BIOLOGICAL ASSESSMENT OF THE KLAMATH PROJECT’S CONTINUING OPERATIONS

ON SOUTHERN OREGON/NORTHERN CALIFORNIA ESU COHO SALMON AND

CRITICAL HABITAT FOR SOUTHERN OREGON/NORTHERN CALIFORNIA ESU COHO

SALMON

U.S. Bureau of Reclamation

Mid-Pacific Region

Klamath Area Office

Klamath Falls, Oregon

January 22, 2001
1

TABLE OF CONTENTS

INTRODUCTION .............................................................. 2

PROJECT DESCRIPTION ....................................................... 3

ENDANGERED SPECIES ACT ................................................. 14

PROPOSED ACTION ......................................................... 15

COHO SALMON GENERAL INFORMATION ..................................... 19

EFFECTS OF KLAMATH PROJECT ON COHO SALMON IN THE KLAMATH RIVER ... 23

CUMULATIVE EFFECTS ...................................................... 41

DETERMINATION OF EFFECTS ............................................... 45

LITERATURE CITED ......................................................... 47

PERSONAL COMMUNICATIONS ............................................... 52
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1.0 INTRODUCTION

The Bureau of Reclamation (Reclamation) is the responsible Federal agency for operation of the

Klamath Project (Project). Operation of the Project has been the subject of numerous previous

consultations with the U.S. Fish and Wildlife Service (Service) and one with the National Marine

Fisheries Service (NMFS) under Section 7 of the Endangered Species Act (ESA). Severe drought

conditions in 1992 and 1994 and resultant associated shortages in project water supplies coupled

with the 1997 listing of the southern Oregon/northern California (SONCC) coho salmon,

Oncorhynchus kisutch, as threatened in the Klamath River downstream from the Project led to a

review of Reclamation’s operations. This biological assessment (BA) describes the effects on

federally-listed species (i.e., coho salmon) and its designated critical habitat from on-going

operation of the project based on historic operations, as described in this BA. The biological

opinion (BO) addressing this BA and any subsequent BA amendments will be among the

information that will inform the development of alternatives of the long-term operations plan and

environmental impact statement (EIS). Reclamation is developing a long-term operations plan and

EIS for the Project. The preferred alternative for implementation from the long-term operations

plan would be the subject of a separate future ESA consultation.

This BA describes the needs of anadromous fish with emphasis on SONCC coho salmon. It was 

developed using the best available scientific and commercial information on anadromous fish in

the Klamath River. 

Coho salmon were listed as threatened on June 6, 1997 (NMFS 1997). The NMFS published a

final rule designating critical habitat for SONCC coho salmon in May, 1999 (NMFS 1999a). 

Designated critical habitat for SONCC coho salmon encompasses accessible reaches of all rivers

(including estuarine areas and tributaries) between the Mattole River in California and the Elk

River in Oregon. Critical habitat includes all waterways, substrate, and adjacent riparian zones

below longstanding, naturally impassable barriers. The areas upstream from Iron Gate Dam (IGD)

(river mile 190) were not proposed critical habitat because areas downstream were considered

sufficient for the conservation of the species. 

Reclamation has not evaluated whether the action that is the subject of this BA is consistent with

its trust responsibility to Klamath Basin Indian Tribes. There are several important scientific

reports and analyses (e.g., Phase II flow study) currently not available to Reclamation concerning

threatened coho salmon, their habitat, and water quality as it relates to appropriate river flows that

may be necessary to operate the Project consistent with the trust responsibility to Klamath Basin

Indian Tribes. When this additional information becomes available, Reclamation intends to

consider it during the development of the Project operations plans and include it in subsequent

consultations with NMFS, as appropriate.
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2.0 KLAMATH PROJECT DESCRIPTION

2.1 General Operations

The Project develops a water supply used for irrigation of approximately 220,000 acres in three

counties in south-central Oregon and northeastern California. The location of the Project is shown

on Figure 1. The Project delivers water primarily from Upper Klamath Lake in the headwaters of

the Klamath River Basin and Gerber and Clear Lake Reservoirs in the Lost River watershed. A

detailed description of Project operations was included in the 1992 BA for Long-Term Operations

of the Klamath Project (Reclamation 1992) and the report describing historic project operation

(Reclamation 2000a).

Figure 1. Klamath Project–location map

2.2 Project Authorities and Institutional Restraints

There are authorities, responsibilities and obligations that affect or influence Project operations. 

These include:

1) Project construction was authorized by the Secretary of the Interior on May 15, 1905, in

accordance with the Reclamation Act of 1902. The Act of February 9, 1905 provides; “The
4

Secretary of the Interior is hereby authorized in carrying out any irrigation project that

may be undertaken by him under the terms and conditions of the national reclamation act

and which may involve the changing of the levels of Lower or Little Klamath Lake, Tule or

Rhett Lake, and Goose Lake, or any river or other body of water connected therewith, in

the States of Oregon and California, to raise or lower the level of said lakes as may be

necessary...”

2) The Klamath River Compact of 1957 entered into between the states of Oregon and

California and approved by the U.S. Congress which established goals and objectives for the

development and management of water resources of the Klamath River Basin. 

3) FERC license, Project No. 2082, establishes terms and conditions for operation of the

Eastside and Westside Powerplants at Link River Dam, J.C. Boyle, Copco No. 1 and No. 2,

and Iron Gate hydroelectric projects and Keno Dam, all of which are operated by PacifiCorp

in accordance with its FERC license. This license sets certain minimum flows for the

Klamath River at IGD (Table 1). Minimum flows, however, are subject to water availability

and senior water rights. Pursuant to a 1956 contract with Reclamation, PacifiCorp operates

Link River Dam and its appurtenant power generation facilities. Reclamation and

PacifiCorp entered into a Letter Agreement on June 5, 1997, to clarify for FERC that

PacifiCorp was operating Link River Dam pursuant to Reclamation authority under the 1956

contract, because the 1997 Klamath Project operations plan required Klamath River flows

that were both greater and less than those included in PacifiCorp's FERC license. The

Agreement has been extended each year to include that year’s operation. 

Table 1. FERC instantaneous minimum flows at Iron Gate Dam.

Month Flow (cfs) Month Flow (cfs) Month Flow (cfs)

April 1,300 August 1,000 December 1,300

May 1,000 September 1,300 January 1,300

June 710 October 1,300 February 1,300

July 710 November 1,300 March 1,300

4) Endangered Species Act - Project operations affect four threatened and endangered species

including the Lost River and shortnose sucker, SONCC coho salmon and bald eagle. In 1992

and 1994, Service issued BOs on the effects of the Project on the endangered suckers and

bald eagles. The Service provided "reasonable and prudent alternatives" (RPAs) regarding

water elevations in project reservoirs that would allow Project operation to continue without

jeopardy to the listed species. A 1996 ESA consultation was on PacifiCorp and New Earth

activities, as permitted by Reclamation (Service 1996a). 

5) The United States has a trust responsibility to protect tribal trust resources. In general, the

trust responsibility requires the United States to protect tribal fishing, gathering, hunting, and

water rights, which are held in trust for the benefit of the tribes. Reclamation is obligated to
5

ensure that Project operations not interfere with the tribes’ senior water rights. With respect

to the tribes’ fishing rights, Reclamation must, pursuant to its trust responsibility and

consistent with its other legal obligations, prevent activities under its control that would

adversely affect those rights, even though those activities take place off reservation. Fishery

and other resources in the Klamath River and Upper Klamath Lake provide religious,

cultural, subsistence, and commercial support values for the Klamath Basin Indian tribes. 

The Klamath Basin Indian tribes include the Klamath, Hoopa Valley, Karuk, and Yurok

Tribes.

6) Reclamation has contractual obligations to Project water users to provide water primarily

for domestic and irrigation uses. The contracts for the majority of the Project area define

this obligation as the amount of water necessary to meet the reasonable beneficial use of

water for irrigation. Approximately 220,000 acres of agricultural lands are served by the

Klamath Project.

7) Refuge Water Supplies - Four national wildlife refuges lie adjacent to or within Project

boundaries--Lower Klamath, Tule Lake, Clear Lake, and Upper Klamath Lake National

Wildlife Refuges. The refuges either receive water from, or are associated with Project

facilities.

2.3 KPOPSIM Model and Project Operation

Reclamation developed a water accounting spreadsheet model (KPOPSIM) that simulates project

operations to help evaluate the impacts of varying water deliveries to overall project operations. 

It defines the available water supply including monthly runoff into Upper Klamath Lake and water

demands at various locations. In addition, estimates of flow accretions downstream of project

facilities have been developed. Criteria for operations, including administrative, legislative,

legal, or contractual requirements, are incorporated into the model. Using the model, monthly

estimates of water deliveries to the various users, reservoir releases, instream flows at specific

locations, reservoir storage, Upper Klamath Lake levels and pumping quantities can be

determined. The model allows alternative operation scenarios to be analyzed with key operations

indicators used to determine the ability of the project to meet various water users’ demands. 

Detailed description of the model components, inputs, and assumptions are found in CH2M Hill

(1997). The model has been presented for preliminary review and comment, and will undergo

further review and refinement. The model is based on 37 years (1961 through 1997) of

hydrological record, and uses expected comparable preceding year types to predict outcomes. 
6

2.4 Project History and Operation

Project facilities, contracts, water rights and operation are described in the 1992 BA (Reclamation

1992) and the report on historic operation (Reclamation 2000a). They are also described in the

1995 and 1997 Regional Solicitor’s memorandums.

Table 2 describes historic operation of the project data regarding Klamath River flows from 1961

through 1997. This period encompasses the time when existing project features/facilities have

been in operation and it is the period of hydrological and project operation records incorporated

into the water accounting spreadsheet model (KPOPSIM) for the Project.

Table 2. Historic Iron Gate Dam flows (1961 through 1997-- values in cfs).

19 Above Average Water Years 11 Below Average Water Years

Time Step Maximum Minimum Average St. Dev. Maximum Minimum Average St. Dev.

Oct 3353 1329 1912 586 2511 1308 1592 345

Nov 5254 1337 2547 1071 2986 1324 1999 621

Dec 6735 1387 2987 1213 6653 1435 2835 1507

Jan 9553 1127 3249 1785 9489 1334 3166 2337

Feb 9150 910 4143 2244 5656 1546 2532 1156

Mar 1-15 12447 1953 4864 2851 5017 1439 2501 1006

Mar 16-31 9219 2101 5268 2008 3682 1748 2391 591

Apr 1-15 9254 1781 4805 1906 3067 1455 2009 587

Apr 16-30 7205 1629 3860 1179 2493 1305 1701 426

May 1-15 5005 1730 3383 1088 2083 1010 1351 372

May 16-31 6247 1026 2761 1329 1714 1003 1188 228

Jun 1-15 4495 760 1764 1150 1480 728 912 230

Jun 16-30 2084 742 1031 365 1295 696 806 163

Jul 1-15 2194 705 870 327 940 709 758 69

Jul 16-31 1122 680 772 107 1023 682 784 94

Aug 1208 1011 1049 46 1094 701 995 104

Sep 2052 1035 1457 206 1428 725 1272 184
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Table 2. Continued

5 Dry Water Years 2 Critical Dry Water Years

Time Step Maximum Minimum Average St. Dev. Maximum Minimum Average St. Dev.

Oct 1382 852 1094 220 937 904 920 16

Nov 1390 873 1218 189 915 909 912 3

Dec 3903 889 2290 1305 944 914 929 15

Jan 4348 888 2588 1307 1191 1011 1101 90

Feb 2217 747 1554 505 730 525 627 103

Mar 1-15 2790 725 1683 817 712 501 607 106

Mar 16-31 2148 724 1464 545 572 521 547 26

Apr 1-15 1767 728 1183 381 843 569 706 137

Apr 16-30 1325 754 1039 241 636 574 605 31

May 1-15 1025 761 968 104 741 525 633 108

May 16-31 1039 924 996 41 714 501 608 106

Jun 1-15 931 712 782 77 706 476 591 115

Jun 16-30 735 612 700 45 702 536 619 83

Jul 1-15 739 547 669 76 572 429 501 71

Jul 16-31 742 542 678 75 575 427 501 74

Aug 1033 647 824 152 636 398 517 119

Sep 1048 749 953 112 906 538 722 184

Historic Project operation has been influenced by events and actions such as: (1) varying hydrological conditions in the watershed

from year to year; (2) changes in the Klamath River watershed and lands adjacent to Upper Klamath Lake; (3) changes in

agricultural cropping patterns; (4) changes in national wildlife refuge operations; (5) previous consultations under Section 7(a)(2) of

the ESA; (6) increased scientific understanding of fish habitat needs has led to a better understanding of trust responsibilities for
1

 Due to the relatively small sample size, the same delineation between dry and critical is

achieved by using the 5th percentile as well as the 3rd percentile.

8

Klamath Basin Indian tribes, both upstream and downstream of the project; and (7) its obligations

and responsibilities described in the July 25, 1995 and January 9, 1997 Regional Solicitor’s

memorandum.

2.5 Water Year Type Description and Development

"Water Year Type" refers to the type of water year predicted based upon hydrologic conditions

that vary from year to year. These conditions determine the volume and timing of water available

for Project use. Annual operation plans are developed in response to the water year type. 

Annually, water year types are determined on April 1 based on Natural Resource Conservation

Service (NRCS) forecasts, and revised monthly thereafter based on these forecasts. 

Thirty-seven years (1961-1997) of historic April through September net inflow data to Upper

Klamath Lake (using 1996 bathymetric data) were used in statistical analyses that shaped the

definition of water year types. The net inflow data was found to have a normal distribution with

an arithmetic mean (average) of 500,400 acre-feet (af) and a standard deviation of 187,600 af. 

This suggests that approximately 68% of the water year types have an inflow that is within the

range of 500,400 +/- 187,600 af. The "above average" water year type is defined as any water

year with an April-September net inflow of over 500,400 af. The average inflow, less one

standard deviation, equals 312,800 af. A "below average" water year type is defined as having an

inflow between 500,000 af and 312,800 af. 

Subtracting the standard deviation again from 312,800 results in a value lower than the driest year

on record, so some other methodology was needed to determine the delineation between "dry" and

"critical" water year types. Percentile ranking of the net inflow data show that the third percentile

falls at 185,000 af, and this value was used for the dry water year indicator. A "critical dry"

water year type is defined as having an inflow less than 185,000 af1. 

In summary, the net inflows for the four water year types (April through September) are: above

average >500,400 af; below average 312,800-500,400 af; dry 185,000-312,800 af; and critical

<185,000 af. 

2.6 Project Operation Description

Since 1995, Reclamation has operated the Klamath Project according to an annual operations plan. 

Each of these years were above average water year conditions. The most recent annual operations

plan is dated April 26, 2000 and covers the period of April 1, 2000 through March 31, 2001. The

annual operation plans have been developed to assist Reclamation in operating the Klamath

Project consistent with its obligations and responsibilities, given varying annual hydrological

conditions. The relationship between forecast inflow for plan development and actual inflow in

September can be illustrated with the 2000 operations. Forecasted inflow in April was 397,000
2

 The FERC minimum flow is an instantaneous value; when operating to meet an

instantaneous value, the average flow is generally 20 to 50 cfs above the minimum value.

9

ac ft (Reclamation 2000b). However, the April to September 2000 inflow to upper Klamath Lake

was 508,400 ac ft.

From 1961 through 1994, prior to increased scientific understanding of fish habitat requirements,

Project operation decisions for flows downstream from IGD were made in coordination with

PacifiCorp with primary consideration for current inflow, projected runoff, and projected

irrigation and refuge needs. Reclamation generally deferred to PacifiCorp’s FERC license flow

schedule requirements when sufficient water supply was available. However, the historic flow

data contained in Table 2 illustrates that actual flows resulted more from hydrologic constraints

and deliveries for agricultural and refuge uses. The data in Table 2 also illustrate a lack of water

storage capability within the Project. 

2.6.1 October - March

Irrigation and refuge water demands from October through March were relatively nominal, and

releases from IGD were primarily the result of filling Upper Klamath Lake while maintaining

downstream flows and meeting flood control purposes. When releases exceeded the FERC

minimum of 1300 cfs during this period2, it was a result of releasing inflow to maintain flood

control elevation in Upper Klamath Lake. The difference between water year types is evident

from the historic record for this period. 

2.6.2 April - June 

April through June is a transition period encompassing the recession of snow pack runoff and the

onset of summer irrigation demand. The timing of runoff is highly dependant on weather and snow

pack conditions. Upper Klamath Lake is operated to fill in accordance to flood control criteria

and considering the projected runoff from remaining snow pack. Inflow to Upper Klamath Lake in

excess of filling and diversion needs is released at Link River Dam. Link River Dam releases and

down stream accretions constitute the flows at IGD. Typically there is a short time lapse or delay

between late winter low elevation runoff and the onset of higher elevation snow melt. This delay

has often resulted in a temporary reduction of flow at IGD. These fluctuations in flow are

dependant on weather conditions that affect snow melt. Figure 2 illustrates these conditions. 

2.6.3 July - September

Snow pack has generally melted and runoff ceased prior to this period. Inflow to Project

reservoirs is the result of springs, stream flow and occasional summer storms. During this period,

the Project draws upon reservoir storage in addition to inflow to provide irrigation for crop

production, meet refuge needs and maintain flows in the Klamath River. 
10

Figure 2. Klamath River Flows (CFS) Below Iron Gate Dam (1998-1999)

0

2000

4000

6000

8000

10000

01-Mar 31-Mar 30-Apr 30-May

Date

Discharge (cfs)

1998

1999

2.7 Klamath River Flows Below Iron Gate Dam

Table 2 contains historical data (1961 through 1997) for IGD flows computed using U.S.

Geological Survey (USGS) daily flow records for the period of operation encompassed by this

BA. This table summarizes the historical minimum, maximum and average flows for the 17 time

steps for each water year type (critical dry, dry, below average and above average). USGS data

for historical flow at IGD are provided in daily cubic feet per second (cfs). Values for average

monthly (or half-monthly) flow were developed for every time step in the period of record. These

values were then aggregated by water year type. For example, consider the "dry" water year type

and the "October" time step. Five years in the period of record are designated as “dry”. The five

average flow values for Octobers in “dry” water year types can be considered together to

calculate an overall average for Octobers in dry water year types. Among these five values is also

a lowest and highest, and these are used as the maximum and minimum values that appear in the

table. This approach was used for every time step and water year type to create Table 2. 

Figures 3a, 3b, 3c, and 3d graph the data in Table 2. The graphs have boxes whose upper and

lower bounds represent the average + 1 standard deviation and the average -1 standard deviation

respectively, and lines running up and down from the boxes which represent the magnitude of the

maximum and minimum values used to compute the average and standard deviation.

2.7.1 Above Average Water Year (See Figure 3a.)

Above average water years occurred in 19 of the 37 hydrologic years utilized for this BA

(51.3%). The minimum value for the time steps ranged from 680 cfs in the later part of July to 
11

Iron Gate Flow Statistics in Above Average Year Types

0

2000

4000

6000

8000

10000

12000

14000

Oct

NovDec

Jan

Feb

Mar 1-15

Mar 16-31

Apr 1-15

Apr 16-30

May 1-15

May 16-31

Jun 1-15

Jun 16-30

Jul 1-15

Jul 16-31

AugSep

Flow in cfs

Figure 3a. Iron Gate Flow Statistics–Above Average Water Year Types

Iron Gate Flow Statistics in Below Average Year Types

0

1000

2000

3000

4000

5000

6000

7000

8000

9000

10000

Oct

NovDec

Jan

Feb

Mar 1-15

Mar 16-31

Apr 1-15

Apr 16-30

May 1-15

May 16-31

Jun 1-15

Jun 16-30

Jul 1-15

Jul 16-31

AugSep

Flow in cfs

Figure 3b. Iron Gate Flow Statistics–Below Average Water Year Types

2,101 cfs in the later part of March. The average value for each time step ranged from 772 cfs in

the later part of July to 5,268 cfs in the later part of March.

2.7.2 Below Average Water Year (See Figure 3b.) 

Below average water years occurred in 11 of the 37 hydrologic years utilized for this BA (29.7%).

The minimum time step flow ranged from 682 cfs in the later part of July to 1748 cfs in the later part

of March. The average time step flow average ranged from 758 cfs in the later part of July to 3166

cfs in January.

2.7.3 Dry Water Year (See Figure 3c.)

Dry water years occurred in 5 of the 37 hydrologic years utilized for this BA (13.5%). The minimum

time step flow ranged from 542 cfs in the later part of July to 924 cfs in the later part of May. The

average time step flow ranged from 669 cfs in the later part of July to 2588 cfs in January. 
12

Iron Gate Flow Statistics in Dry Year Types

0

1000

2000

3000

4000

5000

Oct

NovDec

Jan

Feb

Mar 1-15

Mar 16-31

Apr 1-15

Apr 16-30

May 1-15

May 16-31

Jun 1-15

Jun 16-30

Jul 1-15

Jul 16-31

AugSep

Flow in cfs

Figure 3c. Iron Gate Flow Statistics–Dry Water Year Types

Iron Gate Flow Statistics in Critical Year Types

0

200

400

600

800

1000

1200

1400

Oct

Nov

Dec

Jan

Feb

Mar 1-15

Mar 16-31

Apr 1-15

Apr 16-30May 1-15

May 16-31

Jun 1-15

Jun 16-30

Jul 1-15

Jul 16-31

AugSep

Flow in cfs

Figure 3d. Iron Gate Flow Statistics–Critical Dry Water Year Types

2.7.4 Critical Dry Water Year (See Figure 3d.)

Critical dry water years occurred in 2 of the 37 hydrologic years utilized for this BA (5.5%). The

minimum time step flow ranged from 398 cfs in August to 1011 cfs in January. The average time step

flow ranged from 501 cfs in July to 1101 cfs in January.

2.8 Agricultural and Refuge Water Use

Water is diverted from several sources and delivered to Project facilities for agricultural crop

production and fish and wildlife use on national wildlife refuges located within the Project service

area. Table 3 summarizes the water volumes delivered to support these uses for the portion of the

Project service area served by water deliveries from Upper Klamath Lake.
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Table 3. Crop and Refuge Water Use from Upper Klamath Lake (1961 through 1999–values in

thousands of acre-feet)

19 Above Average Water Years 11 Below Average Water Years

Time Step Maximum Minimum Average Maximum Minimum Average

October 28.9 6.58 17.78 27.77 12.34 18.53

November 15.86 .49 6.78 14.25 2.28 6.81

December 17.28 .39 8.68 16.43 1.52 8.5

January 22.74 5.43 12.43 23.57 6.24 13.79

February 17.64 2.33 7.28 11.10 2.94 8.03

March 12.87 .3 4.69 10.68 1 6.07

April 52.85 5.49 21.14 52.85 21.92 36.17

May 76.70 28.95 55.15 81.83 50.55 65.49

June 103.54 45.33 81.72 102.05 73.11 86.17

July 105.38 75.33 91.35 104.55 75.37 93.25

August 87.20 47.71 74.63 88.58 36.08 71.50

September 61.45 34.63 48.09 60.95 40.15 48.76

 Table 3. Continued

5 Dry Water Years 2 Critical Dry WaterYears

Time Step Maximum Minimum Average Maximum Minimum Average

October 29.13 8.83 20.50 31.17 14.62 22.90

November 16.52 1.5 6.15 9.51 5.57 7.54

December 17.09 6.15 11.99 20.33 15.26 17.80

January 20.67 9.33 13.72 19.70 11.14 15.42

February 12.12 2.23 7.27 12.60 7.35 9.98

March 17.99 1.75 10.15 16.30 11.07 13.69

April 67.32 27.11 41.53 63.63 57.64 60.64

May 58.73 37.60 50.47 90.12 51.50 70.81

June 91.75 70.99 81.70 87.66 78.67 83.17

July 99.81 87.40 95.28 103.77 58.25 81.01

August 83.48 76.26 79.37 90.84 64.91 77.88

September 66.07 49.63 58.56 33.46 32.15 32.81
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3.0 ENDANGERED SPECIES ACT

3.1 Endangered Species Consultation History

In 1995, Reclamation conferred with the NMFS regarding effects of the 1995 Klamath Project

Operations Plan on Klamath Mountains Province steelhead (O. mykiss) which was proposed for

listing at that time. On April 7, 1995, NMFS sent Reclamation a letter of concurrence stating that the

Project’s operations for 1995 were not likely to jeopardize Klamath Mountains Province steelhead. 

The concurrence was based on: 1) an expectation that 1995 Project operations would meet the

minimum flow schedule outlined in the IGD FERC license; and 2) an understanding that proposed

operation of the Project included development and implementation of a long-term operating plan for

the Project that would fully consider the needs of anadromous fish downstream from IGD. 

Subsequent to April 7, 1995, Reclamation revised the schedule and scope of the long-term operations

plan.

Reclamation coordinated with NMFS regarding 1996 Project operations, including the downstream

flows that were implemented that year. A technical review was provided by NMFS of

Reclamation’s memoranda supporting the 1996 Klamath Project Operations Advisory. NMFS

provided similar coordination for the1997 Annual Operations Plan.

Reclamation coordinated with NMFS regarding the1998 Project operations and its consequences on

threatened coho salmon, the proposed Klamath Mountain Province steelhead and candidate species

chinook salmon (O. tshawytscha). On February 11, 1998, Reclamation requested formal consultation

on coho salmon pursuant to the ESA for the 1998 Project operations. On April 1, 1998, Reclamation

provided a BA to NMFS on coho salmon pursuant to ESA for the 1998 Project operations

(Reclamation 1998). The 1998 Project operations met or exceeded the minimum flow schedule for

the Klamath River at IGD as required by the FERC license, August and September excepted.

In March 1999, Reclamation submitted a draft Environmental Assessment (EA) on the 1999 Project

operations to NMFS. The preferred alternative in the 1999 EA was virtually identical to the Project

operations described in the 1998 BA. NMFS agreed that for the purposes of ESA Section 7

consultation, the 1998 BA adequately described proposed 1999 Project operation and potential

impact to coho salmon. NMFS delivered a draft BO to Reclamation regarding the 1999 Project

operations in July 1999 (NMFS 1999b). Reclamation provided a written supplement to the

EA/proposed action (i.e., flows higher than the 1998 Plan minimums). NMFS issued a BO on the

amended proposed action and concluded that the amended proposed action was not likely to

jeopardize SONCC coho salmon. The 1999 BO acknowledged the close operational relation

between the Project and PacifiCorp’s IGD and accordingly the incidental take statement authorized

PacifiCorp’s IGD operations pursuant to Reclamation’s 1999 Plan.

In November 1999, Reclamation provided funding to the Bureau of Indian Affairs and cooperated

with Utah State University (USU), USGS, and the Service to examine incremental changes in flow

and available total habitat (microhabitat plus macrohabitat) in the Klamath River. Dr. Thom Hardy is

with the Institute for Natural Systems Engineering (INSE) of USU and he is the principal investigator

for Phase II. Reclamation anticipates that the results of Phase II analyses will be used in future
3

 Presently, the Phase II report is scheduled to be finalized in early 2001.

15

Section 7 Consultations and for the long-term operations plan EIS. 

On January 31, 2000, USU informed Reclamation that the Phase II instream flow report would not be

completed until late 20003. However, Reclamation’s ESA coverage on coho salmon expired April 1,

2000. Reclamation sent a letter, dated September 14, 2000, to NMFS requesting an updated species

list. On September 25, 2000, NMFS provided Reclamation with a list of Federally listed species

and critical habitat that may occur downstream of IGD on the Klamath River. This BA describes the

Project’s effects on those species. This BA is intended to cover the time period from when a BO is

issued by NMFS until that BO is superceded by another consultation. 

4.0 PROPOSED ACTION

Reclamation proposes ongoing operation of the Klamath Project. A detailed description of project

operations is presented in the BA prepared in 1992 (Reclamation 1992) and the report describing

historic project operation (Reclamation 2000a). The IGD flow releases summarized in Table 4 are

the average minimum flows for each time step taken from historic operations (Table 2). Reclamation

proposes to operate the project to meet these minimum or greater flows, depending on water year

type. In addition, Reclamation will work to develop a plan of closer operational coordination and

data sharing with PacifiCorp to reduce the scope and impacts of depressed flows that occur during

the April to June period (Figure 2). For purposes of this BA, the action area is defined as the

mainstem Klamath River downstream from IGD (river mile190), in northern California.

4.1 PacifiCorp Hydrofacilities Operations

PacifiCorp operates facilities to generate hydroelectrical power at the Westside and Eastside Plants

at Link River Dam, Keno Dam, J. C. Boyle Dam, Copco No. 1 and Copco No. 2 Dams, and IGD. 

This operation is in accordance with Reclamation's annual operations plan for the Project, FERC

license requirements, and the applicable Service BO for Upper Klamath Lake levels (T. Olson,

PacifiCorp pers. comm. 1998). During the last 39 years, project operations pursuant to the contract

between Reclamation and PacifiCorp have been influenced by the FERC license minimum flow

schedule for IGD (FPC 1961). During below average and above average water years, IGD releases

usually exceeded the FERC minimums during the fall and winter while during dry years releases

occasionally dropped below the minimums particularly during the summer months. In critically dry

years (i.e., 1992 and 1994), releases were less than the FERC minimums almost every month of the

year. Between 1962 and 1992, the FERC minimum flows were violated about 30 percent of the total

number of months in this period.
16

Table 4. Proposed average minimum flows at Iron Gate Dam on the Klamath River.

Time Step Above Average Water

Years

Below Average Water

Years

Dry Water Years Critically Dry Water

Years

Oct 1329 1308 852 904

Nov 1337 1324 873 909

Dec 1387 1435 889 914

Jan 1127 1334 888 1011

Feb 910 1546 747 525

Mar 1-15 1953 1439 725 501

Mar 16-31 2101 1748 724 521

Apr 1-15 1781 1455 728 569

Apr 16-30 1629 1305 754 574

May 1-15 1730 1010 761 525

May 16-31 1026 1003 924 501

Jun 1-15 760 728 712 476

Jun 16-30 742 696 612 536

Jul 1-15 705 709 547 429

Jul 16-31 680 682 542 427

Aug 1011 701 647 398

Sep 1035 725 749 538

4.2 Klamath River Anadromous Fish Action Items

The following action items are included in the proposed Federal action that is the subject of this BA. 

These action items have been developed by Reclamation to continue ongoing data collection efforts

or incorporate ongoing activities into the proposed action. They are intended to assist recovery of the

SONCC coho salmon.

4.2.1 Mainstem Klamath River Juvenile Emigration Monitoring 

Reclamation will provide funding for a cooperative program to monitor emigrating anadromous fish

status downstream of IGD. Reclamation will assist with annual funding of the Big Bar monitoring

site. This monitoring program has been conducted since 1989 by the Service, Coastal California Fish

and Wildlife Office (CCFWO) and has been partially funded by the Klamath River Task Force (Task

Force). Temporal abundance indices for various salmonid species will be developed and used in

evaluating the effects of project operations. The objective of this project is to continue the monitoring

of juvenile chinook salmon, coho salmon, and steelhead populations emigrating in the mainstem

Klamath River. Information collected will be used to estimate annual abundance, natural and

hatchery composition, peak emigration timing, size, health, and age class of juvenile salmonids. In
17

addition, data are collected on other fish species including chum salmon, rainbow and brown trout,

American shad, green sturgeon, river and Pacific lamprey. 

4.2.2 Water Supply Initiative 

In 1996, Reclamation’s Klamath Basin Area Office (KBAO) entered into a partnership with the

Oregon Water Resources Department (OWRD), the California Department of Water Resources

(CDWR), and the Klamath River Compact Commission (KRCC) to explore options to increase water

supplies in the Klamath River Basin. The need to increase water supplies has resulted from a need to

provide water for federally-listed threatened and endangered fishes in the Klamath River and Upper

Klamath Lake and to meet the Federal trust obligation to Klamath Basin Indian tribes. These needs

have reduced the ability of Reclamation to provide water to agriculture and national wildlife refuges. 

On July 15, 1998, the Klamath Tribes and certain Project irrigation interests requested in a letter that

the Department of the Interior study certain water supply augmentation projects in the Klamath Basin

that could, if implemented, satisfy the needs of all water users and bring water supply and demand

into balance. 

Potential solutions could include actions that collectively provide operations flexibility, i.e., new

storage facilities (on stream or off stream), raising existing dams, agriculture demand management,

water import/export opportunities, operational changes, groundwater pumping, reducing

evaporation/seepage, and habitat restoration.

A final draft report was released in July 1998. It describes the options that appear feasible for

additional study, based on information currently available. The following options are being actively

investigated by KBAO. Additional studies will be conducted as funding and resources become

available.

4.2.2.1 Raise Upper Klamath Lake

Reclamation’s Technical Service Center (TSC) in Denver, under a service agreement with KBAO,

has conducted an appraisal level study of raising the maximum operating water surface of Upper

Klamath Lake by up to 2 feet (to elevation 4145.3). Two alternatives are being considered: 1)

construction of new dikes and sea walls and modification of existing dikes to contain the lake within

its current boundaries, and 2) acquisition of lands inundated by raising the lake without structural

construction or modification to contain it within current boundaries. 

The Appraisal Study Report (December 2000) estimated a cost of $125 million and $129 million for

options 1 and 2, respectively. Based on these findings, a feasibility study on raising the lake is

recommended and will be undertaken by Reclamation as part of the Klamath Basin Water Supply

Enhancement Act (P.L. 106-498).

4.2.2.2 Groundwater Investigations

While knowledge of local groundwater conditions is increasing, a comprehensive study of the

groundwater system in the Klamath Basin is needed. The ability of this resource to sustain existing
18

uses and to accommodate additional development is not well understood, and there is substantial

uncertainty about the extent to which groundwater development will impact surface water resources

throughout the basin. In FY 1998, OWRD and the USGS began a cooperative groundwater

investigation of the basin. Objectives of the study are to develop a quantitative conceptual

understanding of the system, construct numerical models that accurately simulate the system, describe

the system through reports and presentations, and use hydrologic models to help determine optimal

management alternatives. The study is scheduled for completion in FY 2005. Reclamation will

continue to support and provide funding for completion of this study.

In FY 1999, KBAO entered into a cooperative agreement with OWRD to implement a groundwater

development program in the Klamath and Lost River Basins in Oregon. The program is intended to

assess the feasibility of obtaining supplemental water supplies for the Klamath Project. An existing

well in the Shasta View Irrigation District (SVID) was pumped in the early spring of 1999 to test the

underlying aquifer. Preliminary results of the test indicate good potential for high production wells in

the area with low potential to interfere substantially with other wells. 

KBAO has entered into a cooperative agreement with CDWR to help assess the potential for

groundwater augmentation in the California portion of the Klamath and Lost River Basins. Under the

agreement in FY 1999, CDWR located existing wells, correlating them with available well

completion reports, took initial water level measurements where possible, identified data gaps, and

compiled data obtained in digital format. Beginning in the fall of 1999 (FY 2000), CDWR is

performing semiannual water level measurements on 35 of the wells over a 3-year period. The data

collected will be compiled in digital format.

4.2.2.3 Raise Gerber Dam

The TSC recently completed a cursory review of existing information to determine the feasibility of

raising the active storage capacity of Gerber Dam by 3 feet. The review indicates that raising the

dam is a viable option for increasing water storage in the Klamath Basin, although additional studies

are needed to support this determination. KBAO is developing a service agreement with the TSC to

begin an appraisal study on raising the dam. This study is expected to be completed in 2001.

4.2.2.4 Agency Lake Ranch

In 1998, Reclamation acquired the 7,123-acre Agency Lake Ranch on the west side of Agency Lake at

the north end of Upper Klamath Lake. The ranch property, comprised of former agricultural crop

lands and pasture, is being used to store additional water for Project use which would otherwise be

spilled to the Klamath River during periods of high runoff. In 2000, approximately 15,000 af of

additional water was stored on the ranch. Existing dikes surrounding the ranch could be raised to

store up to 35,000 to 40,000 acre-feet of spill water. A management plan is currently being

developed for the Ranch. 
19

5.0 COHO SALMON GENERAL INFORMATION

5.1 Identification

Coho salmon, also known as silver salmon because of their brilliant silver coloration in the ocean

phase, can be identified from other salmon by a few unique characteristics. Unlike steelhead, coho

have 13 or more anal rays (Wydoski and Whitney 1979). Coho have distinctive small irregular black

spots on their back and caudal fin much like chinook salmon. The difference in spotting between the

two species is coho have spots only on the upper lobe of the fin while chinook have spots on both

lobes (Wydoski and Whitney 1979). Coho can also be distinguished from chinook by the color of the

gums around the base of the teeth. Coho have white gums, chinook black gums (Wydoski and Whitney

1979). Juvenile coho are identified by having long anterior rays on the anal fin (Wydoski and

Whitney 1979). The first three anal rays of the fin are much longer than the other rays giving the fin a

sickle-shaped appearance. 

In describing the species, Scott and Crossman (1973) include the following morphological

characteristics of coho: vertebrae range from 61 - 69, lateral line is complete with 121 - 148 scales,

pyloric caeca vary from 45 - 114, and gill rakers are rough, widely spaced, and range from 18 - 25. 

Some of these characteristics may change if subjected to an exotic habitat (Scott and Crossman 1973).

5.2 Distribution

Historical distribution of coho above IGD is not well known. Pre-dam investigations were focused

on chinook salmon. The absence of coho sightings may be due to the earlier timing of surveys

possibly missing later migrating coho. It is believed that the historical range of coho salmon below

IGD included the mainstem Klamath River and tributaries including the Shasta and Scott rivers. 

Coho salmon still occur in the Klamath River and its tributaries (CH2M Hill 1985; Hassler et al.

1991). Between Seiad Valley and IGD, coho salmon populations are believed to occur in Bogus

Creek, Shasta River, Humbug Creek, Empire Creek, Beaver Creek, Horse Creek, and Scott River

(NMFS 1999b). Between Orleans and Seiad Valley, coho salmon populations are believed to occur

in Seiad Creek, Grider Creek, Thompson Creek, Indian Creek, Elk Creek, Clear Creek, Dillon Creek

(suspected), and Salmon River (NMFS 1999b). Finally, between Orleans and Klamath (mouth of the

river), coho salmon populations are believed to occur in Camp Creek, Red Cap Creek, Trinity River,

Turwar Creek, Blue Creek, Tectah Creek, and Pine Creek (NMFS 1999b). It is estimated that Shasta

River presently maintains approximately 38 miles of coho habitat, which is below pre-development

levels (INSE 1999). Available data suggests that existing coho salmon habitat in the Scott River now

constitutes approximately 88 miles (INSE 1999). The cumulative effects of un-screened diversions,

reduced flows, degraded spawning habitat, and high summer water temperatures have impacted

anadromous fish production within these tributaries (INSE 1999). The Yurok fisheries program and

CCFWO have collected coho salmon outmigration data for tributaries in the lower Klamath River

(CCFWO 1998). 
20

5.3 Historical Run Abundance

Coho populations within the SONCC Evolutionary Significant Unit (ESU) are substantially below

historic levels (NMFS 1995). In the California portion of the ESU, 36 percent of coho streams no

longer have spawning runs (NMFS 1995). In 1983, the Service estimated the annual spawning

escapement to the Klamath River system ranged from 15,400 to 20,000 (Service 1983, cited in Leidy

and Leidy 1984). CDFG (1994 as cited by Weitkamp et al. 1995) concluded that these estimates of

coho abundance, including hatchery stocks, could be less than 6 percent of their abundance in the

1940's and have experienced at least a 70 percent decline in numbers since the 1960's. Recent coho

returns have not been determined (Barnhart 1994). However, river and tributaries in the California

portion of this ESU were estimated to have average recent runs of 7,080 natural spawners and 17,156

hatchery returns, with 4,480 identified as “native” fish occurring in tributaries having little history of

supplementation with non-native fish (NMFS 1999b). Combining recent run-size estimates for the

California portion of this ESU with Rogue River estimates provides a rough minimum run-size

estimate for the entire ESU of about 10,000 natural fish and 20,000 hatchery fish (NMFS 1997 cited

in NMFS 1999b). 

Large hatcheries in the SONCC coho salmon ESU (e.g., Mad River, Trinity River) have released

400,000 - 600,000 coho salmon annually between 1987 and 1991 (NMFS 1999b). In addition, Cole

Rivers Hatchery and Iron Gate Hatchery (IGH) released an average of about 270,000 and 150,000

coho salmon, respectively, during this period. All coho salmon hatchery programs in the California

portion of this ESU have a history of transplants from areas outside of the SONCC coho salmon ESU. 

Although records are incomplete, the frequency and magnitude of out-of-basin-plants in this ESU

appears to be relatively low (Weitcamp et al. 1995). 

Klamath and Trinity Basin coho salmon runs are now composed largely of hatchery fish, although

there still may be wild runs remaining in some tributaries (CDFG 1994 cited in NMFS 1999b). 

Because of the predominance of hatchery stocks in the Klamath River Basin, stock transfers into the

Trinity Hatchery and IGH may have had a substantial impact on natural populations in the basin

(NMFS 1995 cited in NMFS 1999b). 

Coho returns to IGH have been recorded since 1963, and have ranged from zero fish in 1964, to

2,893 fish in 1987. In 1997, 1,872 adult coho and 302 grilse returned to IGH (M. Pisano, CDFG

pers. comm. 1998). Coho returns to the Shasta River have been noted since 1934 (M. Pisano, CDFG

pers. comm. 1995). The Shasta River data is limited since the weir is removed following the fall

chinook run in late November. Coho continue to migrate up the Shasta River into late December, thus

weir counts are incomplete. Based on these available data, Shasta River coho returns have been

variable since 1934, and show a great decrease in returns for the past seven years (M. Pisano, CDFG 

pers. comm. 1995).

The decline of California coho salmon can be attributed to the following: stream alterations brought

about by poor land-use practices, water development/diversions, the effects of periodic floods and

drought, the breakdown of genetic integrity of native stocks, introduced diseases, over harvest, and

climatic change (Brown et al. 1994). In separate petitions to NMFS, both Oregon Trout et al. (1993)

and Pacific Rivers Council et al. (1993, cited in NMFS 1995) indicate freshwater habitat destruction
21

as the primary cause for the decline in coho populations. Pacific Rivers Council et al. (1993) also

cited deteriorating ocean conditions, adverse effects of artificial propagation, intraspecific

hybridization and interspecific hybridization with chinook salmon (Pacific Rivers Council et al. 1993

cited in NMFS 1995).

Recent reviews of Klamath River coho populations have identified these as populations of special

concern; populations are low, however they are not in immediate danger of extinction (Nehlsen et al.

1991, Higgins et al. 1992, Brown et al. 1994). The observation that coho populations in the southern

Oregon/northern California area are depressed relative to past abundance, and noting the large

amount of hatchery production which occurs in Oregon, suggests natural populations are not selfsustaining (NMFS 1995). Although not in danger of extinction, these populations are likely to

become endangered if present trends continue (NMFS 1995).

5.4 Life History

Adult coho migrate into the Klamath River from mid-September through mid-January (Shaw et al.

1997, USFS 1972, cited in Leidy and Leidy 1984). Fish will hold in the estuary with upstream

movement triggered by increased flows due to the fall rains (Scott and Crossman 1973). Upstream

movement occurs during the day (Scott and Crossman 1973). Those fish destined for IGH first arrive

in early October with the greatest number of fish arriving around the first of November (FishPro

1992). Coho returns to the hatchery extend into January.

Adult coho return primarily as 3-year-old fish although some will return as 2-year-old precocious

males (jacks or grilse) (Leidy and Leidy 1984). The percent of jacks within a run can vary greatly

year to year. Coho jacks are not sterile and can actively spawn and fertilize eggs. In some rare cases

a female may return as a 2-year-old (Scott and Crossman 1973). In the Klamath system, coho

normally spawn in tributary streams from November through February (peaking in January) (Leidy

and Leidy 1984). However, coho salmon have been observed spawning in side channels, tributary

mouths and shoreline margins of the mainstem Klamath River between Independence Creek (river

mile 86) and Beaver Creek (river mile 150) (T. Shaw, Service, Service pers. comm. 1996). 

Typically all returns to the IGH are ready to spawn by the first of January (Fish Pro 1992). Coho,

like chinook salmon, die soon after spawning.

Once spawning is complete, eggs will incubate in the gravel for about seven weeks before hatching

(Scott and Crossman 1973). The time period for egg incubation in the Klamath system is from

November through March (Leidy and Leidy 1984, Weitcamp et al. 1995). Fish will remain in the

gravel as alevins for about 2 to 3 weeks until the yolk is absorbed, then emerge as free-swimming,

actively feeding fry (Scott and Crossman 1973). Emergence typically occurs from February to midMay (Leidy and Leidy 1984, Weitcamp et al. 1995). The peak downstream movement usually occurs

between April and May (Leidy and Leidy 1984).

In California, most young coho remain in freshwater for at least one year before migrating to the

ocean (Moyle 1976). In some cases however, fry may migrate to the ocean without rearing in

freshwater (Scott and Crossman 1973). Other fish may never migrate to the ocean, but become

residuals which mature but never spawn (Scott and Crossman 1973).
22

Juvenile coho will initially take up residence in shallow, gravel areas near the streambank (Scott and

Crossman 1973). Later in the summer fish will move into deeper pools seeking slow moving water

and structure for cover.

Fish activity, feeding, and growth rates are dependent on water temperature. Preferred rearing

temperatures of 12 to 14 oC (Bell 1990) allow fish to grow quickly as they feed primarily on insects

(Scott and Crossman 1973). Young coho will also eat other smaller fish when available. 

In the spring, following their first winter, yearling coho will leave their freshwater habitat and

migrate to the ocean. The behavior of the fish is to travel in small schools mainly at night (Scott and

Crossman 1973). Timing of migration varies between individuals based on physiological

development and fish size, and other variables such as photoperiod, stream flows, and water

temperature (Craig 1994). Rate of downstream migration appears to be related to size; larger fish

travel faster (Service 1992). 

Klamath River basin coho will outmigrate from February through mid-June (Leidy and Leidy 1984,

Weitcamp et al. 1995). Trapping on the Klamath River mainstem at Big Bar during the spring of

1994 collected juvenile coho from March through June with peak numbers observed in mid-May

(Craig 1994). Timing of the peak is consistent with observations from trapping conducted in 1988

and 1989 (Service 1992). 

Size of migrating fish increases with later migration times. As yearlings, these fish are approximately

100 mm long when they begin their outmigration (Scott and Crossman 1973). Year-old coho

collected at the Big Bar trap ranged in size from 100 mm to 190 mm and small young-of-the-year

coho ranged from 44 mm to 90 mm (Craig 1994).

Peak numbers of coho smolts generally arrive into the Klamath River estuary in April and May

(Wallace 1994). The number of fish declines to low levels after May and remains low until 

October or November (Wallace 1994). Coho captured in the spring appeared to be smolts, while

fish collected in the fall were young-of-the-year YOY parr (Wallace 1994).

5.5 Reproduction

Hatchery reared coho adults that return to spawn in the Klamath system are primarily 3-year-old fish. 

The jack component of the run can be variable and has ranged from zero to 79 percent. Adult size

may vary based on ocean conditions and run timing. In 1993, female adults returning to IGH typically

ranged from 52 cm to 74 cm (FL) (K. Rushton, CDFG pers. comm. 1995). In the same season males

ranged from small jacks at 41 cm to 70 cm FL (K. Rushton, CDFG pers. comm. 1995). Average

number of eggs per female collected at the IGH is 2,660 eggs (K. Rushton, CDFG pers. comm. 1995).

Spawning activities follow the pattern of other salmonid species. In initiating spawning, the female

fish selects a site in the stream where the stream bottom is of medium to small gravel and the current

swift. At this location, the fish will excavate a long oval to round trough where the female will

deposit her eggs. Van Den Berghe and Gross (1984) found nest depth to be related to fish size; larger

females buried eggs as much as 2.5 times deeper than small females. The range of nest depths
23

observed in the study was from 8.9 cm to 26.7 cm (Van den Berghe and Gross 1984). Once the eggs

are extruded from the female, an adjacent male or males (including jacks) releases sperm fertilizing

the eggs. To secure and protect the eggs, the female will dig upstream covering the eggs with gravel. 

Large female coho may spawn up to four times in different nests, however most females spawn two

times (Van Den Berghe and Gross 1984). Post-spawning, female fish will guard the redd until they

die.

Development of the eggs is dependent on environmental factors, the most obvious is water

temperature. With stable water temperatures of 8.9°C coho eggs can hatch in 48 days (Scott and

Crossman 1973). 

6.0 EFFECTS OF KLAMATH PROJECT ON COHO SALMON IN THE KLAMATH RIVER

6.1 Instream Flows

Reclamation has been actively involved since 1998 in developing analytical tools to identify and

quantify potential flow-related effects on coho salmon and other salmonids in the mainstem Klamath

River. Some of these effects are caused by IGD flow releases in the mainstem Klamath River that

result from Project operations.

A number of hydrology-based analytical methods (such as the modified Tennant method used by

Trihey and Associates on behalf of the Yurok Tribe and the USU - Phase I flow study) have been

employed to determine an instream flow regime that would protect coho, chinook, and steelhead

spawning, rearing and egg incubation. 

In the Phase I report, recommended monthly instream flows were compared with mean historical IGD

releases (1961-1996) (Table 15 in INSE 1999). For purposes of this BA, Reclamation compared

Phase I flow recommendations to the proposed action mean and minimum flows for an above average

water year type (Figure 4 and Table 5). This was because the hydrology for this water year type was

closest to the pre-project (pre-1912) wet water year hydrology used in Phase I. Examination of

Table 5 shows that mean time-step flows with the proposed action during above
24

Figure 4. Iron Gate Flow Comparisons - Above Average Water Year Type

0

1000

2000

3000

4000

5000

6000

Oct

NovDec

Jan

Feb

Mar 1-15

Mar 16-31

Apr 1-15

Apr 16-30

May 1-15

May 16-31

Jun 1-15

Jun 16-30

Jul 1-15

Jul 16-31

Aug

Sep

Time Step

Discharge (cfs)

Minimum flows

Mean flows

Phase I flows

Table 5. Flow comparisons for above average water year - Proposed Action versus Phase I flows.

Time Step Minimum Mean Phase1 % change Phase I vs

minimum

% change Phase I

vs mean

Oct 1329 1912 1476 -9.9 29.5

Nov 1337 2547 1688 -20.8 50.9

Dec 1387 2987 2082 -33.4 43.5

Jan 1127 3249 2421 -53.4 34.2

Feb 910 4143 3008 -69.7 37.7

Mar 1-15 1953 4864 3073 -36.4 58.3

Mar 16-31 2101 5268 3073 -31.6 71.4

Apr 1-15 1781 4805 3307 -46.1 45.3

Apr 16-30 1629 3860 3307 -50.7 16.7

May 1-15 1730 3383 3056 -43.4 10.7

May 16-31 1026 2761 3056 -66.4 -9.7

Jun 1-15 760 1764 2249 -66.2 -21.6

Jun 16-30 742 1031 2249 -67.0 -54.2

Jul 1-15 705 870 1714 -58.9 -49.2

Jul 16-31 680 772 1714 -60.3 -55.0

Aug 1011 1049 1346 -24.9 -22.1

Sep 1035 1457 1395 -25.8 4.4

 average water years would exceed recommended Phase I flows from September to May 15. Mean
25

proposed action flows would be less than Phase I flows from May 16 to the end of August. Lower

flows than recommended by Phase I during this period may adversely affect habitat for rearing and

outmigrating fry and juvenile coho salmon. Minimum proposed action flows would always be less

than recommended Phase I flows during above average water years. The Phase I report recognized

that the “lack of adequate storage may prevent the release of water necessary for the attainment of

the recommended flows due to high demands during the later spring and summer period to meet

existing water allocations within the Upper Klamath Basin (i.e., above Iron Gate Dam)”(INSE

1999).

Hydrology-based methods implicitly assume that macrohabitat conditions, such as water temperature

and dissolved oxygen are not limiting for coho salmon in the longitudinal reach of the Klamath River

studied for this BA. Dr. Hardy acknowledges the limitation of the hydrology-based methods in his

Phase I report, “At this juncture, the various techniques employed implicitly assume that other

factors such as water quality or temperature are not limiting. This of course is not true for the

mainstem Klamath River below Iron Gate Dam where deleterious water temperatures and low

dissolved oxygen have been associated with fish kills during the late summer low flow period”

(INSE 1999).

Although the validity of other criticisms of hydrology-based instream flow methods is debatable (T.

Hardy, INSE, per comm. 2001), the Service (1996b) summarized the following limitations of the

Tennant method, one of the methods used in Phase I:

C no consideration of the biology of individual fish species;

C do not account for differences in the periodicity and magnitude of flow variation from stream

to stream;

C do not account for differences in channel morphology;

C do not apply well to spring-fed streams;

C appear to over-estimate flow requirements in streams with great seasonal variation in flow;

C do not apply well without modification to streams where significant changes of water yield

have occurred as a result of developments such as diversions or consumptive use;

C do not quantify the effects of flow changes on habitat quality; therefore, have no quantitative

impact prediction or tradeoff assessment capabilities; and

C regulated waters need more specific methodology like the Instream Flow Incremental

Methodology (IFIM).

Reclamation has cooperated in development of field-based methods (Phase II) by Dr. Hardy to help

address these limitations. Phase II relies on field-based quantitative methods like IFIM, rather than

solely hydrology-based approaches, to determine availability of total habitat (macrohabitat and

microhabitat) resulting from incremental changes in river flow. The Phase II analytical tools will be

available at a later date and will be used by NMFS (D. Reck, per. comm. 2000) to evaluate the

proposed Project operations. 

The action described in this BA includes an effort to develop a plan of closer operational coordination

and data sharing with PacifiCorp to reduce the scope and impacts of depressed flows that occur during

April-June (see Section 4.0). Implementation of this effort may reduce the impacts of reducing flows

on habitat and stranding fish during this period in certain years (see Figure 2).
26

6.2 Microhabitat - Edge Habitat

Total available habitat is computed by combining macrohabitat such as water quality and temperature

with microhabitat (depth velocity, cover). Cover such as edge habitat, undercut banks, and

overhanging vegetation provide essential velocity shelters, protection from predators and an important

source of terrestrial insects for food.

Habitat events affect recruitment via habitat types directly related to the production and survival of

eggs, larvae and fry. Chronic and acute water temperatures during the summer may reduce

macrohabitat availability and may override benefits derived from the microhabitat component. The

Phase II study will hopefully address this issue. 

“Habitat bottleneck” refers solely to habitat limitations that affect populations of individual species

(Wiens 1977). The basic premise is that populations of aquatic organisms are related to the

availability of habitat through time. Adult populations are frequently determined by recruitment which

is highly correlated to the amount of habitat (microhabitat and macrohabitat) for early life stages of the

species. 

The most critical period for YOY salmonids occurs in March, April, May, and early June (T. Shaw,

Service, per. comm. 1998). YOY begin to emerge from the spawning redds and seek out stream

margins providing vegetated cover which in turn provide low velocity envelopes, protective cover

from predators and sources of food. 

Klamath River chinook fry (FL < 55 mm) show a distinct preference for object and overhead cover

associated with edge habitat. Chinook fry prefer escape cover consisting of grasses, sedges, and

herbacous plants and multistem shrubs. Chinook fry are typically found within 2.0 feet distance of

escape cover (G. Smith, CDFG, per. comm. 2000). 

Coho salmon rearing habitats are available in the Klamath River mainstem and tributaries. Phase II

results should provide further information regarding edge habitat flow needs for YOY salmonids in the

mainstem that could be used to assess the impact of proposed action flows on edge habitat for YOY

coho salmon.

6.3 Rearing Habitat

Rearing and emigrating salmonids are most abundant in the mainstem Klamath River in late spring and

early summer (April - mid July). However, they rear in the mainstem river year-round. Fry and

juvenile salmonids use the mainstem river for rearing and downstream migration to the lower river

and/or estuary. 

The longitudinal distribution of YOY salmonids in the Klamath River and their selection of cooler

thermal refugia near tributary mouths (Bartholow 1995; INSE 1999; NMFS 1999b), instead of warmer

mainstem environs implies that they utilize an avoidance strategy when water temperature may affect

survival. Suboptimal temperatures, even though nonlethal, may reduce fish production. 
27

Experiments with pulse flows in 1994 indicate higher flows (1,500 vs 1,000 cfs) over a two-day

period benefitted hatchery fish by helping to decrease their travel time to the Big Bar area. Reduced

travel time has been shown to increase survival by decreasing the time fish are subjected to in-river

predation, disease, and stress and/or mortality associated with increasing water temperatures in the

river (Craig 1994). Size of fish at time of release also plays an important role in migrational timing. 

Larger YOY chinook marked with adipose clips and coded wire tags migrated at faster rates than

smaller fish (Craig 1994).

The available mainstem Klamath River habitat suitable for juvenile coho salmon rearing is difficult to

estimate (INSE 1999 as cited by NMFS 1999b). There is generally a positive correlation between

summer river flows and rearing habitat for juvenile salmonids (Bjorn and Reiser 1991; Binns and

Eiserman 1979; Havey and Davis 1970; Matthews and Olson 1980 as cited in Satterthwaite 1987). 

The relationship of high river flows in the spring and summer and availability of rearing habitat has

been well documented over the last 30 years of instream flow studies in the United States. The

underlying assumption for all instream flow studies is that suitable macrohabitat (channel

characteristics, water quality, and water temperature) occurs throughout the reach of river for the

target species under investigation. Higher flows in the Klamath River during the summer period may

not provide additional suitable rearing habitat (as is observed in other salmonid-occupied river

systems) because of problems associated with high summer water temperatures, depressed dissolved

oxygen levels, and fish pathogens. Phase II results should provide more information on the

relationship between flow and rearing microhabitat and macrohabitat in the Klamath River for

multiple water year types to allow a better assessment of effects of proposed Project summer flows.

 6.4 Iron Gate Dam Ramping Rates

The 1999 BO for Reclamation’s Klamath Project Operations stated that the rate of flow reduction

(down ramping) at IGD may be a potential cause of fish stranding downstream in the Klamath River

(NMFS 1999b). In the BO, NMFS acknowledged, “...that there is an intimate operational

relationship between the Project and PacifiCorp facilities”, and that, “...associated, intimatelyinvolved IGD operation by PacifiCorp is authorized by this incidental take statement.” As such,

Term and Condition 2 in the BO stated that in coordination with PacifiCorp, Reclamation would

conduct a study to determine the effects of PacifiCorp’s FERC ramp rate on fish resources below IGD. 

This study was carried out in 1999 and the results are described in Hardin Davis, Inc. (2000). The

main conclusions of this study are summarized as follows:

1. PacifiCorp has accurate control over ramping at IGD at flows below 1735 cfs. Ramping at flows

above 1735 cfs must be controlled at Copco, and the degree of control is much less.

2. Past ramping by PacifiCorp has nearly always met current license restrictions (3 inches/hr or 250

cfs/hr). It has also met generally accepted agency guidelines for hourly down-ramping almost

all the time. When flows were below 1800 cfs at the gage, ramp rates were below 1.0 inch

per hour, and below 100 cfs per hour about 97% of the time. At this same flow range, ramp

rates were less than 2 inches per hour about 99% of the time. When IGD was spilling, at flows

above 1800 cfs at the gage, the results were similar. The maximum down-ramp rate in cfs was

higher during spill operations, but this did not translate into a frequency of events of 2 inches

or more because cfs change required to cause a 2-inch stage change increases at higher flows.
28

3. Results from the hydrodynamic model and from the pulse flow study suggest that the magnitude of a

stage decrease per hour reduced by about half at a distance 50 miles down from IGD. The

variables affecting the zone of influence are total flow, ramp rate, and tributary inflow.

4. The existing data did not identify specific areas of potential stranding habitat. However, the

amount of potential stranding habitat (e.g. side channels) appears to be less between IGD and

the Shasta River confluence; the reach where ramping rates at IGD are expected to have the

greatest impact on river stage changes. 

5. During the only reported incidence of stranding, the 1998 Tree of Heaven Event, major flow

decreases (>2000 cfs) occurred over 1-3 day periods. The flows during this time exceeded

the Iron Gate turbine capacity. Current channel morphology at the Tree of Heaven site is the

result of significant past alteration by human activities.

Based on the conclusions of the Hardin-Davis ramp rate study, the following steps will be

implemented in order to minimize and mitigate for any potential impacts of flow reduction (fish

stranding) at IGD: 

Condition 1: PacifiCorp shall target a down-ramp rate below IGD of 150 cfs per hour when the

facility is not spilling. At flows above 1735 cfs, PacifiCorp will follow the current FERC

ramp rate during spill. The FERC ramp rate is 3 inches per hour or 250 cfs per hour,

whichever is less “except for conditions beyond the control of the Licensee (FPC 1961).”

Condition 2: PacifiCorp shall cooperate with CDFG to eliminate the potential for stranding from the

documented stranding site known as Tree of Heaven. This will be done by on-the-ground

manipulation of the point bar.

6.5 Klamath River Flows, Fall Chinook Escapement, and Juvenile Abundance, 1988 - 1998

Given the lack of coho-specific information on relationships between abundance and habitat, general

trends in fall-run chinook salmon populations and their response to changes in mainstem macrohabitat

and microhabitat conditions may provide a good approximation of the expected coho salmon

responses to these changing conditions in the mainstem Klamath River. Chinook prefer faster and

deeper water for spawning than coho salmon. However, both species, when considering the YOY and

juvenile life stages, depend on edge habitat for velocity shelters, protection from predators, and food

sources. 

Klamath fall-run chinook adult returns typically consist of five age classes but are dominated by 3 and

4-year old fish. Historical Klamath runs consisted of 6 year classes (Fortune et. al. 1966). Fall run

escapement to the Klamath River above the Trinity River confluence in 1995 and 1996 represented the

highest returns since 1986-1988, but still well below historical levels. The number of fall chinook

returning to the Klamath River has declined considerably since the 1960's. Fall chinook escapement

consisted of stocks from IGH, and wild stocks from Bogus Creek, mainstem Klamath River, Salmon,

Scott, and Shasta Rivers. Habitat loss in the mainstem and tributaries from logging, water diversions,

mining, elevated water temperatures, and poor water quality has contributed to the decline of chinook,

coho, and steelhead. 
29

There has been speculation that the relatively high escapement observed in 1995 and 1996 reflected

freshwater conditions in1992 and 1994 (Table 6). The relative strength of adult returns in both years

may be attributed to very good ocean conditions and excellent microhabitat rearing conditions in the

Klamath River in 1993. Despite drought conditions in 1992 and 1994, it appears high flow conditions

in the mainstem and tributaries in 1993 compensated somewhat for poor microhabitat and

macrohabitat conditions in the watershed below IGD in 1992 and 1994. 

The relationship between Klamath River fall-run chinook escapement, juvenile chinook abundance,

and Klamath River flows was evaluated by Craig (1998). Data from 1988 to 1998 (Table 6) showed

a weak positive correlation ( r = 0.194) between average daily river flow and natural juvenile

chinook abundance. Data from 1989/1990 (escapement year/juvenile index year) were not included

because unseasonable late spring rains in 1990 severely reduced the ability to conduct monitoring

during a period of significant hatchery and natural stock emigrations (Craig 1998). There was also a

weak positive correlation ( r = 0.261) between spawning escapement and juvenile chinook abundance. 

These correlations improved when the 1993/1994 (escapement year/juvenile index year) data point

was omitted. Craig (1998) speculated that the high juvenile abundance in 1994 was due to several

related factors: 1) relatively low escapement in the fall of 1993 (reduced density-dependant factors);

2) low and consistent (absent significant flow peaks) late fall-spring tributary flows and; 3) the

inherent productivity of Klamath Basin waters. Craig (1998) stated that “... it is a difficult, if not

impossible, task to clearly ascertain which factor or combination of factors most affected a

particular adult run-size or influenced the magnitude and/or health condition of the Basin’s annual

juvenile salmonid production.” Given the complexity involved with attempting to quantify these

relationships, effects of proposed Project flows on salmon escapement and juvenile abundance would

be difficult to assess. 

Total 1999 fall-run chinook salmon spawning escapement into the Klamath River system was

estimated at 52,538 fish (CDFG 2000). This included 19,719 natural adults, 14,915 hatchery returns,

and 17,904 in-river fishing harvest (CDFG 2000). Natural juvenile chinook abundance indices for

1999 and 2000 were 367,036 and 287,000, respectively, at Big Bar (Service 2001). Mean flows

(May-July) in 1999 and 2000 were 9,978 and 5,173 cfs, respectively (Service 2001). For

comparison, indices for natural juvenile coho abundance in1999 and 2000 at Big Bar totalled 6,033

and 4,256, respectively (Service 2001). 
30

Table 6. Natural adult fall chinook spawning escapement (1988-1997, 1989 omitted), natural juvenile

chinook abundance index (1989-1998), 1990 omitted) and average daily Klamath River flow during

May-July (1989-1998, 1990 omitted), with corresponding ranks (1 = highest, 9 = lowest) (Craig

1998).

Year Spawning

Escapement1

Rank Year Juvenile

Index2

Rank River

Flow3

Rank

1988 29783 3 1989 135200 7 5628 5

1990 7102 7 1991 55169 9 3461 7

1991 5905 8 1992 165227 6 1975 9

1992 4135 9 1993 220439 5 11519 2

1993 9453 6 1994 1334078 1 2476 8

1994 20960 5 1995 302581 4 9856 3

1995 79851 1 1996 826188 3 8684 4

1996 31755 2 1997 128465 8 5182 6

1997 28415 4 1998 1038520 2 13900 1

Avg. 24151 467319 6965

1

 Spawning escapement = natural adult fall chinook spawners in the Scott, Shasta, and Salmon Rivers,

Bogus Creek and mainstem Klamath River.

2

 Juvenile abundance index = Sum of daily catch of natural juvenile chinook x (mean daily river flow

(cfs)/volume of river flow sampled (cfs)).

3

 Flow = average mean daily Klamath River flow at Orleans USGS gage during May - July.

 

6.6 Klamath River Water Temperature and Discharge 

Water surface temperatures in the Klamath River basin typically range from 0o C (32o F)

to 30o C (86o F) throughout the year (Deas 2000 a, Bartholow 1995). Average daily water

temperatures in the IGD to Seiad Valley reach may fall below 10o C (50o F) during winter months and

can exceed 25o C (77o F) by mid-summer. Daily average water temperatures typically decline below

16.0o C (60.8o F) by early October. Seasonally the diurnal range in water temperature is greatest in

the summer and smallest in winter. 

Table 7 is a summary of mean hourly water temperatures and discharge averaged over various time

steps based on data collected by Reclamation in 1999. Klamath River water temperatures exceeded

20o C in July and August. The highest average temperature in the 1999 field season was 21.72 o C

with a corresponding average discharge of 1,561 cfs at Seiad Valley (Table 6). These water

temperature data appear to be consistent with the modeling effort by Deas (2000a) and the analysis by

Bartholow (1995).
31

Deas and Orlob (1999) measured hourly water temperature at several locations in the Klamath River

between IGD and Seiad Valley. Observations below the Shasta River for the period June 6 - October

1 1997 show that the diurnal temperature range (difference between the daily maximum and minimum)

varies seasonally. The diurnal range was about 5o C by mid-summer, then decreased to about 2o C by

mid-October (Figure 7.16 in Deas and Orlob 1999). These diel fluctuations are for the “node of

maximum fluctuation” (approximately 1⁄2 days travel distance) and are not characteristic of the entire

Klamath River mainstem downstream from IGD (Deas and Orlob 1999; Vogel 2000). This

phenomenon dampens with distance downstream from IGD.

Table 7. Klamath River water temperatures. Information derived from Reclamation water quality

study in 1999.

Klamath River Below Iron Gate Klamath River Near Seiad

SemiMonthly

Period

Average

Temp.

(

o

 C)

Average

Temp. 

(

o

 F)

Average

Flow

Data

(CFS)

SemiMonthly

Period

Average

Temp.

(

o

 C)

Average

Temp. 

(

o

 F)

Average

Flow

Data

(CFS)

5/1-5/15 11.64 52.95 3,489 5/1-5/15 11.45 52.60 6,894 

5/16-5/31 12.92 55.26 2,668 5/16-5/31 13.55 56.39 7,003 

6/2-6/15 16.76 62.17 1,920 6/1-6/15 14.54 58.16 5,223 

6/16-6/30 18.36 65.05 1,953 6/16-6/30 17.79 64.02 4,708 

7/1-7/15 20.34 68.62 1,353 7/1-7/15 20.23 68.41 2,505 

7/16-7/31 20.76 69.37 1,310 7/16-7/31 na na 1,911 

8/1-8/15 21.34 70.41 1,125 8/1-8/15 21.59 70.86 1,591 

8/16-8/31 21.01 69.82 1,148 8/16-8/31 21.72 71.10 1,561 

9/1-9/15 19.57 67.23 1,323 9/1-9/15 19.49 67.07 1,610 

9/16-9/30 18.47 65.24 1,371 9/16-9/30 18.41 65.15 1,736 

10/1-10/15 16.43 61.57 1,390 10/1-10/15 15.84 60.51 1,712 

10/16-10/31 13.86 56.96 1,490 10/16-10/31 12.60 54.67 1,906 

11/1-11/15 11.64 52.95 1,818 11/1-11/15 11.70 53.06 2,510 

11/16-11/30 10.06 50.10 1,818 11/16-11/30 9.46 49.02 2,579 

Note: All Flow Data Matches Temperature Data Time Period Samples

River flow can directly impact water temperatures in the Klamath River (Deas 2000a). Preliminary

flow and temperature simulations in the sixty-mile reach from IGD to Seiad Valley suggest that during

summer periods lower flows generally lead to higher downstream temperatures. Simulated

temperature response for a typical mid-summer day at various IGD releases illustrates the flowtemperature interdependence. At 500 cfs, simulated daily mean water temperature increases 2.5 o

 C

(4.9 o F) over the sixty mile reach from IGD to Seiad Valley, while at 3,000 cfs the simulated increase

is roughly 0.9 o C (1.6 o F) (Table 8) (Deas 2000a; Figure 8.9 in Deas and Orlob 1999). Water

temperatures are elevated at low flow rates because of an increase in transit time, less thermal mass

allowing greater heating during the day, and shallower river conditions. At 500 cfs, a mean simulated

temperature of approximately 25 oC was recorded at Seiad Valley, compared to about 23.0 oC at 3,000

cfs in mid-August (Figure 17 in Deas 2000a; Figure 8.9 in Deas and Orlob 1999). Thus, high water
32

temperatures can occur at high and low flows, depending on climatic conditions. The extent to which

Project operation affects water temperature is complex and remains unclear (Balance Hydrologics

1996). Available information suggests that proposed Project flows may not influence temperatures

dramatically in the Klamath River at Seiad Valley (Tables 7 and 8).

One limitation of the temperature modeling is described by INSE (1999), “At low flow rates water

temperature results are compromised due to physical representation of river geometry where

modeled flows are excessively shallow due to fixed trapezoidal cross sections. Maximum daily

temperatures are probably too high and minimums too low for flows < 500 cfs. Mean temperatures

are probably representative.”

Table 8. Simulated effects of river flow on water temperature in the Iron Gate Dam to Seiad Valley

reach of the Klamath River for a typical mid-summer day. 

Simulated Iron Gate flow in cubic feet per second

(cfs)

Simulated net temperature increase in the Iron Gate

Dam to Seiad Valley reach in o C and (o F)

500 cfs 2.5 oC (4.5 oF)

1000 cfs 2.1 oC (3.8 oF)

2000 cfs 1.3 oC (2.3 oF)

3000 cfs 0.9 oC (1.6 oF)

Diurnal water temperatures, including maximum and minimum values, are also affected by flow

regime. For low flows, daily maximum temperatures are higher and daily minimum water

temperatures are lower, while at higher flows water temperature daily maximums are lower and

minimum temperatures higher (INSE 1999). 

Tributary influences to the Klamath River mainstem temperatures are seasonally important (Deas and

Orlob 1999). During the spring, certain tributaries contribute significant inflow to the mainstem. For

example, Scott River flows are appreciable and cool, derived from snowmelt runoff in the Marble

mountains, and have a notable impact on the Klamath River downstream of the confluence. 

Conversely, the Shasta River is regulated by Dwinnell Reservoir, is heavily utilized for agriculture,

and experiences a smaller, more moderate snowmelt runoff hydrograph than the Scott River (Deas and

Orlob 1999). By mid- to late-spring, the river base flow drops in response to irrigation demand, and

tributary contributions to the mainstem are minor. In the summer and early fall, tributary flows are

small relative to the mainstem flow. Locally, these tributaries may have an impact, but generally they

provide minor contribution to the water temperature of the system (Deas and Orlob 1999). The

termination of irrigation in late fall results in increased inflow from the Shasta and Scott Rivers. 

These tributaries have small thermal mass compared to the Klamath River (and Iron Gate Reservoir),

and thus can cool quickly to provide local thermal relief to the mainstem. Deas and Orlob (1999)

discussed one day, October 10, 1999, when the Shasta River reduced mainstem temperature by

approximately 1 EC (1.8 EF), while the impact of the Scott River was smaller because it is 30 miles

downstream from the Shasta River and the mainstem cooled appreciably in the interim. 
33

6.7 Water Temperature and Salmonid Physiology

Temperature has direct effects on physical, chemical, and biological processes in most aquatic

systems. High temperatures increase chemical reactions, metabolic rates, and decrease the solubility

of gases such as oxygen, carbon dioxide and nitrogen (Deas 2000a). Excessive water temperature can

reduce productivity and increase mortality of aquatic organisms. Temperature affects fish physiology,

specifically respiration, food intake, digestion, assimilation, and behavior. 

Young-of-the-year (YOY) survival, growth, and recruitment depend on the availability of total

habitat, including suitable macrohabitat (water quality and temperature) and suitable microhabitat

(depth, velocity, and cover) conditions under different river flows. The availability of suitable

microhabitat may not be a primary factor in the survival of YOY salmonids when acute water

temperatures prevail. Chronic (>15o C) and acute (>20o C) water temperatures for salmonids in the

Klamath River are based on an evaluation of existing published information on observed relationships

between water temperature and chinook salmon tolerances (Bartholow 1995). These “thresholds”

may create a population bottleneck by impacting YOY and juvenile coho from June to September

(Table 6). The fact that juvenile salmonids persist in the Klamath River mainstem despite

temperatures that generally exceed these chronic and acute temperature thresholds (Yurok Tribal

Fisheries Program 1999, 2000) illustrates the complexity of this issue. Additional site-specific

studies are needed to better understand the relationships between river flow, water temperature,

microhabitat, and salmonid health in the Klamath River. The Phase II report should provide some of

this information. 

Temperature impacts are well documented for anadromous and resident salmonids, particularly

chinook salmon and rainbow trout. Temperature requirements vary by life stage with the adult life

stage more tolerant to higher temperatures than incubating eggs, larvae, and juveniles (Bartholow

1995).

Adult spring chinook were observed in water temperatures approaching 26o C in the John Day River

(Torgersen et.al 1999). Persistence of these fish in the John Day River at ambient water

temperatures exceeding the thermal optima cited for spring chinook migration (16o C) and spawning

(14o C) and the upper zone of thermal tolerance (22o C) (Bell 1986, Armour 1991, Bjornn and Reiser

1991) limits suggests that the fish have developed a behavioral adaptation to these conditions. 

Studies of spring chinook with temperature sensitive radio transmitters in the Yakima River indicate

spring chinook behaviorally thermoregulate to maintain internal temperatures 2.5o C lower than

ambient stream temperatures in surrounding habitats (Berman and Quinn 1991). Although different

races of chinook salmon have been widely studied with regards to temperature, separate thermal

tolerance criteria have not been developed. Bartholow (1995) found no data supporting the contention

that Klamath River salmonid stocks were more thermally tolerant than other west coast stocks. In fact,

the small amount of information available indicates no difference (Bartholow 1995). However, there

is evidence that juvenile chinook and coho salmon and steelhead persist in the Klamath River

mainstem despite temperatures that generally exceed the chronic and acute temperature thresholds

(Belchik 2000). To improve our knowledge on the ability of Klamath River salmon to acclimate or

adapt to typical summer temperatures, controlled experiments are needed on the physiological

response of Klamath River salmonid juveniles to elevated water temperatures (Williamson and Foott
34

1998).

Only recently, since the early 1990s, have affordable instantaneous temperature measuring devices

been available. Thus, field studies on diurnal temperature effects on fish have not been done. This is

an area that also needs further study (M. Deas and T. Shaw, per. comm. 2000).

In the absence of information on diurnal temperature effects, temperature acclimation studies provide

some indication of effects of temperature changes on fish. Armour (1991) reported on studies of the

acclimation effects in juvenile chinook salmon which found fish subject to higher initial water

temperature could sustain higher maximum temperature than those acclimated to cold water (Table 9). 

The data suggest that, even if fish are acclimated to 20o C, you can expect 50% mortalities if

temperatures reach 25.1o C during the day. 

Table 9. Acclimation response for juvenile chinook salmon (Armour 1991). 

Acclimation Temperature o C (o F) Temperature at 50 % Mortality

Lower o C (o F) Upper o C (o F)

5.0 (41.0) - 21.5 (68.9)

10.0 (50.0) 0.8 (33.4) 24.3 (75.7)

15.0 (59.0) 2.5 (36.5) 25.0 (77.0)

20.0 (68.0) 4.5 (40.1) 25.1 (77.2)

Myrick (1998) evaluated the effects of temperature, ration level, and genetics on the physiology of four

strains of juvenile rainbow trout (Oncorhynchus sp.) by measuring growth rates, food consumption,

acute upper thermal tolerance, oxygen consumption, swimming performance and thermal preference. 

Thermal responses of Eagle Lake rainbow trout (O. m. aquilarum), Mt. Shasta rainbow trout (O.

mykiss ), and Little Kern golden trout (O. m. whitei) at temperatures of 10, 14, 19, and 25o C while

receiving ad libitum rations were studied. Investigations were also conducted evaluating the

physiological responses of juvenile Central Valley steelhead (O. m. irideus) to the combined effects of

water temperature (11, 15, and 19o C) and ration levels at 100 % ad libitum, and 80% ad libitum. 

Eagle Lake trout, Mount Shasta rainbow, and Golden trout exhibited a higher upper critical maxima

than Central Valley steelhead. Eagle Lake rainbow trout upper critical thermal maxima (CTM) with

loss of equilibrium ranged from 27.6o C to 32.0o C. Mount Shasta rainbow exhibited a loss of

equilibrium at temperatures ranging from 27.7o C to 31. 5o C, and Golden trout CTM ranged from

27.69o C to 29.95o C. Age 0 winter-run Central Valley steelhead CTM ranged between 27.8o C and

29.9o C depending on acclimation temperatures and ration size (reduced versus full ration). Central

Valley juvenile steelhead preferred temperature ranges between 17o and 20o C with a mean preferred

temperature of 18.3EC. Acclimation temperature affected the CTM with thermal tolerance increasing

with higher rearing/acclimation temperature. Other studies also indicate an increase in thermal

tolerance at higher acclimation temperatures (Myrick 1998 cited in Cherry et al., 1975; Kowalski et

al., 1978; Lee and Rinne, 1980; Elliot, 1991). Under natural conditions, fish that lose their
35

equilibrium due to thermal stress are no longer capable of evading the thermal stressor and are

considered imminent mortalities. Caution should be used when comparing these results to potential

effects of maximum daily temperatures in the Klamath River on coho salmon. The brief and gradual

exposure of fish to diel temperature fluctuations in a river is different than the relatively rapid

temperature increase experienced by fish in CTM studies (Vogel 2000).

Little information is available on coho salmon temperature tolerance. Preferred temperature ranges

for migration, spawning, egg incubation, and juvenile rearing are presented in Table 10. Studies by

Konecki et al. (1995) of juvenile coho salmon near St. Helens Washington found juvenile coho could

tolerate water temperatures exceeding 24o C (75.2o F) and in some cases were observed in streams

with temperatures as high as 29o C (84.2o F).

6.8 Water Temperature and Fish Diseases

Spawning adults are susceptible to lethal disease at temperatures exceeding 16.0o C (60.8o F) (Armour

1991). Boles (1998) found juvenile salmon more susceptible to diseases, parasites, and predation at

temperatures above 15.5o C (59.9o F). Klamath juvenile salmonids have evolved some resistance to

Ceratomyxa shasta when water temperatures are below 16o C (Foote et al. 1999). However, these 

fish exhibited very high mortality rates from C. shasta at higher temperatures. 

Ceratomyxosis is one of several significant infectious disease in the Klamath River (Hendrickson et

al. 1989 cited in Foote et al. 1999). Elevated water temperatures, often in excess of 18o C during the

late spring and summer have been identified as a negative factor for anadromous fish in the Klamath

River (Klamath R. Basin Fish Task Force 1991, cited in Foott et al. 1999). Foote et al. (1995)

examined IGH chinook juveniles captured in the mid-Klamath River (Indian and Red Cap Creeks,

Orleans, and Big bar) during both their spring and autumn releases in 1995. 
36

Table 10. Coho salmon temperature tolerance (Reiser and Bjorn (1979), Birk (1996), and Hassler (1987)).

Life Stage Preferred Temperature o C (o F) Upper Limit o C (o F)

Migration Hassler (1987) 

7.2 - 15.6 4.0 -14.0

(45.0 - 60.1) (39.2 - 57.2)

Hassler (1987)

25.5 (77.9)

Spawning 4.4 - 9.4 6.0 - 12.0 

(39.9 - 48.9) (42.8 - 53.6) 

25.8 (78.4)

Egg Incubation 4.4 - 13.4 4.4 - 13.3 

(39.9 - 56.1) (39.9 - 55.9) 

n/a 

Juvenile Rearing 11.8 - 14.6 4.4 - 9.4 

(53.2 - 58.3) (39.9 - 48.9)

25.0 (77.0)

Juvenile Outmigration

(Birk)

7.2 - 16.7 4.4 - 9.4

(45.0 - 62.1) (39.9 - 48.9)

25.0 (77.0)

Infectious disease significantly affected the survival of juvenile chinook (broodyear 1994) released

from the IGH in 1995 (Foote et al. 1999). Ceratomyxosis was prevalent in the June release of chinook

juveniles with a high of 92% incidence of infection occurring in the third week after release. This

parasitic infection was associated with intestinal hemorrhage, anemia, and high mortality. Elevated

river temperatures appear to exacerbate the disease as IGH stock tends to be resistant to C. shasta at

temperatures # 16o C. Pancreatitis and inflamation of the associated adipose tissue occurred in the

majority of June out-migrants. Energy reserves were depleted in the June release group but to a lesser

degree in the November release fish. The health and condition of the June released chinook juveniles

captured at Big Bar (July 18) dramatically improved five weeks after release. River temperatures

were above 20o C during this period, thus demonstrating that high temperature at the capture site and

poor fish health are not always related. Foote et al. (1999) speculated these outmigrants may have

been holding in cool-water refugia and now were rapidly moving out of the system to the estuary. 

Crucial characteristics, such as immune defenses, metabolic scope of activity, and smolt development

would be expected to be significantly impaired by long term exposure to elevated temperatures. 

Consequently, thermal refugia appears to play a significant role in the mainstem Klamath River and/or

fry and juveniles rear in cooler water tributaries as they migrate down river to escape the inhospitable

temperature conditions typical of the mainstem river in the summer (NMFS 1999b). 

 

A fish kill involving juvenile chinook salmon and steelhead occurred in the Klamath River between

Happy Camp and Salmon Creek (Coon Creek) confluence in June 2000 (M. Pisano, CDFG, per.

comm., 2000). A large pulse of fish documented between June 18 and July 1 was dominated by

chinook salmon smolts released by IGH between June 9 and June 11 (Buettner 2000). Two pathogens

were found in dead fish, C. shasta and Flexibacter columnaris. Deas (2000b) summarized

hydrologic, meteorologic, and water temperature data during this period. He concluded that during the

period June 15-July 7, 2000 persistent warm conditions dominated the region. There was an apparent

relationship between flow and temperature in the mainstem Klamath River in the area of the fish kill. 

At lower flows, transit time increased, leading to the potential for increased thermal loading. Flows
37

near Seiad Valley declined from approximately 3,000 cfs on June 15 to about 1,500 cfs by July 1, with

over 60% of the decrease occurring by June 21 (Deas 2000b). Warm conditions probably accelerated

the runoff from snowmelt, leaving less water in tributaries to ameliorate mainstem conditions

(temperatures and flows) by late June. Also, tributaries were probably warmer than normal due to

lower flows and associated increased transit times. Dissolved oxygen did not appear to be a water

quality concern (Deas 2000b). Water temperature reached a peak of 24.03o C the afternoon of June 29

at Big Bar (river mile 50) on the Klamath River (Craig 2000). 

Other major fish kills have been documented in 1994, 1995, and 1997 (T. Shaw, Service, per. comm.,

2000). Heavy algal loads and high water temperatures likely cause fish deaths that are observed

annually around mid-August in traps monitored by the Service (T. Shaw, Service, per. comm., 2000). 

In addition, these fish mortalities are a function of confinement and handling stresses associated with

trapping under such conditions (Vogel 2000).

6.9 Water Quality Models

Klamath River water quality is a function of hydrology, upstream operations, tributaries, inflows, and

meteorological conditions (Deas and Orlob 1999). The HEC5Q, and RMA-11 models were used by

Reclamation to assess the impact of Project operations on water quality in the IGD-to-Seiad Valley

reach of the Klamath River. HEC5Q was used to compute the temperature of water released from IGD

using an average daily time step (Hanna and Campbell 2000). The RMA-11 model was used to

compute Klamath River water temperatures in August using an hourly time step (Deas and Orlob

1999). 

6.9.1 HEC5Q Water Quality Model 

The period of record for all model runs was water years 1961-1997. Input flow data for the HEC5Q

model runs was obtained from the KPOPSIM simulations and subsequently the MODSIM outflow

data. The assumptions and conditions assumed in the KPOPSIM and MODSIM simulations are not

presented here, only the assumptions pertinent to the HEC5Q model runs.

6.9.1.1 Systems Impact Assessment Model (SIAM) Multiple Year Model Assumptions

The SIAM developed by the USGS was used to assess the water quality on the Klamath River. Within

SIAM are the MODSIM and HEC5Q models. Binding the models and data is the user interface for

SIAM which tracks the options that are to be simulated, passes data and simulation results as

necessary to the appropriate models, and summarizes the output for convenient display. USGS staff in

late 1999 modified an earlier version of SIAM to enable it to identify of a range of years for a

simulation. The range can be as short as one year or as long as the entire period of record. SIAM was

also modified to allow selection of meteorological data either to match the flow data years or to

evaluate different sets of flow and meteorology. For example, selection of a “critically dry” water

year, such as 1992, and the meteorology for 1996 is now possible. Synthetic meteorological data, if

available, may also be used.

The HEC5Q water quality component is not capable of performing true multiple year simulations. 
38

However, within SIAM, flow and meteorology data are provided to HEC5Q in sequence with the

previous year’s ending simulation results forming the next year’s initial conditions. Therefore, in

multiple year simulations in HEC5Q, the initial water quality for each reservoir at the beginning of

each year is a single value equal to the reservoir discharge water quality on the last day of the

previous year’s simulation. Each reservoir is assumed to be completely mixed at this point resulting

in homogeneous water quality throughout the water column. The output from the HEC5Q model within

SIAM is a 360-day simulation (twelve 30-day months) of average daily temperature (EC) and

dissolved oxygen concentration (mg/L). The computation of daily flows for HEC5Q in cfs from the

MODSIM output in af per month does, however, use the traditional calendar for the number of days

per month. These calculated flows are simulated for 30-day months by HEC5Q. SIAM formats the

output data file to insert five blank days at the end of each year simulated (i.e., days 1-360 are model

output, days 361-365 not predicted, day 366 is the first day of the following year). Thus, all years in

the formatted output file are 365 days in length. 

6.9.1.2 Methods and Assumptions for Historical Meteorology (1961-1997)

There are several weather site locations throughout the basin, such as Klamath Falls, OR, Medford

Jackson County, OR and Montague-Siskiyou, CA airports; the Medford Jackson County, OR record

being the most complete for the period of record desired for model simulations. However, there were

significant differences between the Medford weather data and the Montague-Siskiyou data. Weather

data and estimate of cloud cover based on precipitation and visibility from Montague-Siskiyou airport

had been used for calibration and validation of the water quality component (HEC5Q) of SIAM prior

to these recent simulations (Hanna and Campbell 2000). Therefore, the Medford Jackson County

airport, OR data set was adjusted to more closely emulate the Montague-Siskiyou data set by

comparing data for both weather stations from January, 1994 through December, 1998. The annual

average air temperature, dew point, wind speed, and cloud cover for both locations were computed. 

An adjustment factor was applied to the Medford data to create an annual average value for each of

these parameters identical to the Montague-Siskiyou values (Hanna and Campbell 2000). The

adjustment factors used to modify the Medford data to be applicable in the Klamath River basin were:

_ Decrease Medford Jackson County air temp by 3.4o F.

_ Decrease Medford dew point by 7.7 o F. 

_ Increase Medford wind speed by 0.36 mi/hr.

_ Increase cloud cover by 1.3 tenths.

The resulting meteorological database was used consistently for all requested flow scenario

simulations.

6.9.1.3 Flow Scenario Simulation Methods and Assumptions

The MODSIM output data files used for SIAM water quality simulations were as follows:

1) ferc_esa.xy which uses the FERC release schedule at IGD scenario, 

2) esa_fp1.xy which uses the USU Phase I report recommended minimum instream flows at Iron
39

Gate Dam scenario, and 

3) no_proj.xy which uses the without dam or irrigation project river flow scenario. 

HEC5Q requires a set of inflow water quality conditions for each year simulated. That water quality

data set is currently used for all inflows and accretions throughout the model domain for the

simulation, except Big Springs. The Big Springs accretion below JC Boyle Reservoir is an exception

and is specifically characterized to enter at river mile 224.5 and supply a constant 100 cfs that varies

from 11 - 15o C throughout the year. The measured 1996 water quality data record at Keno was used

to characterize inflow water quality for the simulations identified above. In the final contract

completion report, it was stated that USGS had explored the possibility of synthesizing inflow water

quality data by calculating the equilibrium temperature from the historical Medford meteorology

database using the Corps of Engineers HEATX model that is included in of the suite of models for

HEC5Q. The resulting equilibrium temperatures were averaged by either a 20-day or a 30-day

running average and substituted for the 1996 Keno water quality data set. USGS found that neither

method resulted in a significant improvement in the error statistics compared to using the Keno, 1996

data set. Therefore, the Keno, 1996 data set was used for all flow scenario simulations. It may be

possible to improve the inflow water quality characterization for the historical period of record, but

additional data and time would be required to allow this estimation process to occur.

6.9.1.4 Meteorological and Water Year Type Determination

Individual year simulations that combine different meteorological and water year types are based on

meteorological year types (hot, cool, and median); and the water year types (wet, average and dry). 

The adjusted Medford air temperature data base was statistically evaluated and average air

temperature during the April 1 - September 30 period for each year of record was used to categorize

the years into hot, median and cool meteorologic year types. 1992, 1964, and 1979 correspond to the

hot, cool, and median meteorological year types, respectively. Determination of water year types was

performed in coordination with Reclamation Klamath Area Office and Denver TSC staff. The total

Upper Klamath Lake inflow for April through September of each year was evaluated. 1983, 1989, and

1992 correspond to wet, average, and dry water year types, respectively. The final contract

completion report contains the list of data used for determining meteorological and water year types. 

Table 11 summarizes the year types.
4 This elevation is higher than the original reef elevation before excavation of the channel at the

Upper Klamath Lake outlet and simply signifies the minimum lake level for the KPOPSIM simulations.

40

Table 11. Summary of Meteorological and Water Year Types.

Meteorological Year Type Water Year Type

Type Year Type Year

Hot 1992 Dry 1992

Median 1979 Average 1989

Cool 1964 Wet 1983

6.9.1.5 No Irrigation Project Model Methods and Assumptions

The HEC5Q model application for this scenario was developed to expand the model domain upstream

from Keno, Oregon to Upper Klamath Lake, Oregon, which is now the upstream boundary/reservoir

for the without irrigation project model. Simplified bathymetric data for Upper Klamath Lake was

included in this model. The data were developed using an elevation/storage/surface area table for the

lake. The outlet elevation of Upper Klamath Lake in this HEC5Q model application is 4139 ft which

is the same elevation as the minimum Upper Klamath Lake elevation used by KPOPSIM4. River bed

elevations from historic USGS gage records were used and the channel cross-section of the river

reach between Upper Klamath Lake and Keno was estimated to have a bottom width of 78 feet and a

side slope ratio of 3:1 (trapezoidal cross section). Data characterizing channel shapes for the reach

between Upper Klamath Lake and Keno were unavailable. All downstream reservoirs in the HEC5Q

model domain were removed. The inflow water quality used was the Keno, 1996 data set, as

discussed above. The basin-wide flows were obtained from the no_proj.xy MODSIM file. It should

be noted that in the MODSIM application that the downstream reservoirs, J.C. Boyle, Copco, and Iron

Gate remain in the model with a small capacity (1 acre-foot) that is held constant throughout the

simulation. The inclusion of reservoirs in the water quantity model simulation does not effect the

water quality model prediction. The meteorology used for this simulation was the adjusted Medford

data set previously discussed. 

The resultant model runs were provided to Dr. Hardy in January 2000 for use in the PHABSIM and

bioenergetic modeling for Phase II. Water quality modeling (HEC5Q) indicated changes in reservoir

management such as maintaining maximum storage capacity in the spring would reduce IGD outfall

water temperature slightly (1 to 3o C). Temperature changes at Seiad Valley would range from 1 to 2o

C (S. Campbell, per. comm. 1998). The RMA-11 modeling results showed that reducing storage

provided little benefit to downstream temperatures, while increasing storage increased potential for

moderate temperature control well into the summer months (Deas and Orlob 1999). The HEC5Q

results were not comparable to the RMA-11 modeling results of Deas (2000 a) and Deas and Orlob

(1999) because of different objectives. The HEC5Q model was used for general planning purposes

with longer flow time steps, whereas the Deas (2000 a) and Deas and Orlob (1999) studies were more

detailed and used shorter time steps in a shorter reach of river (60 miles) (M. Deas, per. comm. 2000).
41

7.0 CUMULATIVE EFFECTS 

Cumulative effects of State and private activities on anadromous fish species in the Klamath Basin are

significant. Since 1906, fish habitat conditions throughout the watershed including headwater streams,

Upper Klamath Lake (UKL), the Klamath River from Link River Dam to Klamath California, IGD and

tributaries below IGD have been altered by human activities. Operation of the Project has altered

UKL elevations and Klamath River flows downstream from IGD. Marsh lands surrounding UKL have

been converted to agricultural use diminishing the capacity of the lake to reduce nutrient levels. 

Klamath Basin anadromous fisheries have declined precipitously since the early 1900's (INSE 1999). 

Steelhead and chinook salmon above the confluence with the Trinity River have been determined by

NMFS to not be at risk of extinction. A decision to list steelhead will be made by NMFS in the future. 

Chinook stocks below the confluence of the Trinity and Klamath Rivers are being considered for

listing as threatened. Normally, robust populations can withstand environmental perturbations and

recover over time; however, this is not case for anadromous fishes in the Klamath River for the

following reasons. 

Loss of fish habitat, problems with chronic and acute water temperatures and excessive nutrients,

commercial over harvest, and climatic changes have resulted in declining populations of steelhead,

chinook and coho salmon. The combination of timber management practices, agricultural practices,

placer mining, water diversions in the Scott and Shasta River watersheds and the construction of

hydroelectric dams appear to have individually and cumulatively caused significant reduction in

spawning, rearing, and emigration habitat throughout the watershed. Loss of these habitats has resulted

in declining populations. 

During the last 40 years, a large body of information has been collected regarding the effects of water

temperature on salmonid adult migration, spawning, egg incubation, alevin emergence, fry and juvenile

rearing. Bartholow’s (1995) literature review of salmonid temperature tolerances and study of

Klamath River water temperatures support the premise that high summer temperatures 

(>15E C from late June through early September) have a detrimental effect on coho and chinook

salmon and steelhead trout.

High water temperatures found in the river are primarily a function of climate and massive landscape

changes that have occurred throughout the Klamath River watershed. Water temperatures recorded at

Klamathon in the early 1900's (pre-project) indicate the Klamath River was, on average, several

degrees cooler than present (M. Belchik, Yurok Tribe, per. comm.1998). Additionally, flow blockage

by dams and degradation of tributary habitat have eliminated most or all of the thermal refugia areas in

the upper portion of the Klamath River below IGD thus forcing greater reliance on mainstem habitat

(M. Belchik, Yurok Tribe, per. comm.1998). 

Fish kills occur in the lower Klamath River and Upper Klamath Lake due to poor water quality. For

example, bacterial fish diseases such as F. columnaris thrive in high water temperatures typical of the

summer months in the lower river. Aeromonus hydrophylla, another bacterial disease and

anchorworm, a parasitic copepod, are also indicators of the stresses affecting the fisheries. High
42

water temperatures and low dissolved oxygen combined with bacterial diseases and parasites were

largely responsible for the 1997 and 2000 fish kills downstream from IGD. Dead salmon are typically

collected annually during the second week in August in fish traps monitored by the Service at Big Bar

(river mile 50). These deaths are attributed to heavy algal loads and high water temperatures (T.

Shaw, Service, per. comm. 2000). 

Water diversions from Klamath River basin tributaries have played a significant role in the decline of

Klamath River salmonids. Historically, tributaries played a vital role in sustaining coho, steelhead,

and chinook stocks in the Klamath Basin. Diversions on tributaries during the irrigation season (May

to October) reduce stream flow. These low flows prevent fall chinook from migrating up the Scott

River past Etna Creek (river mile 42.2) during average to dry years (D. Rogers, CDFG. per. comm.,

cited in Vogel 1997). Low flows also limit coho and steelhead juvenile rearing habitat and can strand

juvenile fall chinook, coho, and steelhead when the irrigation season begins (CH2M Hill 1985 cited in

Vogel 1997). These activities have also altered water temperature, water quality, and the duration,

frequency, and magnitude of Klamath River flows. 

Watershed conditions in the Klamath River Basin exhibit a legacy of over a hundred years of livestock

grazing, some of which was very intensive. The Shasta and Scott Rivers has a long history of stream

diversions. Diversion dams block salmon from migrating upstream. Riparian vegetation has been

extensively reduced or removed along the Shasta and Scott rivers, as well as other tributaries, causing

increased water temperatures and lack of instream cover for salmon and steelhead. Unscreened or

ineffectively screened diversions have resulted in fish strandings. In one documented case on a

tributary of the Scott River, the following stranded fish were counted: 1,488 young steelhead and 105

young coho salmon (Taft and Shapovalov 1935 cited in Vogel 1997). Agricultural practices in the

Lost, Shasta, and Scott River watersheds may have released herbicides and pesticides into the

Klamath River. However, no evidence exists indicating adverse affects of pesticides or herbicides on

Klamath River resident or anadromous fish. Livestock wastes and fertilizer runoff contributes excess

nutrients (nitrogen and phosphorus) to the stream. As a result, aquatic plant and algae growth is

stimulated. After these plants die, the decomposition process by bacteria can demand more oxygen

than the living plants produce, which lowers the oxygen levels in the stream (Vogel 1997). In

combination with high temperatures and low streamflow, these decreased oxygen levels can be

stressful or lethal to adult and juvenile salmon. Critically low levels of oxygen have been measured in

the Shasta River in recent years (D. Maria, CDFG, per. comm. cited in Vogel 1997). 

Upper Klamath Lake and the Klamath River are highly eutrophic systems from naturally and mancaused phosphorous and nitrogen compounds and pollution in the form of ammonia and nitrates. 

Waste water from Klamath sewage treatment plant, U.S. Timberlands, and South Suburban sewage;

leachates from the Columbia Plywood log storage facility; return water from the Klamath Project area;

and irrigation returns in the Scott and Shasta watersheds all contribute to the high nutrient load and

biological oxygen demand in the Klamath River above and below IGD. High nutrient levels promote

plant and algal growth, which cause diel fluctuations in the river’s dissolved oxygen level because of

plant respiration. Water quality degradation as a result of these activities cannot be discounted as a

major factor contributing to the decline of Klamath River steelhead, coho, and chinook. 

Commercial ocean fisheries have also reduced salmonid stock abundance in the Klamath River system
43

up to 70 percent (Rankel 1980 cited in Vogel 1997). Marine harvest in the Oregon Coast and SONCC

ESUs occurs primarily in nearshore waters off Oregon and California (Weitkamp et al. 1995). 

Commercial landings of coho salmon in Washington, Oregon, and California show relatively constant

landings between 1882 and 1982, ranging between 1.0 and 2.5 million fish, with a low of 390,000 fish

in 1920 and a high of 4.1 million fish in 1971 (Shepard et al. as cited in Weitkamp et al. 1995). Coho

salmon landings off the California and Oregon coast ranged from 0.7 to 3.0 million in the 1970s, were

consistently below 1 million in the 1980s, and averaged less than 0.4 million in the early 1990s prior

to closure of the fisheries in 1994 (Pacific Fishery Management Council (PFMC) 1995 cited in NMFS

1997a). This decline largely reflects reductions in allowable harvest, which were imposed in

response to perceived declines in production (Weitkamp et al. 1995). 

Timber harvest activities and silvicultural practices dating back to the early 1930's have resulted in

extensive degradation of fish habitat in the lower Klamath River watershed and has contributed to the

decline of Klamath River salmonids. Road construction associated with these activities and practices

created impassable barriers to steelhead and salmon spawning areas in Coon, Crawford, Little Girder,

and Beaver Creeks (Taft and Shapovalov 1935 cited in Vogel 1997). Logging caused aggradation in

the lower reaches of Blue and Roach Creeks, blocking spawning access during low water (ESA 1980,

Payne 1989 cited in Vogel 1997).

Mining in the Klamath River Basin has damaged fish habitat from heavy silt loads. One study of

mining impacts was performed in 1934 by the U.S. Bureau of Fisheries (Taft and Shapovalov 1935

cited in Vogel 1997). An analysis of hydraulic mine operations on the East Fork Scott River involved

taking samples of benthic macroinvertebrates located on riffles above and below a tributary carry

considerable mining silt. Above the silted site, the gravels contained an average of 249 organisms per

square foot while below the muddy tributary the average was 36 organisms per square foot (Vogel

1997). These stream fauna represent important food for salmon and steelhead and their loss reduces

the capacity of the stream to support fish populations.

In addition to reduction in fish food, silt from placer mining covers salmon redds and suffocates the

salmon eggs (Smith 1939 cited in Vogel 1997). The level of egg mortality seems related to the amount

of silt. Also, pools filled in with silt leave no hiding or rearing places for fish (Vogel 1997).

Generally, the available water supplies in the Upper Klamath River Basin are insufficient to meet the

competing demands for water supplies of the basin in every water year type. Water rights in most of

the Upper Klamath Basin are currently unquantified and unadjudicated. The State of Oregon is

proceeding with an adjudication of the Klamath River in Oregon. The Upper Klamath Basin Working

Group is working with private entities throughout the Upper Klamath Basin to prioritize watershed

restoration projects and implement restoration projects on a large and small scale using federal and

private funding. It is likely that additional wetland areas will be reclaimed and restored, and

degraded riparian areas fenced and restored. Reclamation is seeking additional sources of water and

storage capacity to assist in meeting the competing demands for water in the basin.

The timing of flow events is also important because the life cycles of many aquatic and riparian

species are timed to either avoid or exploit flow events of different magnitudes. The timing of high or

low flow events provides environmental cues for fish to initiate spawning (Montgomery et al. 1983),
44

egg hatching (Naesje et al. 1995), rearing (Seegrist and Gard 1972), and migration (Trepanier et al.

1996). 

Although no Klamath River-specific data exists, generally a positive flow-versus-survival

relationship has been found in most geographic areas where this relationship has been studied (Cada et

al. 1994). This generally means that as river flows increase, fish survival increases. However, there

are studies that have demonstrated that a positive relationship does not occur uniformly for all ranges

of flows (Vogel 1998). 

Studies have shown that high flows maintain ecosystem productivity and diversity. For example, high

flows remove and transport fine sediments which otherwise would fill interstitial spaces in productive

gravel habitats (Beschta and Jackson 1979). Other studies support the premise that higher flows

would result in higher salmonid smolt survival because these fish would outmigrate faster and reduce

exposure time to poor mainstem habitat conditions (Wagner 1974, Lundquist and Ericksson 1985,

Glova and McInerney 1977, and Smith 1982 cited in McCormick and Saunders 1987). 

High mainstem river spring flows may be necessary to provide rearing habitat for fry and juvenile

coho and other salmonids outmigrating from the tributaries. Degraded fish habitat and poor water

quality conditions in some tributaries, especially in low water years, may prematurely force the

outmigration of salmonids into the mainstem Klamath River. The results of Phase II studies should

provide additional information regarding flow needs for rearing salmonids.

Additional baseline studies are needed on fish distribution and relative abundance, location of crucial

spawning and rearing areas in the mainstem and tributaries, and flow studies determining habitat

conditions for all life stages of chinook, coho and steelhead under a range of flows and water year

types. Further, data are not available to quantitatively determine the survival benefits for each species

and life stage or the requirements to achieve long-term conservation and restoration of the 

Klamath River fisheries. Without this information, it is very difficult for Reclamation to completely

assess the cumulative impacts of the action that is the subject of this BA.
45

8.0 DETERMINATION OF EFFECTS

Reclamation has determined that the effects of on-going operation of the Project, that is the subject of

this BA, is likely to adversely affect the SONCC coho salmon. Further, Reclamation has determined

the proposed action may adversely modify critical habitat for that species. PacifiCorp’s operation of

IGD, subject to the FERC license restrictions, Reclamation’s annual plans, and Conditions 1 and 2

described in Section 6.7 will not jeopardize coho salmon. These determinations are made considering

the following information:

• On-going operation of the Project will result in flows in the Klamath River downstream from

IGD that may affect rearing and outmigrating fry and juvenile coho salmon. 

• On-going operation of the Project could place rearing salmonids at risk (depending on water

year type) because the operation could result in a combination of high water temperature ($15o

C), low dissolved oxygen, and low flows. The relationship between the Project’s effects on

water temperature and summer/fall mainstem river flows is complex (Balance Hydrologics

1996), thus limiting Reclamation’s ability to assess the Project’s effects. 

• The Klamath River has likely always been a relatively warm river system. Insolation (solar

radiation) and ambient air temperatures are primary factors affecting water temperatures in

most rivers, including the Klamath. These climatic factors are completely independent and are

not affected by Project operations. These factors influence water temperatures as distance

increases downstream from IGD (Balance Hydrologics 1996; Hanna 1997). Currentlydepressed salmonid populations combined with successful introduction of numerous warm

water fish species into the reservoir system suggests that natural climatic factors combined

with major landscape alterations in the Klamath River watershed and its tributaries have

caused higher water temperatures, thus favoring fish species other than salmonids.

• Additional research is needed to assess the impact of on-going Project operations and other

activities in the Klamath Basin on anadromous fish. Over the last 50 years, much information

has been collected by federal, state, tribal, and corporate entities regarding Klamath River

salmonids. The information describes fish habitat and their populations in the Klamath River

watershed dating back to the 1940's. Recent studies by CCFWO, the Yurok Tribe of

California and the Karuk Tribe are valuable in understanding the Klamath River fisheries and

the overall mechanics of the watershed. Additional studies are needed to gain a

comprehensive understanding of the Klamath Basin aquatic ecosystem and should focus on

obtaining 1) information on spatial distribution and temporal abundance of fish (all life stages)

within the mainstem river and it’s tributaries, 2) the relationship of flow and the availability of

spawning, incubation, rearing, and outmigration habitat, 3) the effects of water quality on egg

to smolt survival, 4) reliable data on run strength in the mainstem using direct enumeration, 5)

detailed information on pollution sources and relative contribution of each source to the

nutrient loads in the Klamath River, and 6) diurnal temperature effects on fish.

• Macrohabitat conditions, primarily elevated water temperature from late June through

September, may outweigh the benefits of suitable microhabitat (depth, velocity and cover) for
5 A fish kill in 2000 coincided with a water temperature of 24.03o

 C and a discharge of about 1,500

cfs in July. Releases at IGD were approximately 1,000 cfs.

6

 Care should be exercised when applying laboratory results of thermal preferences of wild fish

because there may be unquantified interactive effects from other factors including predation, inter- and

intra-specific competition for microhabitat, availability of food for maintaining high metabolic rates, and

instream hydraulics. These factors can influence the temperature regimes tolerated by wild and hatchery

fish (Myrick, 1998). 

46

YOY and juvenile salmonids. Phase II results will hopefully provide additional information

on this issue. Microhabitat appears to be most limiting during the spring (March, April, May,

and early June) and relates to river stage and availability of mainstem Klamath River edge

habitat. Reclamation will work to develop a plan of closer operational coordination and data

sharing with PacifiCorp to reduce the scope and impacts of depressed flows that occur during

the April to June period. In addition, ramping rate conditions implemented by PacifiCorp may

minimize potential stranding impacts and should benefit coho salmon.

• Elevated water temperatures in the river downstream from IGD from late June through

September create a population bottleneck because water temperature exceeds chronic (> 15o

C) and acute (>20o C) thermal thresholds for YOY and juvenile salmonids. Bartholow (1995)

reported acute thermal effects on salmonids, especially egg and larval life stages, could be

expected at mean daily water temperatures of 20o C, or for consecutive exposures at a weekly

mean temperature at 15o C. 

• Implementing river flows greater than those resulting from on-going Project operation

downstream from IGD from July through September (Table 4) will not likely reduce mean

water temperature to levels below chronic and acute levels for salmonids (Table 6). Deas and

Orlob (1999) reported that higher flows from IGD in August resulted in water temperatures

being reduced approximately 0.6o C, but not reduced below the chronic or acute levels typical

of summer conditions. The temperature of water released from IGD and temperature records

at Seiad from late June through early September in many water year types approach or exceed

acute thermal thresholds and may be a contributing factor to fish kills in the mainstem5. 

Although fish do survive these temperatures, the complex relationship of river flows and water

temperatures, and their effects on the fishery in the Klamath River warrants further

investigation. Phase II results will hopefully provide additional information on this issue6.
47

9.0 LITERATURE CITED

Armour, C.L. 1991. Guidance for evaluating and recommending temperature regimes to protect fish. 

U.S. Fish and Wildlife Service Biological Report 90(22). 13 pp.

Balance Hydrologics, Inc. 1996. Initial assessment of pre- and post-project hydrology on the Klamath

River and impacts of the project on instream flows and fishery habitat.

Barnhart, R.A. 1994. Salmon and steelhead populations of the Klamath-Trinity Basin, California. In

Klamath Basin Fisheries Symposium, Proceedings of a symposium held in Eureka, California,

March 1994. Editor Thomas J. Hassler, California Cooperative Fishery Research Unit,

Humboldt State University, Arcata, California.

Bartholow, J. M. 1995. Review and analysis of Klamath River basin water temperatures as a factor

in the decline of anadromous salmonids with recommendations for mitigation. River Systems

Management Section, Midcontinent Ecological Science Center, U. S. National Biological

Service, Fort Collins, Colorado. Final draft.

Belchik, M. 2000. Technical comments provided to the Bureau of Reclamation on December 22,

2000, on the draft biological assessment for the Klamath Project’s Continuing Operations Plan

on coho salmon. 

Bell, M.C. 1986. Fisheries handbook of engineering requirements and biological criteria. U.S. 

Army Corps of Engineers, Office of the Chief of Engineers, Fish Passage Development and

Evaluation Program, Portland, Oregon.

Bell, M.C. 1990. Fisheries handbook of engineering requirements and biological criteria. U.S. 

Army Corps of Engineers, North Pacific Division, Portland, Oregon.

Berman, C.H. and T.P. Quinn. 1991. Behavioral thermoregulation and homing by spring chinook

salmon, Oncorhynchus tshawytscha (Walbaum), in the Yakima River. J. Fish Biology. 

39:301-312.

Beschta, R.L. and W.L. Jackson. 1979. The intrusion of fine sediments into a stable gravel bed. J.

Fish. Res. Board Can. Vol. 36:204-210.

Binns, N.A., and F.M. Eiserman. 1979. Quantification of fluvial trout habitat in Wyoming. 

Transactions of the American Fisheries Society 108:215-228.

Bjornn, T. C., and D.W. Reiser. 1991. Habitat requirements of salmonids in streams. Influences of

Forest and Rangeland Management on Salmonid Fishes and Their Habitats. American

Fisheries Society Special Publication 19: 83-138.

Brown, L.R., P.B. Moyle, and R.M. Yoshiyama. 1994. Historical decline and current States of coho

salmon in California. North American Journal of Fisheries Management. Volume 14, No. 2. 
48

Pages: 237-261.

Buettner, M. 2000. Klamath River Fish Kill. U.S. Bureau of Reclamation Memorandum. July 10,

2000.

Cada, G.F., M.D. Deacon, S.V. Mitz, and M.S. Bevelhimer. 1994. Review of information pertaining

to the effect of water velocity on the survival of juvenile salmon and steelhead in the Columbia

River basin. Report prepared for the Northwest Power Planning Council (94-9), Portland

Oregon, by the Oak Ridge National Laboratory. 70 pp.

California Department of Fish and Game (CDFG). 2000. Klamath River Basin fall chinook salmon

run-size in-river harvest, and spawner escapement - 1999 season. Summary Report.

CH2M Hill. 1997. Klamath River water accounting model (KPOPSIM) documentation.

CH2M Hill. 1985. Klamath River Basin Fisheries Resource Plan. Prepared for U.S. Department of

Interior.

Craig, J.L. 1994. Klamath River Juvenile Salmonid Emigration Monitoring Pulsed Flow Evaluation

and Klamath Basin Drought Impacts 1994 Salmon Production. Preliminary Report, U.S. Fish

and Wildlife Service, Coastal California Fishery Resource Office, Arcata, California.

Craig, J.L. 1998. Information request regarding the 1995 adult fall-run chinook escapement to the

Klamath River Basin and factors affecting abundance and health condition of Klamath River

juvenile salmonids. Memorandum to Larry Dugan, Bureau of Reclamation, U.S. Fish and

Wildlife Service, Coastal California Fishery Resource Office, Arcata, California

Craig, J.L. 2000. 2000 Klamath and Trinity River Rotary Trap Catch Summary for Julian Week (JW)

27 (7/02-7/08). U.S. Fish and Wildlife Service Facsimile Transmittal.

Deas, M.L., and G.T. Orlob. 1999. Klamath River Modeling Project- Assessment of Alternatives for

Flow and Water Quality Control in the Klamath River below Iron Gate Dam. Completion

Report No. 99-04. Department of Civil and Environmental Engineering. University of

California, Davis.

Deas, M. L. 2000a. Application of Numerical Water Quality Models in Ecological Assessment. 

PhD. dissertation. University of California, Davis. 409 pp.

Deas, M. L. 2000b. Brief Synopsis of Available Hydrologic, Meteorologic, and Water Temperature

Data June 15-July 7, 2000.

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49

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Foote, J.S., J.D. Williamson, and K.C. True. 1999. Health, physiology, and migration characteristics

of Iron Gate Hatchery Chinook, 1995 Releases. U.S. Fish and Wildlife Service, CaliforniaNevada Fish Health Center, Anderson, CA.

Fortune, J.D. Jr., A.R. Gerlach, and C.J. Hanel. 1966. A Study to Determine the Feasibility of

Establishing Salmon and Steelhead in the Upper Klamath Basin. Oregon State Game

Commission.

Hanna, R.B. and S.G. Campbell. 2000. Water quality modeling in the System Impact Assessment

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Geological Survey, Open-File Report 99-113. Fort Collins, Colorado. 82 pp.

Hanna, B.R. 1997. Water quality modeling in the System Impact Assessment Model Case Study:

Klamath Basin. Prototype Final Report. Prepared for United States Department of Interior,

United States Geological Survey, Denver Colorado. 72 pp.

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Fish and Wildlife Service Final Report submitted to California Department of Fish and Game. 

Contract No. FG7292.

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Extinction. Unpublished manuscript, Humboldt Chapter of the American Fisheries Society,

Arcata, California.

Institute for Natural Systems Engineering (INSE). 1999. Evaluation of Interim Instream Flow Needs

in the Klamath River. Phase I Final Report, August 1999. Prepared for Department of

Interior.

Konecki, J.T., C.A. Woody, and T.P. Quinn. 1995. Critical thermal maxima of coho salmon

(Oncorhynchus kisutch) fry under field and laboratory acclimation regimes. Canadian Journal

of Zoology. 73:993-996.

Leidy, R.A. and G.R. Leidy. 1984. Life stage periodicities of anadromous salmonids in the Klamath

River basin, northwestern California. U.S. Fish and Wildlife Service. Division of Ecological

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salmonids: Osmoregulation, growth, and metabolism. American Fisheries Society Symposium

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50

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Moyle, P.B. 1976. Inland Fishes of California. Berkeley: Univ. of California Press. 405 pp.

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Naesje, T., B. Jonsson, and J. Skurdal. 1995. Spring flood: a primary que for hatching of river 

Coregoninae. Can. J. Fisheries and Aquatic Sciences 52:2190-2196.

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Threatened Status for Three Contiguous ESUs of Coho Salmon Ranging from Oregon Through

Central California. Federal Register. 60 CFR 38011. July 20, 1995.

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Status for Southern Oregon/Northern California Coast Evolutionary Significant Unit (ESU) of

Coho Salmon. Final Rule. Federal Register 62 (87): 24588-24609.

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Register 64. 24049.

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2000 Klamath Project Operations.

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Office. April 26, 2000
51

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U.S. Fish and Wildlife Service Biological Report 90(22). 13 pp.

 

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Trepanier, S., M.A. Rodriguez, and P. Magnan. 1996. Spawning migrations in landlock Atlantic 

salmon: time series modeling of river discharge and water temperature effects. Journal 

of Fish Biology 48: pages 925-936.

U. S. Fish and Wildlife Service (Service). 1992. Klamath River fisheries assessment program -

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Lost River Sucker and Shortnose Sucker and Their Proposed Critical Habitat. July 15, 1996. 

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Water Users Association. 19 pp.
52

Vogel, D.A. 1998. Technical comments provided to the Bureau of Reclamation on May 14, 1998, on

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2000, on the draft biological assessment for the Klamath Project’s Continuing Operations Plan

on coho salmon. 

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funding.

10.0 PERSONAL COMMUNICATIONS

Belchik, Mike: Fishery Biologist, Yurok Tribe of California, Klamath, California. Personal

conversation with L. Dugan, Senior Fishery Biologist, U.S. Bureau of Reclamation, Klamath

Falls, Oregon, January 1998.

Campbell, Sharon: Aquatic Biologist, U.S. Geological Survey, Denver, Colorado. Personal

conversation with L. Dugan, Senior Fishery Biologist, U.S. Bureau of Reclamation, Klamath

Falls, Oregon, February, 1998.

Deas, Mike: Personal conversation with R. Sutton, Fishery Biologist, U.S. Bureau of Reclamation,

Denver, Colorado, September, 2000.

Hardy, Thom: Personal conversation with R. Sutton, Fishery Biologist, U.S. Bureau of Reclamation,

Denver, Colorado, January, 2001.

Olsen, Todd: Fishery Biologist, PacifiCorp, Portland, Oregon. Personal conversation with 
53

L. Dugan, Senior Fishery Biologist, U.S. Bureau of Reclamation, Klamath Falls, Oregon. 

March 1998.

Pisano, Mark: Fisheries Biologist, California Department of Fish and Game, Yreka, California. 

Personal conversation and fax transmission to T. Olson, Fishery Biologist, PacifiCorp,

Portland, Oregon, December 1995.

Pisano, Mark: Fisheries Biologist, California Department of Fish and Game, Yreka, California. 

Personal conversation with L. Dugan, Senior Fishery Biologist, U.S. Bureau of Reclamation,

Klamath Falls, Oregon, February 1998.

Pisano, Mark: Fisheries Biologist, California Department of Fish and Game, Yreka, California. 

Personal conversation with Ron Sutton, Fishery Biologist, U.S. Bureau of Reclamation,

Denver, Colorado, August 2000.

Reck, Don: Fishery Biologist, National Marine Fisheries Service, Arcata, California. Personal

conversation with R. Sutton, Fishery Biologist, U.S. Bureau of Reclamation, Denver,

Colorado, August 2000.

Rushton, Kim: Fish Hatchery Manager I, California Department of Fish and Game, Hornbrook,

California. Personal conversation and fax transmission to T. Olson, Fishery Biologist,

PacifiCorp, Portland, Oregon, December 1995.

Shaw, Thomas: Fisheries Biologist, U.S. Fish and Wildlife Service, Arcata, California. Personal

conversation with M.Buettner, Senior Fisheries Biologist, U.S. Bureau of Reclamation,

Klamath Falls, Oregon, November 1996.

Shaw, Thomas: Fishery Biologist, U.S. Fish and Wildlife Service, Arcata, California. Personal

communication with L. Dugan, Fishery Biologist, U.S. Bureau of Reclamation, Klamath Falls,

Oregon, March 1998.

Shaw, Thomas: Fishery Biologist, U.S. Fish and Wildlife Service, Arcata, California. Personal

communication with R. Sutton, Fishery Biologist, U.S. Bureau of Reclamation, Denver,

Colorado, September 2000.

Smith, Gary: Fishery Biologist, California Department of Fish and Game, Yreka, California. Personal

communication with R. Sutton, Fishery Biologist, U.S. Bureau of Reclamation, Denver,

Colorado, November 2000.