laws, 

ordinances, and regulations.

14. No unset cement, concrete, grout, damaged concrete, concrete spoils, or wash 

water used to clean concrete surfaces shall contact or enter surface waters. Any 

area containing wet concrete shall be completely bermed and isolated. The berm 

shall be constructed of sandbags or soil and shall be lined with plastic to prevent 

seepage. No leachate from truck or grout mixer cleaning stations shall percolate 

into Project area soils. Cleaning of concrete trucks or grout mixers shall be 

performed in such a manner that wash water and associated debris is captured, 

contained and disposed of in compliance with State and local laws, ordinances and 

regulations. Washout areas shall be of sufficient size to completely contain all 

liquid and waste concrete or grout generated during washout procedures. Hardened 

concrete or grout shall be disposed at an authorized landfill, in compliance with 

State and local laws, ordinances and regulations.

15. All equipment must be washed prior to transport to the Project site and must be 

free of sediment, debris, and foreign matter. Any equipment used in direct contact 

with surface water shall be steam cleaned prior to use. All equipment using gas, 

oil, hydraulic fluid, or other petroleum products shall be inspected for leaks prior 

to use and shall be monitored for leakage. Stationary equipment (e.g., motors, 

pumps, generator, etc.) shall be positioned over drip pans or other types of 

containment. Spill and containment equipment (e.g., oil spill booms, sorbent pads, 
F-7

etc.) shall be maintained onsite at all locations where such equipment is used or 

staged.

16. Onsite containment for storage of chemicals classified as hazardous shall be 

away from watercourses and include secondary containment and appropriate 

management as specified in California Code of Regulations, title 27, section 

20320.

17. Unless otherwise specified in this WQC or at the request of the Deputy 

Director, data and/or reports must be submitted electronically in a format accepted 

by the State Water Board to facilitate the incorporation of this information into 

public reports and the State Water Board's water quality database systems in 

compliance with California Water Code section 13167.

18. The State Water Board's approval authority includes the authority to withhold 

approval or to require modification of a proposal or plan prior to approval. The 

State Water Board may take enforcement action if the Licensee fails to provide or 

implement a required plan in a timely manner.

19. The State Water Board reserves the authority to add to or modify the 

conditions of this WQC to incorporate load allocations developed in a total 

maximum daily load developed by the State Water Board or the Central Valley 

Water Board.

20. The State Water Board reserves the authority to add to or modify the 

conditions of this WQC: (1) if monitoring results indicate that continued operation 

of the Project could violate water quality objectives or impair the beneficial uses 

of the Merced River or tributaries to the Merced River; (2) to coordinate the 

operations of this Project and other hydrologically connected water development 

projects, where coordination of operations is reasonably necessary to achieve 

water quality standards or protect beneficial uses of water; or (3) to implement any 

new or revised water quality standards and implementation plans adopted or 

approved pursuant to section 303 of the CWA

21. Future changes in climate projected to occur during the license term may 

significantly alter the baseline assumptions used to develop the conditions of this 

certification. The State Water Board reserves authority to add to or modify the 

conditions in this certification to require additional monitoring and/or other 

measures, as needed, to verify that Project operations meet water quality 

objectives and protect the beneficial uses assigned to the Project-affected stream 

reaches.

22. The Licensee shall comply with all applicable requirements of the SR/SJR 

Basin Plan. Licensee must notify the Deputy Director and Executive Officer 

within 24 hours of any unauthorized discharge to surface waters.

23. Notwithstanding any more specific conditions in this WQC, the Project shall 

be operated in a manner consistent with all water quality standards and 
F-8

implementation plans adopted or approved pursuant to section 303 of the CWA.

The Licensee must take all reasonable measures to protect the beneficial uses of 

waters of the Merced River and tributaries to the Merced River.

24. This WQC does not authorize any act which results in the taking of a 

threatened, endangered or candidate species or any act, which is now prohibited, 

or becomes prohibited in the future, under either the California ESA (Fish & Game 

Code §§ 2050 2097) or the federal ESA (16 U.S.C. §§ 1531 - 1544). If a "take" 

will result from any act authorized under this WQC or water rights held by the 

Licensee, the Licensee must obtain authorization for the take prior to any 

construction or operation of the portion of the Project that may result in a take. 

The Licensee is responsible for meeting all requirements of the applicable ESAs 

for the Project authorized under this WQC.

25. In the event of any violation or threatened violation of the conditions of this 

WQC, the violation or threatened violation is subject to all remedies, penalties, 

processes, or sanctions as provided for under applicable state or federal law. For 

the purposes of section 401(d) of the CWA, the applicability of any state law 

authorizing remedies, penalties, process, or sanctions for the violation or 

threatened violation constitutes a limitation necessary to ensure compliance with 

the water quality standards and other pertinent requirements incorporated into this 

WQC.

26. In response to a suspected violation of any condition of this WQC, the Deputy 

Director or the Executive Officer may require the holder of any federal permit or 

license subject to this WQC to furnish, under penalty of perjury, any technical or 

monitoring reports the Deputy Director or the Executive Officer deems 

appropriate, provided that the burden, including costs, of the reports shall bear a 

reasonable relationship to the need for the reports and the benefits to be obtained 

from the reports. (Wat. Code, §§ 1051, 13165, 13267 & 13383). The State Water 

Board may add to or modify the conditions of this WQC as appropriate to ensure 

compliance.

27. No construction shall commence until all necessary federal, state, and local 

approvals are obtained.

28. Any requirement in this WQC that refers to an agency whose authorities and 

responsibilities are transferred to or subsumed by another state or federal agency 

will apply equally to the successor agency.

29. The Licensee must submit any change to the Project, including changes in 

Project operation, technology, upgrades, or monitoring, that could have a 

significant or material effect on the findings, conclusions, or conditions of this 

WQC, to the State Water Board for prior review and written approval. The State 

Water Board shall determine significance and may require consultation with state 

or federal agencies. If the State Water Board is not notified of a potentially 
F-9

significant change to the Project, it will be considered a violation of this WQC. If 

such a change would also require submission to FERC, the change must first be 

submitted and approved by the State Water Board, unless otherwise noted in this 

certification.

30. The Deputy Director and the Executive Officer shall be notified one week 

prior to the commencement of ground disturbing activities. Upon request, a 

construction schedule shall be provided to agency staff in order for staff to be 

present onsite to answer any public inquiries during construction and to document 

compliance with this WQC. The Licensee must provide State Water Board and 

Central Valley Water Board staff reasonable access to Project sites to document 

compliance with this WQC.

31. This WQC is subject to modification or revocation upon administrative or 

judicial review, including review and amendment pursuant to California Water 

Code section 13330 and California Code of Regulations, title 23, division 3, 

chapter 28, article 6 (commencing with section 3867).

32. The State Water Board shall provide notice and an opportunity to be heard in 

exercising its authority to add to or modify the conditions of this WQC.

33. Activities associated with operation and maintenance of the Project that 

threaten or potentially threaten water quality shall be subject to further review by 

the Deputy Director and Executive Officer.

34. Nothing in this certification shall be construed as State Water Board approval 

of the validity of any water rights, including pre-1914 claims. The State Water 

Board has separate authority under the Water Code to investigate and take 

enforcement action if necessary to prevent any unauthorized or threatened 

unauthorized diversions of water.

35. This WQC is not intended and shall not be construed to apply to any activity 

involving a hydroelectric facility and requiring a FERC license or an amendment 

to a FERC license unless the pertinent certification application was filed pursuant 

to California Code of Regulations, title 23, section 3855, subdivision (b) and that 

application specifically identified that a FERC license or amendment to a FERC 

license for a hydroelectric facility was being sought.

36. This WQC is conditioned upon total payment of any fee required under 

California Code of Regulations, title 23, division 3, chapter 28.
F-10

This page intentionally left blank.