United States Department of the Interior 

In Response Refer To: FWS/ AES/DERIBCH/OS6189 

Mr. Robert Wood 

Director 

FISH AND WILDLIFE SERVICE 

Washington, D.C. 20240 

Engineering and Analysis Division 

Office of Water 

U.S. Environmental Protection Agency 

Washington, D.C. 20460 

Dear Mr. Wood: 

In accordance with section 7 of the Endangered Species Act (ESA) of 1973, as amended (16 

U.S.C. 1531 et seq.), and the Interagency Cooperation Regulations (50 CFR 402), this transmits 

our final biological opinion (Opinion) on the U.S. Environmental Protection Agency's (EPA) 

issuance and implementation of the final regulations implementing Section 316(b) of the Clean 

Water Act (CWA). Section 7(a)(2) ofthe ESA of1973, as amended (16 U.S.C. 1536(a)(2)), 

requires Federal agencies to insure that any action they authorize, fund, or carry out is not likely 

to jeopardize the continued existence of any endangered or threatened species or result in the 

destruction or adverse modification of critical habitat. When a Federal agency's action may 

affect listed species or critical habitat, formal consultation with the National Marine Fisheries 

Service (NMFS) and/or the U.S. Fish and Wildlife Service (USFWS) is required (50 CFR 

402.14(a)). EPA requested formal consultation even though EPA was ofthe opinion that its 

action would not cause adverse effects to listed species and critical habitat. After review of the 

proposed regulation, biological evaluation, and other available information we determined that 

the proposed action is likely to adversely affect threatened and endangered species and 

designated critical habitat. 

Federal agencies may request a conference on a proposed action that may affect proposed species 

or proposed critical habitat. While the EPA request for consultation indicates proposed species 

were addressed in the biological evaluation, a conference opinion was not requested, nor was the 

information presented in the biological evaluation sufficient to complete a conference opinion for 

all proposed species. Therefore, we are not providing a conference opinion at this time. 

EPA proposes to issue and implement final regulations (40 CFR 122 and 125; Rule) to establish 

requirements for cooling water intake structures (CWIS) at existing facilities under section 

316(b) of the CW A. This document transmits a joint NMFS and USFWS Opinion on the 

proposed action and its effects on ESA-listed species and designated critical habitat. We based 

our Opinion on information provided in the draft Rule and Preamble, the Services' 

interpretations ofthat rule as agreed upon by EPA on AprilS, 2014, the biological evaluation for 

the CW A section 316(b) Rulemaking provided by EPA on June 18, 2013, consultation meetings, 

peer-reviewed publications, recovery plans, government reports, grey literature, scientific and 
commercial data, and other sources of information. We prepared our Opinion in accordance with 

section 7(a)(2) of the statute (16 U.S.C. 1536(a)(2)), associated implementing regulations (50 

CFR 402), and agency policy and guidance (USFWS and NMFS 1998). 

We appreciate your commitment in the conservation of endangered species. If you require 

further assistance or have any questions, please contact Ms. Cathy Tortorici, Chief, Interagency 

Cooperation Division, NMFS, at 301-427-8495 or by e-mail at cathy.tortorici@noaa.gov, or 

Ms. Patrice Ashfield, Chief, Branch of Consultations and Habitat Conservation Planning, 

USFWS, at 703-358-2478 or by e-mail at patrice_ashfield@fws.gov. 

Donna Wieting 

Director for 

Office of Protected Resources 

Attachment 

Sincerely, 

¢h ary Frazer 

~- ~ssistant Director for 

Ecological Services 
Endangered Species Act Section 7 Consultation

Programmatic Biological Opinion 

on the

U.S. Environmental Protection Agency’s

Issuance and Implementation of the Final Regulations

Section 316(b) of the Clean Water Act

U.S. Fish and Wildlife Service

Endangered Species Program

Division of Environmental Review

Arlington, Virginia

National Marine Fisheries Service

Office of Protected Resources

Endangered Species Act

Interagency Cooperation Division

Silver Spring, Maryland

May 19, 2014
i

Table of Contents

1.0 Consultation History................................................................................................... 1

2.0 Description of the Proposed Action......................................................................... 2

2.1 EPA Requirements....................................................................................................................4

2.2 Owner or Operator Requirements.............................................................................................4

2.2.1 Permit Application.............................................................................................................5

2.2.3 BTA Standards for Impingement Mortality .........................................................................7

2.2.4 BTA Standards for Entrainment..........................................................................................9

2.2.5 Monitoring........................................................................................................................9

2.2.6 Reporting ........................................................................................................................10

2.2.7 Incidental Take................................................................................................................11

2.3 Director Requirements ...........................................................................................................11

2.3.1 Permit Application...........................................................................................................12

2.3.2 Permitting Requirements.................................................................................................12

2.3.3 Impingement...................................................................................................................14

2.3.4 Entrainment....................................................................................................................14

2.3.5 Monitoring and Reporting................................................................................................16

2.3.6 Incidental Take ...............................................................................................................16

2.3.7 Permit Notification .........................................................................................................16

2.3.8 Permit Modification........................................................................................................17

3.0 Approach to the Assessment.................................................................................. 17

4.0 Action Area ................................................................................................................ 18

5.0 Status of the Species................................................................................................ 21

6.0 Environmental Baseline ........................................................................................... 28

7.0 Effects of the Action ................................................................................................. 35

7.1 Programmatic Approach...................................................................................................35

1.1.1 Scope.........................................................................................................................37

1.1.2 Stressors...................................................................................................................40

1.1.3 Minimization of likely adverse effects...................................................................56

1.1.4 Identifies, informs, encourages, and screen applicants for potential eligibility under the 

Rule 62

1.1.5 Monitoring and evaluation of adverse effects...............................................................63

1.1.6 Compliance..................................................................................................................64

1.1.7 Adaptive management.................................................................................................65

8.0 Cumulative Effects......................................................................................................... 66

9.0 Integration and Synthesis of Effects ............................................................................... 67

10.0 Conclusion ................................................................................................................... 71
ii

11.0 Incidental Take Statement ........................................................................................... 75

12.0 Reasonable and Prudent Measures .............................................................................. 76

13.0 Terms and Conditions .................................................................................................. 76

14.0 Conservation Recommendations.................................................................................. 78

15.0 Reintiation Notice........................................................................................................ 78

16.0 Literature Cited............................................................................................................ 80
1

1.0 Consultation History

On July 9, 2004, U.S. Environmental Protection Agency (EPA) promulgated regulations 

establishing requirements for Cooling Water Intake Structures (CWIS) at existing facilities (69 

FR 41576). On January 25, 2007, the Second Circuit remanded parts of the regulations to EPA 

(Riverkeeper, Inc., v. EPA, 475 F.3d 83 (2nd Circuit2007) holding that EPA impermissibly 

balanced costs and benefits in developing the requirements. On July 9, 2007, EPA suspended the 

regulations (72 FR 37107). On April 1, 2009, the U.S. Supreme Court reversed, holding that 

EPA could consider costs and benefits in its regulatory decisions under section 316(b) (Entergy 

Corp. v. Riverkeeper, Inc., 556 U.S. 208 (2009).

On November 22, 2010, EPA signed a settlement agreement with Riverkeeper, Inc. to establish 

rulemaking dates, which included final action by July 27, 2012. On July 17, 2012, the parties 

agreed to an amendment to extend the date for the final Rule until July 27, 2013. 

On April 20, 2011, pursuant to section 316(b) of the Clean Water Act (CWA), EPA proposed 

regulations establishing requirements for CWISs at existing facilities (76 FR 22174). In its 

proposed Rule, EPA replaces with amendments the suspended regulations establishing 

requirements for CWISs at existing facilities. 

On July 20, 2012, EPA met with the National Marine Fisheries Service (NMFS) to commence 

informal ESA Section 7(a)(2) consultation. 

On October 1, 2012, EPA met with the U.S. Fish and Wildlife Service (USFWS) to commence 

informal ESA section 7 consultation. The USFWS and NMFS (i.e., the Services) met with EPA 

numerous times to discuss their action, its impacts to listed species, and measures to minimize 

impacts. 

On April 4, 2013, EPA sent the Services an early draft of the Rule. 

On April 12, 2013, the Services provided comments on the early draft of the Rule. 

On June 18, 2013, EPA submitted a section 7 consultation initiation package, which included the 

draft Rule, draft Preamble, and biological evaluation. We initiated formal consultation on June 

18, 2013. 

On June 27, 2013, EPA signed a modified settlement agreement with Riverkeeper, Inc. to extend 

the date for the final Rule until November 4, 2013, to allow for the completion of formal section 

7 consultation with the Services. This deadline was subsequently extended to January 14, 2014

and then to April 17.

Between June 27 and November 4, the Services met with EPA frequently to discuss EPA’s 

action.
2

On November 4, 2013, we received a revised version of the proposed 316(b) Rule from Office of 

Management and Budget.

On November 15, 2013, we sent the Description of the Action to EPA for review. 

On November 26, 2013, EPA sent corrections and comments on the Description of the Action

and we incorporated their edits into the final Description of the Action. 

From December 6, 2013, through March 11, 2014, the Services and EPA engaged in numerous 

exchanges about possible revisions to the processes embodied in EPA’s draft final Rule.

On March 14, 2014, EPA sent the Services the final Rule and Preamble.

On March 31, 2014, the Services provided EPA with a document seeking clarification on the 

Services’ understandings of key elements in EPA’s proposed action).

On April 8, 2014, EPA provided confirmation on the Services’ description and understanding of 

the key elements of EPA proposed action. (Attached as Appendix A)

2.0 Description of the Proposed Action

EPA proposes to issue and implement a final Rule to establish requirements for CWIS at existing 

facilities and modify certain requirements for new facilities under an existing rule. EPA will 

amend specific parts of the Rule, which implement section 316(b) of the CWA, that had 

previously been suspended (72 FR 37107) in response to the 2nd Circuit Court of Appeals’ 

decision in Riverkeeper, Inc., v. EPA. These parts include: 40 CFR 122.21 (r) (1)(ii) and (5), 

125.90 (a), (c), and (d), and 125.91 through 125.99. In response to the Court’s remand, EPA in 

its final regulation also proposes to remove the restoration-based compliance alternative and 

associated monitoring and demonstration requirements for new facilities (125.84(c) and (d)(1))1. 

In addition, EPA proposes to modify other parts of its regulations implementing section 316(b) 

to establish new requirements for all existing power generating facilities and existing 

manufacturing and industrial facilities that withdraw more than two million gallons of water per 

day (mgd) from waters of the United States and use at least 25 percent of the water they 

withdraw exclusively for cooling purposes (76 FR 22173). In summary, in response to litigation, 

EPA will issue a final Rule to establish modified or new requirements for facilities that withdraw 

water for CWIS. 

Section 316(b) of the CWA requires that the location, design, construction, and capacity of 

CWIS reflect the best technology available (BTA) for minimizing adverse environmental 

impacts. Under the regulation, the term “cooling water intake structure” means the total physical 

structure and any associated waterways used to withdraw cooling water from waters of the 

United States. For purposes of the final Rule, adverse environmental impacts include, but are not 

 

1 The removal of the restoration-based compliance alternative and associated monitoring and documentation requirements for new facilities are 

non-discretionary actions on the part of EPA and therefore, the effects of these actions are not being addressed in this biological opinion. 
3

limited to, impingement and entrainment at CWIS, including adverse effects to federally-listed 

species (species listed as threatened or endangered under the ESA or ESA-listed species) and 

designated critical habitat, and changes in flow regime, caused by the withdrawal of water. 

Impingement is defined as the entrapment of any life stages of fish and shellfish on the outer part 

of an intake structure or against a screening device during periods of intake water withdrawal. 

Entrapment is defined as the condition where impingeable fish and shellfish lack the means to 

escape the cooling water intake. Entrainment is defined as any life stages of fish and shellfish in 

the intake water flow entering and passing through a cooling water intake structure and into a 

cooling water system, including the condenser or heat exchanger.

EPA tailored the Rule toward the protection of fish and shellfish. However, federally-listed 

aquatic organisms that do not fall into the classification of fish and shellfish are also impacted by 

impingement, entrainment, and entrapment (e.g., manatees, turtles). The Rule provides that the 

Director may establish in the permit additional control measures, monitoring and reporting 

requirements that are designed to minimize incidental take, reduce or remove more than minor 

detrimental effects (as defined on page 4 of this Opinion) to federally-listed species and 

designated critical habitat, or avoid jeopardizing federally-listed species or destroying or 

modifying designated critical habitat. As such, and based on communication received from EPA 

on April 8, 2014, (Appendix A), the Rule’s application to “fish and shellfish” and the Director’s 

authority to establish additional measures to protect listed species and habitat will encompass all 

taxa of listed species, including their critical habitat. This consultation also considers the direct 

and indirect effects to federally-listed species caused by facilities operating CWIS under 

requirements of the Rule, including but not limited to; impingement, entrainment, loss of prey, 

changes in water quality, and flow alteration. 

The Rule regulates existing facilities and new units at existing facilities that withdraw cooling 

waters from waters of the United States and have, or require, a National Pollutant Discharge 

Elimination System (NPDES) permit, issued under section 402 of the CWA. The NPDES permit 

program is administered by State Directors in authorized States. However, EPA retains the 

NPDES permit program for facilities located in: Idaho, Massachusetts, New Hampshire, New 

Mexico, District of Columbia, American Samoa, Guam, Johnston Atoll, Midway Island, 

Northern Mariana Islands, Puerto Rico, and Wake Island, as well as certain Federal facilities and 

facilities located on Tribal Lands.

The Rule applies to owners or operators of existing facilities with CWISs that withdraw > 2 mgd 

and use at least 25 percent of the water for cooling purposes. It also applies to the State or EPA 

Regional Director (i.e., the Director2), who establishes controls under CWA Section 316(b) 

authority on withdrawals through the NPDES permitting process. Regulatory requirements are 

described in full in the Rule (40 CFR 122 and 40 CFR 125) and further explained in the 

Preamble. Here, we summarize the Rule, Preamble and relevant correspondence from EPA to 

describe EPA’s action with sufficient detail to evaluate its impact on ESA-listed species and 

designated critical habitat. 

 

2

See 40 CFR 122.2 for the Definition of Director as used in the Rule.
4

2.1 EPA Requirements

When EPA is the NPDES permitting authority and has determined the issuance of the permit 

may affect ESA-listed species or designated critical habitat, they then must request consultation 

under section 7(a)(2) of the ESA. As discussed in Section 2.3, regarding State or Tribal-issued 

CWIS permits, in the Preamble, EPA reaffirms its commitment to the procedures stipulated in 

the 2001 Memorandum of Agreement (MOA) signed by EPA, and the Services (66 FR 11202). 

EPA has incorporated as part of its action relevant sections of the MOA, as described in the 

Preamble to the Rule and, based on correspondence with EPA received on April 8, 2014

(attached as Appendix A), EPA commits to the following implementation of their NPDES 

oversight authorities in situations where the Services contact EPA with concerns that a State or 

Tribal permit will have more than minor detrimental effects on federally-listed species or critical 

habitat that cannot be resolved with the State or Tribal permitting authority: 

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply with all 

applicable CWA requirements and will discuss appropriate measures protective of 

federally-listed species and critical habitat;

ii. EPA will work with the State or Tribe to reduce or remove the detrimental impacts of the 

permit, including, in appropriate circumstances, by objecting to and federalizing the 

permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit proposed by 

a State where EPA finds (giving deference to the views of the Services) that a State or 

Tribal permit is likely to jeopardize the continued existence of such species or result in 

the destruction or adverse modification of such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will give 

deference to the views of the Services with regard to effects on federally-listed 

fish and wildlife resources.

EPA has stated adverse environmental impacts include adverse effects to listed species (USEPA 

2013f), and Section 316(b) of the CWA requires that the location, design, construction, and 

capacity of CWIS reflect the BTA for minimizing adverse environmental impacts. Further, the 

phrase “more than minor detrimental effects” as used in the Rule, Preamble to the Rule, the 2001 

MOA, and in EPA’s commitment to the implementation of their NPDES oversight authorities as 

described above, means “adverse effects” as that term is used in the ESA implementing

regulations, consultation handbook, and MOA (66 FR 11207) and is one type of “adverse 

environmental impact” as that term is used under section 316(b) of the CWA. EPA has also 

defined minimize in the Rule as “to reduce to the smallest amount, extent, or degree reasonably 

possible.” In summary, EPA will exercise its oversight authority on proposed/draft permits 

where the Services contact EPA with concerns that a State or Tribal permit will have more than 

minor detrimental effects on Federally-listed species or designated critical habitat. Such 

situations may include where a permit does not minimize adverse effects to listed species to the 

smallest amount, extent, or degree reasonably possible. 

2.2 Owner or Operator Requirements

In the Rule, EPA establishes certain requirements of the owner or operator of an existing facility 
5

with CWIS by indicating the owner or operator “must” or “shall” perform some action. EPA 

also allows discretion by indicating that the owner or operator “may” or “should” perform some 

optional task. For the purposes of this biological opinion (Opinion), we focus on requirements of 

the rule because we must evaluate the Federal action (not the discretionary decisions of owners,

operators, or Directors) and whether EPA has met their obligations under section 7(a)(2) of the 

ESA. Therefore, we focus on the requirements (i.e., “must” or “shall”) established in the Rule; 

however, we describe and consider optional tasks (i.e., “may” or “should”) to characterize 

discretion allowed in the Rule. 

2.2.1 Permit Application

EPA requires the owner or operator of a facility with CWIS to submit information to the 

Director, as described in Table 1. 

Table 1. Summary of information requirements, based on facility and unit type. For details, see 40 CFR 122.21(r) 

and 125.95. Numbers 2 – 14 refer to sections in §122.21(r), described in brief below table; “X” means required. 

Abbreviations: million gallons per day (mgd); actual intake flow (AIF); design intake flow (DIF).

Information 

required

Existing facilities

Closed 

cycle*

Open cycle

Existing units New units

≤125 mgd >125 mgd

2-Source water 

physical data

X X X X

3-CWIS data X X X X

4-Source water 

baseline 

biological data

X

Applicable 

provisions

Applicable 

provisions

Applicable provisions

5-CWIS system 

data

X X X X

6-Impingement 

mortality 

standard 

method

X X X Applicable provisions

7-Entrainment 

performance 

studies

X X Applicable provisions

8-Operational 

status

X X X X

9-Entrainment 

characterization 

study

Unless 

waived

X X if > 125 mgd or if 125.94(e)(2)

10-

Comprehensive 

technical 

feasibility and 

cost evaluation 

Unless 

waived

X X if > 125 mgd
6

Information 

required

Existing facilities

Closed 

cycle*

Open cycle

Existing units New units

≤125 mgd >125 mgd

study

11-Benefits 

valuation study

Unless 

waived

X X if > 125 mgd

12-Non-water 

quality 

environmental 

and other 

impacts study

Unless 

waived

X X if > 125 mgd

13-Peer review Unless 

waived

X X if > 125 mgd

14-Method of 

compliance for 

new units

X

Additional 

information 

required

See §125.98

See § 122.21(r)(14), 125.95(d), and 

125.98(i)

*Closed-cycle recirculating system is defined by EPA as a system designed and properly operated using minimized 

make-up and blowdown flows withdrawn from a water of the United States to support contact or noncontact cooling 

uses within a facility, or a system designed to include certain impoundments; it passes cooling water through the 

condenser and other components of the cooling system and reuses the water for cooling multiple times. It may include 

a facility with wet, dry, or hybrid cooling towers; it withdraws new source water (make-up water) only to replenish 

losses that have occurred due to blowdown, drift, and evaporation. The definition also includes a system with 

impoundments of waters of the U.S. where the impoundment was constructed prior to the effective date of this rule and 

created for the purpose of serving as part of the cooling water system as documented in the project purpose statement 

for any required Clean Water Act section 404 permit obtained to construct the impoundment.

2. Water body description, characterization, and drawings/maps; 3. Configuration, coordinates, operation schedule, 

flow regime, and drawings; 4. Species, life stages, abundance, reproduction/recruitment, impingement/entrainment 

potential, protective measures; 5. Description, calculations, performance, impingement/entrainment technology 

performance; 6. Impingement mortality standard compliance method and studies; 7. Entrainment technology efficacy, 

entrainment survival data; 8. Description of units, capacity, upgrades, operating status; 9 – 13. For facilities with an 

actual intake flow of greater than 125 mgd. 14. Compliance method for new unit. 

In lieu of the information required at 122.21(r)(4)(vi), the owner or operator of an existing 

facility or new unit at an existing facility must, based on readily available information at the time 

of the permit application, identify all federally-listed species and/or designated critical habitat 

that are or may be present within their action area. In correspondence received from EPA on 

April 8, 2014, EPA verified the following clarifications to the preceding statement:

i. “Readily available information” means information that is publicly available 

information, and includes information obtained from the Services. “Readily 

available information” is not limited to information that is in the facility’s 
7

possession; however, facilities are not required to create new information (e.g. 

new studies or surveys) in order to identify federally-listed threatened and 

endangered species and/or designated critical habitat in their action area; and 

ii. In the Preamble to the Rule, EPA describes the phrase “action area” in the 

following way: “The action area can generally be considered the area in the 

vicinity of the cooling water intake structure.” In the April 8, 2014,

correspondence, EPA verified that whenever the phrase “action area” is used in 

the Preamble and Rule, it is to be interpreted in a manner consistent with the 

definition as found in the Services’ regulations implementing ESA Section 7 at 50 

CFR 402.02. In other words, “action area” includes all areas that may be directly 

or indirectly affected by the operation of a facility’s CWIS.

The owner or operator of a facility may, in subsequent permit applications, request to reduce the 

information required, if conditions at the facility and in the water body remain substantially 

unchanged since the previous application so long as the relevant previously submitted 

information remains representative of current source water, intake structure, cooling water 

system, and operating conditions. Any habitat designated as critical or species listed as 

threatened or endangered after issuance of the current permit, whose range of habitat or 

designated critical habitat includes waters where a facility’s intake is located constitutes potential 

for a substantial change that must be addressed by the owner/operator in subsequent permit 

applications, unless the facility received an exemption pursuant to 16 U.S.C. 1536(o) or permit 

pursuant to 16 U.S.C. 1539(a) or there is no reasonable expectation of take. The owner or 

operator of a facility must submit a request for reduced information requirements regarding 

cooling water intake structure and waterbody information to the Director at least two years and 

six months prior to the expiration of its current NPDES permit. The owner or operator’s request 

must identify each element that it determines has not substantially changed since the previous 

permit application and the basis for the determination. The Director has the discretion to accept 

or reject any part of the request. The owner or operator of a facility must certify that its permit 

application is true, accurate and complete pursuant to § 122.22(d). 

The Director may waive some or all information requirements of 40 CFR 122.21(r) if the intake 

is located in a manmade lake or reservoir and the fisheries are stocked and managed by a State or 

Federal natural resources agency or the equivalent. If the man-made lake or reservoir contains 

federally-listed threatened or endangered species or designated critical habitat, such a waiver 

shall not be granted.

2.2.3 BTA Standards for Impingement Mortality

EPA requires owners or operators to comply with one of following BTA Standards for 

Impingement Mortality, explained in detail in 40 CFR 125.94(c) and summarized below: 

1) Closed-cycle recirculating system and daily monitoring of actual intake flows; or

2) Demonstrated ≤ 0.5 ft/sec through-screen design velocity; or

3) Demonstrated ≤ 0.5 ft/sec through-screen actual velocity* and daily monitoring of 

velocity; or

4) Existing offshore velocity cap and daily monitoring of intake flow; or

5) Modified traveling screens, optimized to minimize impingement mortality; or

6) BTA** systems of technology, management practices, and operational measures; or
8

7) 12-month impingement mortality performance standard and monthly monitoring:

# fish killed*** < 24 percent

# fish impinged

*Director may authorize the operator to exceed 0.5 fps for brief periods

**Determined by the Director

***After collected or retained in ≤ 0.56 inch sieve and held for 18 to 96 hours, or other Director specified period

Pursuant to the Rule, the owner or operator must also comply with any additional measures for 

shellfish and fragile species, as established by the Director. Fragile species as defined in the 

Rule means those species of fish and shellfish that are least likely to survive any form of 

impingement and have an impingement survival rate of less than 30 percent. The owner or 

operator of an existing facility with CWIS used for electric generating unit(s), each with an 

annual average capacity utilization rating of less than 8 percent (averaged over a 24-month 

contiguous period), may request that the Director establish site-specific BTA standards for 

impingement mortality that are less stringent than the Impingement Mortality Standards 

described above. 

The Rule includes provisions for de minimis rates of impingement. In limited circumstances, 

rates of impingement may be so low at a facility that additional impingement controls may not be 

justified. In correspondence received from EPA on April 8, 2014 (attached as Appendix A), 

EPA verified that “where a Director determines, pursuant to §125.94(c)(11), that a facility’s rate 

of impingement is so exceptionally low as to not warrant additional impingement controls, the 

Services may still consider the detrimental effects of the facility operation to be more than minor 

if Federally-listed threatened or endangered species are subject to impingement.” The Services 

may therefore still recommend species protection measures. For threatened and endangered 

species, all unauthorized take is prohibited by the ESA.

Where required by the Director, the owner or operator must implement any requirements for 

additional control measures, monitoring, and reporting that are designed to minimize incidental 

take, reduce or remove more than minor detrimental effects to federally-listed species and 

designated critical habitat, or avoid jeopardizing federally-listed species or destroying or 

adversely modifying designated critical habitat (e.g., prey base). Such control measures, 

reporting, and monitoring requirements may include measures or requirements that may have 

been identified by the Services during their 60 day review of the permit application or the public 

comment period.

Prior to the effective date of this rule , the owner or operator of an existing facility with a 

cumulative design intake flow (DIF) greater than 2 mgd is subject to site-specific impingement 

mortality and entrainment requirements as determined by the Director on a case-by-case Best 

Professional Judgment basis. On or after the effective date of this rule, the owner or operator of 

an existing facility with a cumulative design intake flow (DIF) greater than 2 mgd is subject to 

the BTA standards for impingement mortality under paragraph 125.94(c) of the rule, and 

entrainment under paragraph 125.94(d) of the rule including any measures to protect Federallylisted threatened and endangered species and designated critical habitat established under 

paragraph 125.94(g) of the rule. After issuance of a final permit that establishes the entrainment 
9

requirements, EPA requires the owner or operator of an existing facility to comply with the 

impingement mortality standard as soon as practicable. The owner or operator of a new unit at 

an existing facility must comply with the BTA standards in paragraph § 125.94(e) with respect to 

the new unit upon commencement of the new unit’s operation. 

2.2.4 BTA Standards for Entrainment

The Rule requires the Director to establish requirements that reflect the BTA standards for 

entrainment for each CWIS on a site-specific basis that must reflect the maximum reduction in 

entrainment warranted by §125.98 of the Rule. The owner or operator of an existing facility 

must comply with BTA standard for entrainment, as determined by the Director. 

The owner or operator of a new unit at an existing facility must achieve the impingement 

mortality and entrainment standards by: (1) reducing design intake flow for the new unit, at a 

minimum, to a level commensurate with that which can be attained by the use of a closed-cycle 

recirculating system for the same level of cooling for the new unit; or (2) demonstrating to the 

Director that they will operate and maintain technologies for the intake flow serving the new unit 

that demonstrate entrainment reductions equivalent to at least 90 percent of the reduction that 

could be achieved through compliance with intake flow commensurate with a closed-cycle

system (i.e., 125.92(c)(1)). Exceptions are described in the Rule, and the Director may establish 

alternative requirements or additional BTA standards for entrainment on a site-specific basis. 

Where required by the Director, the owner or operator must implement any requirements for 

additional control measures, monitoring, and reporting that are designed to minimize incidental 

take, reduce or remove more than minor detrimental effects to federally-listed species and 

designated critical habitat, or avoid jeopardizing federally-listed species or destroying or 

adversely modifying designated critical habitat. Such control measures, reporting, and 

monitoring requirements may include measures and requirements that may have been identified 

by the Services during their 60 day review of the permit application or the public comment 

period. 

Prior to 42 months after the effective date of the rule, the Director determines on a case-by-case 

basis when the facility becomes subject to site-specific entrainment requirements; after 42 

months after the effective date of the rule, the owner or operator is subject to the entrainment 

standard. After issuance of a final permit that establishes the entrainment requirements, EPA 

requires the owner or operator of an existing facility to comply with the entrainment standard as 

soon as practicable, based on a schedule of requirements established by the Director. The owner 

or operator of a new unit at an existing facility must comply with the impingement mortality 

standard upon commencement of the new unit’s operation.

2.2.5 Monitoring

EPA has established monitoring requirements for some of the BTA Standards for Impingement 

Mortality, described above. The owner or operator complying with the 12-month impingement 

mortality performance standard (§125.94(c)(7)) may request the Director to reduce monitoring 

requirements after the first full permit term in which these monitoring requirements are 

implemented, if the facility’s CWIS does not directly or indirectly affect federally-listed species 

or designated critical habitat. To do so, the results of the monitoring to date must demonstrate 

that the owner or operator of the facility has consistently operated the intake as designed and is 
10

meeting the impingement mortality standard. In addition, the Director will determine 

entrainment monitoring requirements on a site-specific basis, as appropriate, to achieve the 

maximum reduction in entrainment warranted. The Director may require additional monitoring 

for a variety of reasons as specified in §125.96 of the Rule, including additional monitoring for 

federally-listed species. Where the Director requires additional monitoring for federally-listed 

species or critical habitat, the owner/operator must implement such monitoring. 

The owner or operator of a new unit at an existing facility must either: (option 1) monitor flow 

intake daily and under normal operating conditions, to determine whether the levels are 

commensurate with that which can be attained by the use of a closed-cycle recirculating system; 

or (option 2) continue monitoring entrainment, to demonstrate entrainment reductions are 

commensurate with a closed-cycle recirculating system. If an owner/operator chooses to 

continue monitoring entrainment (option 2), the owner or operator of a new unit at an existing 

facility must monitor entrainable organisms at a proximity to the intake that is representative of 

the entrainable organisms in the absence of the intake structure. They must also monitor the 

latent entrainment mortality in front of the intake structure. Latent mortality is defined as the 

delayed mortality of organisms that were initially alive upon being impinged or entrained but 

that do not survive the delayed effects of impingement and entrainment during an extended 

holding period. Mortality after passing the cooling water intake structure must be counted as 100 

percent mortality, unless the owner or operator has demonstrated to the approval of the Director 

that the mortality for each species is less than 100 percent. 

Monitoring must be representative of the cooling water intake when the structure is in operation. 

In addition, sufficient samples must be collected to allow for calculation of annual average 

entrainment levels of all life stages of fish and shellfish. The Director will determine specific 

monitoring protocols and frequency of monitoring. The owner or operator of a new facility must 

follow the monitoring frequencies identified by the Director for at least 2 years after the initial 

permit issuance. After that time, the Director may approve a request for less frequent monitoring 

in the remaining years of the permit term and when subsequent permits are issued. The 

monitoring must measure the total count of entrainable organisms or density of organisms, unless 

the Director approves of a different metric for such measurements. In addition, the owner or 

operator must monitor the actual intake flow for each intake. The actual intake flow must be 

measured at the same time as the samples of entrainable organisms are collected. The Director 

may require additional monitoring necessary to demonstrate compliance with the entrainment 

standard.

EPA requires an owner or operator of an existing facility to either conduct visual inspections or 

employ remote monitoring devices during the period the cooling water intake structure is in 

operation. The owner or operator must conduct such inspections at least weekly to ensure that 

any technologies operated to minimize adverse environmental impact using BTA standards are 

maintained and operated to function as designed, including those installed to protect federallylisted species or designated critical habitat. The Director may establish alternative procedures if 

this requirement is not feasible (e.g., an offshore intake, velocity cap, or during periods of 

inclement weather).

2.2.6 Reporting

EPA requires the owner or operator to submit to the Director the following information: 
11

 Monitoring Reports (Discharge Monitoring Reports or equivalent state reports and results 

of all monitoring; demonstrations, and other information required by the permit sufficient 

to determine compliance with the permit conditions and requirements established under § 

125.94(g);

 Status reports required by the Director; 

 Signed annual certification statement and report (indicating substantial modifications, if 

any); 

 Additional supplemental permit reporting, as determined by the Director; and

 Where the Director requires additional reporting for federally-listed species or critical 

habitat, the owner/operator must provide such reporting. 

In addition, the Director may require supplemental recordkeeping, such as compliance and other 

monitoring or supplemental data collection required in the permit application. 

The owner or operator of a facility must keep records of all permit application submissions until 

the subsequent permit is issued to document compliance. If the Director approves a request for 

reduced permit application studies, the owner or operator of a facility must keep records of all 

submissions that are part of the previous permit application until the subsequent permit is issued. 

The owner or operator must keep all records supporting the Director’s determination of BTA for 

the entrainment standard until it is revised by the Director. 

2.2.7 Incidental Take

The Rule does not authorize take of endangered or threatened species. Under the ESA, take 

means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to 

engage in any such conduct (16 USC 1532(19)), of endangered or threatened species. Harm is 

defined by the Services to include significant habitat modification or degradation that results in 

death or injury to listed species by significantly impairing behavioral patterns such as breeding, 

feeding, or sheltering. Harass is further defined by the USWFS as actions that create the 

likelihood of injury to listed species by annoying them to such an extent as to significantly 

disrupt normal behavior patterns which include, but are not limited to, breeding, feeding or

sheltering (50 C.F.R. 17.3). Because EPA defines impingement as entrapment and entrainment 

as entering or passing through a CWIS and into the cooling water system, and we interpret these 

as examples of “trap,” “capture,” and “harass,” we have determined that any impingement or 

entrainment of federally-listed species constitutes take. As cited in the Rule, incidental take of 

endangered species (and threatened species, as applicable, under 16 U.S.C. 1533(d)) is 

prohibited under the ESA (16 U.S.C. 1538), unless it is permitted (16 U.S.C. 1539(a)) or 

exempted (16 U.S.C. 1536(o)) by the Services. Absent such exemption or permit, any facility 

operating under the authority of this Rule must not take federally threatened or endangered 

species.

2.3 Director Requirements

In the Rule, EPA establishes many requirements of the Director by indicating that the Director 

“must” or “shall” perform some action. EPA also provides discretion by indicating that the 

Director “may” or “should” perform some optional task. For the purposes of this Opinion, we 

focus on requirements because we must evaluate the Federal action (not the discretionary 

decisions of Directors) and whether EPA’s action is not likely to jeopardize the continued 
12

existence of any federally-listed species or result in the destruction or adverse modification of 

designated critical habitat. Therefore, we focus on the requirements (“must” or “shall”) 

established in the Rule; however, we describe and have considered the optional elements of the 

Rule (“may” or “should”) to characterize the extent of discretion allowed in the Rule. 

2.3.1 Permit Application

EPA requires the Director to review the materials submitted by the applicant (see Table 1) for 

completeness at the time of initial permit application and before each permit renewal or 

reissuance. 

2.3.2 Permitting Requirements

Section 316(b) requirements are implemented through a NPDES permit. EPA requires the 

Director to determine the requirements and conditions to include in the permit, based on the 

information submitted in the permit application, and EPA’s 316(b) regulations. Under the 

regulation, the permit must include: 

 The following language as a permit condition: “Nothing in this permit authorizes take for 

the purposes of a facility’s compliance with the Endangered Species Act.”

 At minimum, the monitoring and reporting requirements described above.

 For permits issued after 42 months after the effective date of the rule:

o At a minimum, conditions to implement and ensure compliance with the impingement

mortality and entrainment standards, including any measures to protect ESA-listed 

species and designated critical habitat required by the Director.

o Conditions, management practices, and operational measures necessary to ensure 

proper operation of any technology used to comply with the impingement mortality 

standard and the entrainment standard.

 For permits issued before 42 months after the effective date of the rule, or permits issued 

after but applied for before the effective date of the final rule, the Director must establish 

interim BTA requirements in the permit on a site-specific basis, based on the Director’s 

best professional judgment. 

 If modified screens or BTA systems of technology, management practices, and 

operational measures are selected as the BTA Standard for Impingement Mortality, the 

permit must include operational measures and best management practices identified in 

the impingement technology performance optimization study as described in 

§122.21(r)(6) of the Rule and deemed as necessary by the Director to ensure optimized 

operation of the modified traveling screens or other systems of technologies. 

The permit may include requirements for the protection of federally-listed species and designated 

critical habitat, including:

 Additional control measures, monitoring requirements, and reporting requirements that 

are designed to minimize incidental take, reduce or remove more than minor detrimental 

effects to federally-listed species and designated critical habitat, or avoid jeopardizing 

federally-listed species or destroying or adversely modifying designated critical habitat 

(e.g. prey base). Such control measures, monitoring requirements, and reporting 

requirements may include measures or requirements identified by the U.S. Fish and 

Wildlife Service and/or the National Marine Fisheries Service during the 60 day review 
13

period pursuant to 125.98(h) or the public notice and comment period pursuant to 40 

C.F.R. 124.10; 

o As described in the Preamble of the Rule and further clarified in correspondence 

received from EPA on April 8, 2014, in situations where the Services have provided 

the Director control measures, monitoring, or reporting recommendations for the 

protection of federally-listed species or designated critical habitat, and the permit will 

have more than minor detrimental effect on federally-listed species or critical habitat 

that cannot be resolved with the State or Tribal permitting authority:

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply 

with all applicable CWA requirements and will discuss appropriate measures 

protective of federally-listed species and critical habitat;

ii. EPA will work with the State or Tribe to reduce or remove the detrimental 

impacts of the permit, including, in appropriate circumstances, by objecting to and 

federalizing the permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit 

proposed by a State where EPA finds (giving deference to the views of the 

Services) that a State or Tribal permit is likely to jeopardize the continued 

existence of such species or result in the destruction or adverse modification of 

such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA 

will give deference to the views of the Services with regard to effects 

on federally-listed fish and wildlife resources.

The Director may require additional permit requirements if: 

 There are migratory or sport or commercial species subject to entrainment that may be 

directly or indirectly affected by the CWIS, based on information submitted to the 

Director by any fishery management agency or other relevant information; or

 It is determined by the Director, based on information submitted by any fishery 

management agencies or other relevant information, that the facility, after meeting the 

entrainment standard of this section, would still result in undesirable cumulative stressors 

to ESA-listed and proposed species and designated and proposed critical habitat.

 For permits expiring prior to or on the date 42 months after the effective date of the rule, 

for which the Director has established an alternate schedule for submission of the permit 

application information (see Table 1), permit conditions to ensure that, for any 

subsequent permit, the Director will have all the information required to establish BTA 

impingement and entrainment requirements.

 For permits applied for before, but issued after the final Rule, the Director may include 

permit conditions to ensure that all the information necessary to establish BTA 

impingement and entrainment requirements for the subsequent permit is included. 

 For new units at existing facilities, the Director may establish alternative requirements if: 

1) the data specific to the facility indicate that compliance with the requirements is 

commensurate with closed cycle recirculating system design intake flow; 2) or 

entrainment reductions for each new unit would result in compliance costs wholly out of 

proportion to the costs EPA considered in establishing the requirements at issue, would 
14

result in significant adverse impacts on local air quality or local water resources other 

than impingement or entrainment, or significant adverse impacts on local energy markets:

o The alternative requirements must achieve a level of entrainment reduction that is 

equivalent to 90 percent or greater of the reduction that could be achieved with closed 

cycle recirculating system, as described above;

o The alternative requirements must ensure compliance with these regulations other 

provisions of the CWA and state and tribal law;

o The burden is on the owner or operator of the facility requesting the alternative 

requirement to demonstrate that alternative requirements should be authorized for the 

new unit.

 Additional measures are needed, such as seasonal deployment of barrier nets, to protect 

shellfish; 

 Additional technologies are needed for protection of fragile species; and

 Additional study and monitoring if a threatened or endangered species has been identified 

in the vicinity of the intake.

The Director may waive some or all of the information requirements (see Table 1) if the intake is 

located in a man-made lake or reservoir and the fisheries are stocked and managed by a State or 

Federal natural resources agency or the equivalent; however, if the man-made lake or reservoir 

contains federally-listed species or designated critical habitat, such a waiver shall not be granted.

2.3.3 Impingement

When the Director establishes a schedule of BTA requirements, the schedule must provide for 

compliance with impingement mortality and entrainment standards as soon as practicable. 

If the owner or operator chooses to comply with the BTA Standard for Impingement Mortality 

with modified traveling screens or systems of technology, management practices, and 

operational measures, and the Director concludes that the study does not establish that the 

proposed technology is the best technology available for impingement reduction for the site, then 

the Director must determine other impingement reduction controls for the facility. The Director 

may request further monitoring and information as part of the “impingement technology 

performance optimization study,” including extending the study period beyond two years. The 

Director may waive all or part of the impingement technology performance optimization study 

after the first permit cycle after the rule wherein the permittee is deemed in compliance with the 

BTA Standard for Impingement Mortality.

Depending on a facility’s choice to comply with the BTA Standard for Impingement Mortality, 

the Director may approve of impinged fish being returned to water sources other than the 

original source water, taking into account any recommendations from the Services with respect 

to endangered or threatened species. Based on correspondence received from EPA on April 8, 

2014, EPA verified that Directors will address any concerns from the Services regarding the 

return of aquatic species to waters other than their source waters. If the Services’ concerns are 

not addressed and the permit would cause more than minor detrimental effects, the permit will be 

subject to the EPA oversight provisions as described above.

2.3.4 Entrainment

When the Director establishes a schedule of BTA requirements, the schedule must provide for 
15

compliance with impingement mortality and entrainment standards as soon as practicable. 

The Rule requires the Director to establish BTA requirements for entrainment for each intake on 

a site-specific basis. The Director must establish site-specific requirements for entrainment after 

reviewing the information submitted by the owner or operator (see Table 1). These entrainment 

requirements must reflect the Director’s determination of the maximum reduction in entrainment 

warranted after consideration of factors relevant for determining the BTA for minimizing 

adverse environmental impact at each facility. These entrainment requirements may also reflect 

any control measures to reduce entrainment of federally-listed species and designated critical 

habitat (e.g. prey base). The Director may reject an otherwise available technology as a basis for 

entrainment requirements if the Director determines, among other things, there are unacceptable 

adverse impacts, including: impingement, entrainment, or other adverse effects to federallylisted species or designated critical habitat. Prior to any subsequent permit issuance after the 

date 42 months after the effective date of the rule, the Director must review the performance of 

the facility’s installed entrainment technology to determine whether it continues to meet the 

requirements of the BTA entrainment standards for existing facilities. 

The Director must provide a written explanation of the proposed entrainment determination in 

the fact sheet or statement of basis for the proposed permit. The written explanation must 

describe why the Director has rejected any entrainment control technologies or measures that 

perform better than the selected technologies or measures, and must reflect consideration of all 

reasonable attempts to mitigate any adverse impacts of otherwise available better performing 

entrainment technologies. The proposed determination in the fact sheet or statement of basis 

must be based on consideration of any additional information required by the Director and the 

following factors:

 Numbers and types of organisms entrained, including, specifically, the numbers and 

species (or lowest taxonomic classification possible) of ESA-listed species and 

designated critical habitat (e.g., prey base);

 Impact of changes in particulate emissions or other pollutants associated with 

entrainment technologies;

 Land availability inasmuch as it relates to the feasibility of entrainment technology and 

remaining useful plant life; and 

 Quantified and qualitative social benefits and costs of available entrainment technologies 

when such information on both benefits and costs is of sufficient rigor to make a 

decision.

The proposed determination in the fact sheet or statement of basis may be based on consideration 

of the following factors:

 Entrainment impacts on the waterbody;

 Thermal discharge impacts;

 Credit for unit retirements occurring within the past 10 years;

 Impacts on water consumption; and/or

 Availability of process water, gray water, waste water, reclaimed water, or other waters 

of appropriate quantity and quality for reuse as cooling water.
16

In implementing their responsibilities under the entrainment requirements, the Director is 

authorized to inspect the facility and to request additional information needed to determine 

permit conditions and requirements. 

2.3.5 Monitoring and Reporting

At a minimum, the Director must require the permittee to monitor as required at § 125.94 (BTA 

standards compliance requirements for owners and operators), § 125.96 (monitoring 

requirements for owners and operators) and report as specified at §125.97 (reporting 

requirements for owners and operators). The Director shall determine monitoring requirements 

for entrainment on a site-specific basis. The Director may establish additional monitoring and 

reporting requirements, including monitoring and reporting requirements monitoring for 

federally-listed species. The Rule requires State Directors submit at least annually the results of 

such monitoring and reporting in facilities’ annual reports, to the appropriate EPA Regional 

Office.

 EPA verified on April 8, 2014, that in circumstances where the Services have provided 

State Directors recommendations for control measures or monitoring and reporting 

requirements designed to minimize incidental take, reduce or remove more than minor 

detrimental effects to Federally-listed species and designated critical habitat, or avoid 

jeopardizing Federally-listed species or destroying or adversely modifying designated 

critical habitat, and the Services are concerned that without such control measures or 

monitoring and reporting requirements the permit may result in more than minor 

detrimental effects to federally-listed species or designated critical habitat, a State 

Director’s failure to include these recommendations or requirements will subject the 

permit to EPA oversight provisions as outlined in the Preamble of the Rule, the April 8, 

2014, correspondence from EPA, and in section 2.1 of this Opinion. 

The Director may reduce monitoring requirements as follows:

 For new units at existing facilities, after 2 years following the initial permit issuance, the 

Director may approve a request for less frequent monitoring for impingement and 

entrainment in the remaining years of the permit term and when the permit is reissued. 

 Where the facility’s CWIS does not directly or indirectly affect federally-listed species or 

designated critical habitat, an owner or operator choosing the impingement mortality 

performance standard, may request the Director to reduce monitoring requirements after 

the first full permit term in which these monitoring requirements are implemented, on the 

condition that the results of the monitoring to date demonstrate that the owner or operator 

of the facility has consistently operated the intake as designed and is meeting the 

impingement mortality standard requirements.

2.3.6 Incidental Take

EPA requires the Director to include the following language as a permit condition: “Nothing in 

this permit authorizes take for the purposes of a facility’s compliance with the Endangered 

Species Act.” 

2.3.7 Permit Notification

EPA requires the Director to transmit all permit applications received from existing facilities to 
17

the appropriate Field Office of the U.S. Fish and Wildlife Service and/or Regional Office of the 

National Marine Fisheries Service upon receipt for a 60 day review prior to public notice of the 

draft or proposed permit. Directors may not propose/publish the draft permit until the 60 day 

Service review period has ended. Under current EPA NPDES regulations, Directors are also 

required to provide for public notice and a public comment period (40 CFR §§ 124.10 & 124.11) 

and to submit a copy of the fact sheet or statement of basis (prepared in the case of EPA-issued 

permits), the permit application (if any), and the draft permit (if any) to the Services. This 

includes notice of specific CWIS requirements and notice of the draft permit and any specific 

information the Director has about threatened or endangered species and critical habitat that are 

or may be present in the action area, including any proposed control measures and monitoring 

and reporting requirements for such species and habitat. 

2.3.8 Permit Modification

As described in the Preamble, “the NPDES regulations also allow a Director to modify a permit 

during the term of the permit, consistent with the Federal regulations at 40 CFR sections 122.62, 

122.63, 122.64, and 124.5. Among other things, under 40 CFR 122.62, causes for permit 

modification include new information, not available at the time of permit issuance, including 

information on newly listed threatened or endangered species or federally-designated critical 

habitat (or unanticipated impacts thereto) received that would have justified the application of 

different permit conditions at the time of issuance.”

3.0 Approach to the Assessment

Section 7(a)(2) requires every Federal agency, in consultation with and with the assistance of the 

Services, insure that any action it authorizes, funds, or carries out is not likely to jeopardize the 

continued existence of any ESA-listed species or result in the destruction or adverse modification 

of critical habitat (16 U.S.C. 1539). During the consultation summarized by this Opinion, we 

reviewed all relevant information provided by EPA to describe the action, including interrelated 

and interdependent actions. Interrelated actions are part of a larger action and depend on the 

larger action for their justification. Interdependent actions have no independent utility apart from 

the proposed action (50 CFR 402.02). We also described the action area, which includes all 

areas affected directly or indirectly by the action (50 CFR 402.02) and evaluated the current 

status of ESA-listed and designated critical habitat that may be affected by this proposed action.

 

We evaluated the direct and indirect effects of the action on ESA-listed species and designated 

critical habitat. Indirect effects are caused by the proposed action and are later in time, but still 

are reasonably certain to occur (50 CFR 402.02). We assessed the exposure to physical, 

chemical, or biotic stressors produced by the proposed action, whether such exposure is likely to 

reduce the survival and reproduction of individuals, and whether fitness reductions would 

threaten the viability of populations and species. We assessed whether the action would 

appreciably reduce the likelihood of recovery of listed species. We assessed whether the action 

is likely to reduce the conservation value of critical habitat. We did not rely on the regulatory 

definition of “destruction or adverse modification of critical habitat (50 CFR 402.02); instead, 

we relied upon the statutory provisions of the ESA to complete our critical habitat analysis. We 

also searched for data on cumulative effects of non-Federal activities (i.e., State and private) that 

are reasonably certain to occur within the action area. For all analyses, we used the best 
18

available scientific and commercial data. For this consultation, we relied on information 

submitted by the action agency, government reports, and the general scientific literature. 

We used the above process to formulate this Opinion. Because we are consulting on the issuance 

and implementation of a Federal Rule, which regulates many activities conducted over several 

geographic areas and long periods of time, there is substantial uncertainty about the number, 

location, timing, frequency, and intensity of individual activities. Therefore, we conducted a 

programmatic consultation to determine whether EPA’s issuance and implementation of the Rule 

as described in the Description of the Proposed Action is likely to jeopardize the continued 

existence of listed species or result in the destruction or adverse modification of critical habitat. 

4.0 Action Area

Under section 7 implementing regulations, action area is defined as “all areas to be affected

directly or indirectly by the Federal action and not merely the immediate area involved in the 

action ( 50 CFR 402.02). As the effects of CWIS can extend well beyond the footprint of the 

structure, for purposes of this consultation, the action area consists of waters over which EPA 

has jurisdiction, see Section 502(7-10), 33 U.S.C. 1362(7-10), from which existing facilities 

withdraw water for cooling purposes (Figure 1). 

Although not necessarily regulated by EPA, the action area also includes other wetland or 

aquatic sites that do not meet the definition of “Waters of the U.S.” and/or adjacent upland areas 

that may be affected by water intake associated with CWIS (i.e., impingement, entrainment, or 

other adverse effects caused by resultant environmental changes, including but not limited to loss 

of prey, changes in water quality, and flow alteration). 

The location of all facilities that may be within the action area of the rule is unknown. From a 

survey that EPA conducted, however, EPA knows the names and location of 575 electric 

generating facilities and 230 manufacturers that may be within action area of the rule. The 

survey was a census of electric generating facilities. For manufacturers, however, a weighted 

sample was collected. For the purpose of analyzing the rule, EPA estimated that 544 electric 

generating facilities and 521 manufacturing facilities, or a total of 1,065 facilities, will be subject 

to the rule (ABT 2014). 

While EPA is confident that in its estimate that there are 1,065 total facilities with one or more 

cooling water intake structures, because of the sample of manufacturers, EPA does not know the 

location of roughly 315 of these facilities (ABT 2014). Consequently, in order to produce a 

better sense of manufacturers’ locations for the purpose of the biological evaluation, EPA 

developed an upper-bound set of manufacturers. This set included all manufacturers that may 

potentially be within the Agency’s action area of the rule, found by searching its permit database 

for facilities that hold a NPDES permit and share a North American Industry Classification code 

with manufacturing facilities that responded to the survey that they had a CWIS. This search 

identified the location of an additional 2,925 manufacturing facilities that may be within action 

area of the rule. EPA added the 2,925 additional manufacturing facilities to the 575 electric 

generating facilities and 230 manufacturers with known locations to estimate that a total of 3,730

facilities may potentially be within the action area of the rule. It is important to note that EPA is 
19

confident that only 1,065 of these 3,730 facilities have a cooling water intake structure (ABT 

2014). Nonetheless the set of 3,730 facilities, which represents an upper bound estimate of the 

number off facilities that may possibly have cooling water intakes, allows the Services to 

identify the broadest set of ESA-listed species that may be affected CWISs.
20
21

5.0 Status of the Species

In the biological evaluation, EPA identified 312 species that may be affected by the proposed 

Rule (Table 2-2 of biological evaluation). Table 2 represents a refinement of EPA’s list of 312 

to include only those species under the jurisdiction of the USFWS we believe may be affected by 

the proposed action (n=195). Table 3 includes those species distinct population segments, 

evolutionarily significant units, or subspecies under the jurisdiction of the NMFS we believe may 

be affected by the proposed action (n=71). We reach this conclusion based on the overlap 

between the species’ habitats and facilities with CWISs, and/or the level of effect on the species 

from CWISs that may result in incidental take.

For more information regarding the individual species and critical habitats listed in Table 2, and 

the factors affecting their conservation status, please refer to proposed and final listing 

determinations, critical habitat designations, recovery plans, and five-year reviews available at: 

http://ecos.fws.gov/ecos/indexPublic.do. For more information regarding the individual species 

and critical habitats listed in Table 3 and the factors affecting their conservation status, please 

refer to Appendix B. The discussion that follows focuses on attributes of life history and 

distribution that influence the manner and likelihood that species may be exposed to the 

proposed action, as well as the species potential response and risk when exposure occurs.

Table 2. ESA-listed species and critical habitat that may be adversely affected by EPA’s proposed 

316(b) regulation under the jurisdiction of USFWS.

Common Name Scientific Name Status Critical Habitat 

 Amphibians

Ozark Hellbender Cryptobranchus alleganiensis 

bishopi

Endangered No*

Barton Springs Salamander Eurycea sosorum Endangered Yes

California Red-Legged Frog Rana draytonii Threatened Yes

 Birds

Hawaiian (=Koloa) Duck Anas wyvilliana Endangered No*

Marbled Murrelet Brachyramphus marmoratus Threatened No

Western Snowy Plover Charadrius alexandrinus nivosus Threatened Yes

Piping Plover Charadrius melodus: Great Lakes Endangered No

Piping Plover Charadrius melodus: Non-Great 

Lakes

Threatened No

Hawaiian Coot Fulica americana alai Endangered No*

Hawaiian Common Moorhen Gallinula chloropus sandvicensis Endangered No*

Whooping Crane Grus americana Endangered Yes

Mississippi Sandhill Crane G. canadensis pulla Endangered No

Hawaiian Stilt Himantopus mexicanus knudseni Endangered No*

Wood Stork Mycteria americana Endangered No*

Eskimo Curlew Numenius borealis Endangered No*

Short-Tailed Albatross Phoebastria (=Diomedea) albatrus Endangered No*

Steller's Eider Polysticta stelleri Threatened No

Light-Footed Clapper Rail Rallus longirostris levipes Endangered No*

California Clapper Rail R. longirostris obsoletus Endangered No*

Yuma Clapper Rail R. l. yumanensis Endangered No*
22

Common Name Scientific Name Status Critical Habitat 

Everglade Snail Kite Rostrhamus sociabilis plumbeus Endangered No*

Least Tern Sterna antillarum Endangered No*

California Least Tern S. antillarum browni Endangered No*

Roseate Tern S. dougallii dougallii Threatened No*

 Bivalves

Cumberland Elktoe Alasmidonta atropurpurea Endangered No

Dwarf Wedgemussel A. heterodon Endangered No*

Appalachian Elktoe A. raveneliana Endangered No

Fat (Mussel) Three-Ridge Amblema neislerii Endangered No

Ouachita Rock Pocketbook Arkansia wheeleri Endangered No*

Spectaclecase (Mussel) Cumberlandia monodonta Endangered No*

Fanshell Cyprogenia stegaria Endangered No*

Dromedary Pearlymussel Dromus dromas Endangered No*

Chipola Slabshell Elliptio chipolaensis Threatened Yes

Altamaha Spinymussel E. spinosa Endangered No

Tar River Spinymussel E. steinstansana Endangered No*

Purple (Mussel) Bankclimber Elliptoideus sloatianus Threatened No

Cumberlandian Combshell Epioblasma brevidens Endangered Yes

Oyster Mussel E. capsaeformis Endangered Yes

Curtis Pearlymussel E. florentina curtisii Endangered No*

Yellow (Pearlymussel) Blossom E. f. florentina Endangered No*

Tan Riffleshell E. f. walkeri (=E. walkeri) Endangered No*

Upland Combshell E. metastriata Endangered No

Purple Cat's Paw (=Purple Cat's Paw Pearlymussel) E. obliquata obliquata Endangered No*

White (Pearlymussel) Catspaw E. o. perobliqua Endangered No*

Southern Acornshell E. othcaloogensis Endangered No

Southern Combshell E. penita Endangered No*

Green (Pearlymussel) Blossom E. torulosa gubernaculum Endangered No*

Northern Riffleshell E. t. rangiana Endangered No*

Tubercled (Pearlymussel) Blossom E. t. torulosa Endangered No*

Snuffbox Mussel E. triquetra Endangered No*

Turgid (Pearlymussel) Blossom E. turgidula Endangered No*

Tapered Pigtoe Fusconaia burkei Threatened No

Shiny Pigtoe F. cor Endangered No*

Finerayed Pigtoe F. cuneolus Endangered No*

Narrow Pigtoe F. escambia Threatened No

Round Ebonyshell F. rotulata Endangered No

Cracking Pearlymussel Hemistena lata Endangered No*

Pink (Pearlymussel) Mucket Lampsilis abrupta Endangered No*

Finelined Pocketbook L. altilis Threatened No

Higgins Eye (Pearlymussel) L. higginsii Endangered No*

Orangenacre Mucket L. perovalis Threatened Yes

Arkansas Fatmucket L. powellii Threatened No*
23

Common Name Scientific Name Status Critical Habitat 

Shinyrayed Pocketbook L. subangulata Endangered Yes

Speckled pocketbook L. streckeri Endangered No*

Alabama Lampmussel L. virescens Endangered No*

Carolina Heelsplitter Lasmigona decorata Threatened No

Birdwing Pearlymussel Lemiox rimosus Endangered No*

Scaleshell Mussel Leptodea leptodon Endangered No*

Louisiana Pearlshell Margaritifera hembeli Threatened No*

Alabama Pearlshell M. marrianae Endangered No

Alabama Moccasinshell Medionidus acutissimus Threatened No

Coosa Moccasinshell M. parvulus Endangered No

Gulf Moccasinshell M. penicillatus Endangered Yes

Ochlockonee Moccasinshell M. simpsonianus Endangered Yes

Ring Pink (Mussel) Obovaria retusa Endangered No*

Littlewing Pearlymussel Pegias fabula Endangered No*

White (Pearlymussel) Wartyback Plethobasus cicatricosus Endangered No*

Orangefoot (Pearlymussel) Pimpleback P. cooperianus Endangered No*

Sheepnose Mussel P. cyphyus Endangered No*

Clubshell Pleurobema clava Endangered No*

James Spinymussel P. collina Endangered No*

Black Clubshell P. curtum Endangered No*

Southern Clubshell P. decisum Endangered Yes

Dark Pigtoe P. furvum Endangered No

Southern Pigtoe P. georgianum Endangered No

Cumberland Pigtoe P. gibberum Endangered No*

Georgia Pigtoe P. hanleyianum Endangered No

Flat Pigtoe P. marshalli Endangered No*

Ovate Clubshell P. perovatum Endangered No

Rough Pigtoe P. plenum Endangered No*

Oval Pigtoe P. pyriforme Endangered Yes

Fuzzy Pigtoe P. strodeanum Threatened No

Heavy Pigtoe P. taitianum Endangered No*

Fat Pocketbook Potamilus capax Endangered No*

Alabama (=Inflated) Heelsplitter P. inflatus Threatened No*

Triangular Kidneyshell Ptychobranchus greenii Endangered No

Southern Kidneyshell P. jonesi Endangered No

Rough Rabbitsfoot Quadrula cylindrica strigillata Endangered Yes

Winged Mapleleaf Q. fragosa Endangered No*

Cumberland (Pearlymussel) Monkeyface Q. intermedia Endangered No*

Appalachian (Pearlymussel) Monkeyface Q. sparsa Endangered No*

Stirrupshell Q. stapes Endangered No*

Pale (Pearlymussel) Lilliput Toxolasma cylindrellus Endangered No*

Choctaw Bean Villosa choctawensis Endangered No*

Rayed Bean V. fabalis Endangered No*
24

Common Name Scientific Name Status Critical Habitat 

Purple Bean V. perpurpurea Endangered Yes

Cumberland (Pearlymussel) Bean V. trabalis Endangered No*

 Fish

Gulf Sturgeon Acipenser oxyrinchus desotoi Threatened Yes

White Sturgeon A. transmontanus Endangered No

Santa Ana Sucker Catostomus santaanae Threatened No

June Sucker Chasmistes liorus Endangered No

Laurel Dace Chrosomus saylori Endangered No

Blue Shiner Cyprinella caerulea Threatened No*

Spotfin Chub Erimonax monachus Threatened No

Slender Chub Erimystax cahni Threatened No

Slackwater Darter Etheostoma boschungi Threatened No

Relict Darter E. chienense Endangered No*

Etowah Darter E. etowahae Endangered No*

Niangua Darter E. nianguae Threatened No

Duskytail Darter E. percnurum Endangered No*

Rush Darter E. phytophilum Endangered No

Bayou Darter E. rubrum Threatened No*

Cherokee Darter E. scotti Threatened No*

Maryland Darter E. sellare Endangered No

Cumberland Darter E. susanae Endangered No

Boulder Darter E. wapiti Endangered No*

Tidewater Goby Eucyclogobius newberryi Endangered No

Unarmored Threespine Stickleback Gasterosteus aculeatus williamsoni Endangered No*

Hutton Tui Chub Gila bicolor ssp. Threatened No*

Mohave Tui Chub G. b. ssp. mohavensis Endangered No*

Humpback Chub G. cypha Endangered No

Bonytail Chub G. elegans Endangered No

Gila Chub G. intermedia Endangered No

Virgin River Chub G. seminuda (=robusta) Endangered No

Rio Grande Silvery Minnow Hybognathus amarus Endangered No

Delta Smelt Hypomesus transpacificus Threatened Yes

White River Spinedace Lepidomeda albivallis Endangered No

Little Colorado Spinedace Lepidomeda vittata Threatened No

Spikedace Meda fulgida Endangered No

Waccamaw Silverside Menidia extensa Threatened No

Palezone Shiner Notropis albizonatus Endangered No*

Cahaba Shiner N. cahabae Endangered No*

Arkansas River Shiner N. girardi Threatened No

Cape Fear Shiner N. mekistocholas Endangered No

Pecos Bluntnose Shiner N. simus pecosensis Threatened No

Topeka Shiner N. topeka (=tristis) Endangered No

Chucky Madtom N. crypticus Endangered No
25

Common Name Scientific Name Status Critical Habitat 

Yellowfin Madtom N. flavipinnis Threatened No

Neosho Madtom N. placidus Threatened No*

Pygmy Madtom N. stanauli Endangered No*

Scioto Madtom N. trautmani Endangered No*

Greenback Cutthroat Trout O. clarki stomias Threatened No*

Lahontan Cutthroat Trout O. clarkii henshawi Threatened No*

Paiute cutthroat Trout O. clarkii seleniris Threatened No*

Oregon Chub Oregonichthys crameri Threatened No

Amber Darter Percina antesella Endangered No

Goldline Darter P. aurolineata Threatened No*

Conasauga Logperch P. jenkinsi Endangered No

Leopard Darter P. pantherina Threatened No

Roanoke Logperch P. rex Endangered No*

Snail Darter P. tanasi Threatened No*

Blackside Dace Phoxinus cumberlandensis Threatened No*

Woundfin Plagopterus argentissimus Endangered No

Gila (Incl. Yaqui) Topminnow Poeciliopsis occidentalis Endangered No*

Colorado Pikeminnow (=Squawfish) Ptychocheilus lucius Endangered No

Foskett Speckled Dace R. osculus ssp. Threatened No*

Atlantic Salmon Salmo salar Endangered No

Bull Trout Salvelinus confluentus Threatened No

Pallid Sturgeon Scaphirhynchus albus Endangered No*

Alabama Sturgeon Scaphirhynchus suttkusi Endangered No

Loach Minnow Tiaroga cobitis Endangered No

Razorback Sucker Xyrauchen texanus Endangered Yes

 Mammals

Northern Sea Otter Enhuydra lutris kenyoni Threatened No

Southern Sea Otter E.l. nereis Threatened No*

West Indian Manatee Trichechus manatus Endangered Yes

Grizzly Bear Ursus arctos horribilis Threatened No*

 Reptiles

American Crocodile Crocodylus acutus Threatened No

Yellow-Blotched Map Turtle Graptemys flavimaculata Threatened No*

Alabama Red-Belly Turtle Pseudemys alabamensis Endangered No*

 Snails

Pecos Assiminea Snail Assiminea pecos Endangered No

Anthony's Riversnail Athearnia anthonyi Endangered No*

Slender Campeloma Campeloma decampi Endangered No*

Lacy (Snail) Elimia Elimia crenatella Threatened No*

Koster's Springsnail Juturnia kosteri Endangered No

Round Rocksnail Leptoxis ampla Threatened No*

Interrupted (=Georgia) Rocksnail Leptoxis foremani Endangered No

Plicate Rocksnail Leptoxis plicata Endangered No*
26

Common Name Scientific Name Status Critical Habitat 

Painted Rocksnail Leptoxis taeniata Threatened No*

Flat Pebblesnail Lepyrium showalteri Endangered No*

Cylindrical (Snail) Lioplax Lioplax cyclostomaformis Endangered No*

Snake River Physa Snail Physa natricina Endangered No*

Rough Hornsnail Pleurocera foremani Endangered Yes

Bliss Rapids Snail Taylorconcha serpenticola Threatened No*

Tulotoma Snail Tulotoma magnifica Threatened No*

*Critical habitat has not been designated for these species. 

Table 3. ESA-listed species and critical habitat that may be adversely affected by EPA’s proposed 

316(b) regulation under the jurisdiction of NMFS.

Common name (Distinct population segment, 

evolutionarily significant unit, or subspecies)

Scientific name Status Critical habitat

 Cetaceans

Blue whale Balaenoptera musculus Endangered No

Bowhead whale Balaena mysticetes Endangered No

Fin whale Balaenoptera physalus Endangered No

Humpback whale Megaptera novaeangliae Endangered No

Killer whale (Southern Resident*) Orcinus orca Endangered Yes

North Atlantic right whale* Eubalaena glacialis Endangered Yes

Sei whale Balaenoptera borealis Endangered No

Sperm whale Physeter macrocephalus Endangered No

Beluga whale (Cook Inlet)* Delphinapterus leucas Endangered Yes

False killer whale (Main Hawaiian Island insular) Pseudorca crassidens Endangered No

 Pinnipeds

Guadalupe fur seal Arctocephalus townsendi Threatened No

Hawaiian monk seal*,** Monachus schauinslandi Endangered Yes, Proposed

Steller sea lion (Western*) Eumetopias jubatus Endangered Yes

Bearded seal (Beringia) Erignathus barbatus nauticus Threatened No

Ringed seal (Arctic) Phoca hispida hispida Threatened No

 Sea turtles

Green sea turtle (Florida & Mexico’s Pacific coast 

colonies) Chelonia mydas Endangered No

Green sea turtle (all other areas*) Threatened Yes

Hawksbill sea turtle* Eretmochelys imbricate Endangered Yes

Kemp’s ridley sea turtle Lepidochelys kempii Endangered No

Leatherback sea turtle* Dermochelys coriacea Endangered Yes

Loggerhead sea turtle (North Pacific Ocean) Caretta caretta Endangered No

Loggerhead sea turtle (Northwest Atlantic Ocean**) Threatened Proposed

Olive ridley sea turtle (Mexico’s Pacific coast breeding 

colonies) Lepidochelys olivacea Endangered No

Olive ridley sea turtle (all other areas) Threatened No

 Sturgeons

Shortnose sturgeon Acipenser brevirostrum Endangered No
27

Common name (Distinct population segment, 

evolutionarily significant unit, or subspecies)

Scientific name Status Critical habitat

Green sturgeon (southern*) Acipenser medirostris Threatened Yes

Gulf sturgeon* Acipenser oxyrhynchus desotoi Threatened No

Atlantic sturgeon (Gulf of Maine) Acipenser oxyrhynchus Threatened No

Atlantic sturgeon (New York Bight) Endangered No

Atlantic sturgeon (Chesapeake Bay) Endangered No

Atlantic sturgeon (Carolina) Endangered No

Atlantic sturgeon (South Atlantic) Endangered No

 Salmonids

Atlantic salmon (Gulf of Maine*) Salmo salar Endangered Yes

Chinook salmon (CA Coastal*) Oncorhynchus tschawytscha Threatened Yes

Chinook salmon (Central Valley Spring-run*) Threatened Yes

Chinook salmon (Lower Columbia River*) Threatened Yes

Chinook salmon (Upper Columbia River Spring-run*) Endangered Yes

Chinook salmon (Puget Sound*) Threatened Yes

Chinook salmon (Sacramento River Winter-run*) Endangered Yes

Chinook salmon (Snake River Fall-run*) Threatened Yes

Chinook salmon (Snake River Spring/Summer-run*) Threatened Yes

Chinook salmon (Upper Willamette River*) Threatened Yes

Chum salmon (Columbia River*) Oncorhynchus keta Threatened Yes

Chum salmon (Hood Canal Summer-run*) Threatened Yes

Coho salmon (Central CA Coast*) Oncorhynchus kisutch Endangered Yes

Coho salmon (Lower Columbia River**) Threatened Proposed

Coho salmon (Southern Oregon & Northern California 

Coast*) Threatened Yes

Coho salmon (Oregon Coast*) Yes

Sockeye salmon (Ozette Lake*) Oncorhynchus nerka Threatened Yes

Sockeye salmon (Snake River*) Endangered Yes

Steelhead (Central California Coast*) Oncorhynchus mykiss Threatened Yes

Steelhead (California Central Valley*) Threatened Yes

Steelhead (Lower Columbia River*) Threatened Yes

Steelhead (Middle Columbia River*) Threatened Yes

Steelhead (Northern California*) Threatened Yes

Steelhead (Puget Sound) Threatened No

Steelhead (Snake River*) Threatened Yes

Steelhead (South-Central California Coast*) Threatened Yes

Steelhead (Southern California*) Threatened Yes

Steelhead (Upper Columbia River*) Threatened Yes

Steelhead (Upper Willamette River*) Threatened Yes

 Other fishes

Pacific eulachon* Thaleichthys pacificus Threatened Yes

Bocaccio (Georgia Basin**) Sebastes paucispinis Endangered Proposed

Yelloweye rockfish (Georgia Basin**) Sebastes pinniger Threatened Proposed
28

Common name (Distinct population segment, 

evolutionarily significant unit, or subspecies)

Scientific name Status Critical habitat

Canary rockfish (Georgia Basin**) Sebastes ruberrimus Threatened Proposed

Smalltooth sawfish* Pristis pectinata Endangered Yes

 Marine invertebrates

Elkhorn coral* Acropora palmata Threatened3 Yes

Staghorn coral* Acropora cervicornis Threatened1 Yes

White abalone Haliotis sorenseni Endangered

Black abalone* Haliotis cracherodii Endangered Yes

 Marine plants

Johnson’s seagrass* Halophilia johnsonii Threatened Yes

6.0 Environmental Baseline

The Environmental Baseline includes the past and present impacts of all Federal, State, or private 

actions and other human activities in the action area, the anticipated impacts of all proposed 

Federal projects in the action area that have already undergone formal or early section 7 

consultation, and the impact of State or private actions, which are contemporaneous with the 

consultation in process (50 CFR 402.02). The key purpose of the Environmental Baseline is to 

describe the condition of the listed species/critical habitat that exist in the action area in the 

absence of the action subject to consultation. This Environmental Baseline focuses primarily on 

the status and trends of the aquatic ecosystems in the United States and the consequences of that 

status for listed resources.

Consistent with case law, we include in the Environmental Baseline the existence of CWIS at 

existing facilities, but not their operation. We acknowledge that facilities with CWIS exist, and 

that those facilities impinge and entrain aquatic organisms on a daily basis. However, the 

operation of those CWIS is within EPA’s discretion. Therefore, for this baseline, we assume the 

CWIS are in place, but are not in operation. In re Operation of Missouri River System Litigation, 

421 F.3d. 618 (8th Cir. 2005), the Eighth Circuit upheld the Service’s use of a ‘run of the river’ 

baseline, “in which the dams and physical channel modifications are assumed to be in place, but 

all floodgates are assumed to be wide open, with no flood control, “...the hypothetical continued 

operation [sic] (of the dams) under the previous version of the Master Manual in future years, as 

the alternative to the proposed action of updating the Master Manual, does not in any sense 

constitute a “past impact” of federal action.” The Ninth Circuit reached a similar conclusion in 

National Wildlife Federation v. NMFS: “Although we acknowledge that the existence of the 

dams must be included in the environmental baseline, the operation of dams is within the federal 

agencies’ discretion under both the ESA and the Northwest Power Act, 16 U.S.C. §839.” 524 

F.3d 917 (9th Cir.2008): Using the same logic, the continued operation of CWIS does not 

constitute a past impact of Federal action and is not included in the environmental baseline.

All of the endangered and threatened species and designated critical habitat considered in this 

Opinion depend on the health of aquatic ecosystems for their survival. These species were listed 

 

3

Proposed endangered
29

as endangered or threatened, at least in part, because of the consequences of human activities on 

the aquatic ecosystems to include estuaries, rivers, lakes, streams, and associated wetlands, 

floodplains, and riparian ecosystems of the United States, its Territories and possessions. The 

status and trends of those aquatic ecosystems determines the status and trends of these species 

and the critical habitat that has been designated for them. 

Habitat

Freshwater habitats are among the most threatened ecosystems in the world (Leidy and Moyle 

1998). Reviews of aquatic species’ conservation status over the past three decades have 

documented the cumulative effect of anthropogenic and natural stressors on freshwater aquatic 

ecosystems, resulting in a significant decline in the biodiversity and condition of indigenous fish, 

mussel and crayfish communities (Taylor et al. 2007; Jelks et al. 2008). Anthropogenic stressors 

are present to some degree in all water bodies of the United States, and are the result of many 

different impacts. These stressors often lead to long-term environmental degradation associated 

with lowered biodiversity, reduced primary and secondary production, and a lowered capacity or 

resiliency of the ecosystem to recover to its original state in response to natural perturbations 

(Rapport and Whitford 1999). 

Many of our nation’s rivers and streams have been altered by dams, stream channelization, and 

dredging to stabilize water levels in rivers or lakes. When examining the impacts of large dams 

alone, it is estimated that 75,000 large dams have modified at least 600,000 miles of rivers across 

the country (IWSRCC 2011). For example, more than 400 dams exist in the Columbia River 

Basin alone (Columbia Basin Trust 2014). Habitat loss coupled with other stressors has led to 

impacts on fish communities as well. By the early 80’s, approximately 81 percent of the native 

fish communities in the United States had been adversely affected by human activities (Judy et 

al. 1984).

Wetland habitats have been drained to make land available for agriculture; they have been filled 

to make land available for residential housing, commerce, and industry; they have been diked to 

control mosquitoes; and they have been flooded for water supply. Efforts to create and restore 

wetlands and other aquatic habitats by agencies of Federal, State, and local governments, nongovernmental organizations, and private individuals have dramatically reduced the rate at which 

these ecosystems have been destroyed or degraded, but many aquatic habitats continue to be lost 

each year. Between 2006 and 2009, approximately 13,800 acres of wetlands were lost per year 

(Dahl 2011). While this is significantly less than losses experienced in the previous decades 

(Figure 2), an estimated 72 percent of U.S wetlands have already been lost when compared to 

historical estimates (Dahl 2011). 

Estuaries are some of the most productive ecosystems in the world. Thousands of species of 

birds, mammals, fish, and other wildlife depend on estuarine habitats as places to live, feed, and 

reproduce. Many marine organisms, including most commercially-important species of fish, 

depend on estuaries at some point during their development. Estuaries are important nursery and 

rearing habitat for fishes such as salmon and sturgeon, sea turtles, and many other species. For 

example, in estuaries that support salmon, changes in habitat and food-web dynamics have 

altered their capacity to support juvenile salmon (Bottom et al. 2005, Fresh et al. 2005, NMFS 

2006d, LCFRB 2010). Diking and filling activities have reduced the tidal prism and eliminated
30

emergent and forested wetlands and floodplain habitats. These changes likely have reduced 

these estuary’s’ salmon-rearing capacity. Restoration of estuarine habitats, particularly diked 

emergent and forested wetlands, reduction of avian predation by terns, and flow manipulations to 

restore historical flow patterns may have begun to enhance the estuary’s productive capacity for 

salmon, although historical changes in population structure and salmon life histories may prevent 

salmon from making full use of the productive capacity of estuarine habitats.

Figure 2. Average annual net wetland acreage loss and gain estimates for the conterminous U.S. (Taken from Dahl 

2011)

Pollution

In addition to direct loss and alteration of aquatic habitat, many aquatic ecosystems have been 

impacted by various contaminants and pollutants. In 2008, the Heinz Center for Science, 

Economics and the Environment (Heinz Center) published a comprehensive report on the 

condition of our nation’s ecosystems. In their report, the Heinz Center noted the following:

 From 1992 to 2001, benchmarks for the protection of aquatic life were exceeded in 50 

percent of streams tested nationwide—83 percent of streams in urbanized areas—and 94 

percent of streambed sediments.

 Contaminants were detected in approximately 80 percent of sampled freshwater fish and 

most of these detected contaminants exceeded wildlife benchmarks (1992–2001 data) 

(Gilliom et al 2006)

 Nearly all saltwater fish tested had at least five contaminants at detectable levels, and 

concentrations exceeded benchmarks for the protection of human health in one-third of 

fish tissue samples—most commonly DDT, PCBs, PAHs, and mercury (USEPA 2007.)

Toxic contaminants, as noted above have, been documented in the Lower Columbia River and its 

tributaries (LCREP 2007). More than 41,000 waters are listed as impaired by pollutants that 

include mercury, pathogens, sediment, other metals, nutrient, and oxygen depletion, and other 

causes (USEPA 2013a). Pennsylvania reported the greatest number of impaired waters (6,957), 

-458,000

-290,000

-58,550

32,000

-13,800

-500,000

-400,000

-300,000

-200,000

-100,000

0

100,000

1950-1970 1970-1980 1980-1990 1998-2004 2004-2009

Acres of Wetlands
31

followed by Washington (2,420), Michigan (2,352), and Florida (2,292). These figures likely 

underestimate the true number of impaired waterbodies in the U.S. For example, EPA’s 

National Aquatic Resource Surveys (NARS) is a probability based survey that provides a 

national assessment of the nation’s waters and is used to track changes in water quality over 

time. Through this method, EPA estimates that 50 percent of the nation’s streams 

(approximately 300,000 miles) and 45 percent of the nation’s lakes (approximately seven million 

acres) are in fair to poor condition for nitrogen or phosphorus levels relative to reference 

condition waters (USEPA 2013b). However, data submitted by the States indicates that only 

about half of the NARS estimate (155,000 miles of rivers and streams and about four million 

acres of lakes) have been identified on EPA’s 303(d) impaired waters list for nutrient related 

causes (USEPA 2013b).

Water quality problems, particularly the problem of non-point sources of pollution, have resulted 

from changes humans have imposed on the landscapes of the United States over the past 100 to 

200 years. The mosaic or land uses associated with urban and suburban centers has been cited as 

the primary cause of declining environmental conditions in the United States (Flather et al. 1998) 

and other areas of the world (Houghton 1994). Most land areas covered by natural vegetation 

are highly porous and have very little sheet flow; precipitation falling on these landscapes 

infiltrates the soil, is transpired by the vegetative cover or evaporates. The increased 

transformation of the landscapes of the United States into a mosaic of urban and suburban land 

uses has increased the area of impervious surfaces such as roads, rooftops, parking lots, 

driveways, sidewalks, etc., in those landscapes. Precipitation that would normally infiltrate soils 

in forests, grasslands and wetlands falls on and flows over impervious surfaces. That runoff is 

then channeled into storm sewers and released directly into surface waters (rivers and streams), 

which changes the magnitude and variability of water velocity and volume in those receiving 

waters.

Increases in polluted runoff have been linked to a loss of aquatic species diversity and 

abundance, including many important commercial and recreational fish species. Nonpoint 

source pollution has also contributed to coral reef degradation, fish kills, seagrass bed declines 

and algal blooms (including toxic algae) (NOAA 2013). In addition, many shellfish bed and 

swimming beach closures can be attributed to polluted runoff. As discussed in EPA’s latest 

National Coastal Condition Report (NCCR), nonpoint sources have been identified as one of the 

stressors contributing to coastal water pollution (USEPA 2012). Since 2001, EPA has 

periodically released these reports detailing condition of the nation’s costal bays and estuaries 

and assessing trends in water quality in coastal areas. The latest NCCR report indicates that 

coastal water conditions have remained “fair” and the trend assessment demonstrates no

significant change in the water quality of U.S. coastal waters since the publication of the NCCR 

II in 2004 (USEPA 2012).

In many estuaries, agricultural activities are major source of nutrients to the estuary and a 

contributor to the harmful algal blooms in summer, although according to McMahon and 

Woodside 1997 (EPA 2006a) nearly one-third of the total nitrogen inputs and one-fourth of the 

total phosphorus input to the estuary are from atmospheric sources. The National Estuary 

Program Condition Report found that nationally, 37% of national estuary program estuaries are 

in poor condition (http://water.epa.gov/type/oceb/nep/nepccr-factsheet.cfm).
32

Throughout the 20th century, mining, agriculture, paper and pulp mills, and municipalities 

contributed large quantities of pollutants to many estuaries. For example, the Roanoke River and 

the Albemarle-Pamlico Estuarine Complex which receives water from 43 counties in North 

Carolina and 38 counties and cities in Virginia. This estuarine system supports an array of 

ecological and economic functions that are of regional and national importance. Both the lands 

and waters of the estuarine system support rich natural resources that are intertwined with 

regional industries including forestry, agriculture, commercial and recreational fishing, tourism, 

mining, energy development, and others. The critical importance of sustaining the estuarine 

system was reflected in its Congressional designation as an estuary of national significance in 

1987. Even so, today the Albemarle-Pamlico Estuarine Complex is rated in good to fair 

condition in the National Estuary Program Coastal Condition Report despite that over the past 

40-year period data indicate some noticeable changes in the estuary, including increased 

dissolved oxygen levels, increased pH, decreased levels of suspended solids, and increased 

chlorophyll a levels (EPA 2006b). 

Since 1993 EPA has compiled information on locally issued fish advisories and safe eating 

guidelines. This information is provided to the public to limit or avoid eating certain fish due to 

contamination of chemical pollutants. EPA’s 2010 National Listing of Fish Advisories database 

indicates that 98 percent of the advisories are due (in order of importance) to: mercury, PCBs, 

chlordane, dioxins, and DDT (USEPA 2010). Fish advisories have been issued for 36 percent of 

the total river miles (approximately 1.3 million river miles) and 100 percent of the Great Lakes 

and connecting waterways (USEPA 2010). Fish advisories have been steadily increasing over 

the National Listing of Fish Advisories period of record (1993-2010), but EPA interprets these 

increases to reflect the increase in the number of waterbodies being monitored by States and 

advances in analytical methods rather than an increase in levels of problematic chemicals 

(USEPA 2010).

Water-quality concerns related to urban development include providing adequate sewage 

treatment and disposal, transport of contaminants to streams by storm runoff, and preservation of 

stream corridors. Water availability has been and will continue to be a major, long- term issue in 

many areas. It is now widely recognized that ground-water withdrawals can deplete streamflows 

(Morgan and Jones 1999), and one of the increasing demands for surface water is the need to 

maintain instream flows for fish and other aquatic biota.

Climate Change

All species discussed in this Opinion are or will be threatened by the direct and indirect effects of 

global climatic change. Climate change is projected to have substantial direct and indirect 

effects on individuals, populations, species, and the structure and function of marine ecosystems 

in the near future (IPCC 2002). The Intergovernmental Panel on Climate Change (IPCC) 

estimated that average global land and sea surface temperature has increased by 0.85°C (± 0.2) 

since the late-1800s, with most of the change occurring since the mid-1900s (IPCC 2013). This 

temperature increase is greater than what would be expected given the range of natural climatic 

variability recorded over the past 1,000 years (Crowley and Berner 2001). The IPCC estimates 

that the last 30 years were likely the warmest 30-year period of the last 1,400 years, and that 

global mean surface temperature change will likely increase in the range of 0.3 to 0.7°C over the 

next 20 years.
33

Warming water temperatures attributed to climate change can have significant effects on 

survival, reproduction, and growth rates of aquatic organisms (Staudinger et al 2012). For 

example, warmer water temperatures have been identified as a factor in the decline and 

disappearance of mussel and barnacle beds in the Northwest (Harley 2011). Shifts in migration 

timing of pink salmon (Oncorhynchus gorbuscha) which may lead to high pre-spawning 

mortality have also been tied to warmer water temperatures (Taylor 2008). Increasing 

atmospheric temperatures have already contributed to changes in the quality of freshwater, 

coastal, and marine ecosystems and have contributed to the decline of populations of endangered 

and threatened species (Karl et al. 2009; Littell et al. 2009; Mantua et al. 1997). Ocean 

acidification, as a result of increased atmospheric carbon dioxide, can interfere with numerous 

biological processes in corals including: fertilization, larval development, settlement success, 

and secretion of skeletons (Albright et al. 2010).

Climate change is also expected to impact the timing and intensity of stream seasonal flows 

(Staudinger et al 2012). Warmer temperatures are expected to reduce snow accumulation and 

increase stream flows during the winter, cause spring snowmelt to occur earlier in the year, and 

reduced summer stream flows in rivers that depend on snow melt. As a result, seasonal stream 

flow timing will likely shift significantly in sensitive watersheds (Littell et al. 2009). Warmer 

temperatures may also have the effect of increasing water use in agriculture, both for existing 

fields and the establishment of new ones in once unprofitable areas (ISAB 2007). This means 

that streams, rivers, and lakes will experience additional withdrawal of water for irrigation and 

increasing contaminant loads from returning effluent. Changes in stream flow due to use 

changes and seasonal run-off patterns may alter predator-prey interactions and change species 

assemblages in aquatic habitats. For example, a study conducted in an Arizona stream 

documented the complete loss of some macroinvertebrate species as the duration of low stream 

flows increased (Sponseller et al 2010). As it is likely that intensity and frequency of droughts 

will increase across the southwest (Karl et al. 2009), similar changes in aquatic species 

composition in the region is likely to occur. 

Warmer water also stimulates biological processes which can lead to environmental hypoxia. 

Oxygen depletion in aquatic ecosystems can result in anaerobic metabolism increasing, thus 

leading to an increase in metals and other pollutants being released into the water column 

(Staudinger et al 2012). In addition to these changes, climate change may affect agriculture and 

other land development as rainfall and temperature patterns shift. Aquatic nuisance species 

invasions are also likely to change over time, as oceans warm and ecosystems become less 

resilient to disturbances (USEPA 2008). If water temperatures warm in marine ecosystems, 

native species may shift poleward to cooler habitats, opening ecological niches that can be 

occupied by invasive species introduced via ships’ ballast water or other sources (Ruiz et al. 

1999, Philippart et al. 2011). Invasive species that are better adapted to warmer water 

temperatures would outcompete native species that are physiologically geared towards lower 

water temperatures; such a situation currently occurs along central and northern California 

(Lockwood and Somero 2011)

In summary, the direct effects of climate change include increases in atmospheric temperatures, 

decreases in sea ice, and changes in sea surface temperatures, patterns of precipitation, and sea 

level. Indirect effects of climate change include altered reproductive seasons/locations, shifts in 
34

migration patterns, reduced distribution and abundance of prey, and changes in the abundance of 

competitors and/or predators. Climate change is most likely to have its most pronounced effects 

on species whose populations are already in tenuous positions (Isaac 2008).

Clean Water Act

Several laws and regulations have been put in place to help improve the state of our aquatic 

resources, the principal one being the CWA. The original 1948 statute was totally re-written in 

1972 to produce its current purpose: “to restore and maintain the chemical, physical, and 

biological integrity of the Nation's waters” (Federal Water Pollution Control Act, Public Law 92 

–500). Congress made substantial amendment to the CWA in the Water Quality Act of 1987 (P. 

L. 100-4) in response to the significant and persistent water quality problems.

To achieve its objectives, the CWA generally prohibits all point source discharges into the 

nation’s waters, unless otherwise authorized under the CWA. One of the main ways that point 

source discharges are regulated is through permits issued under the NPDES authorized under the 

CWA. For example, the NPDES program regulates discharges of pollutants like bacteria, 

oxygen-consuming materials, and toxic pollutants like heavy metals, pesticides, and other

organic chemicals. EPA has also promulgated regulations setting effluent limitations guidelines 

and standards under sections 301, 304, and 306 of the CWA for more than 50 industries [40 CFR 

parts 405 through 471]. These effluent limitations guidelines and standards for categories of 

industrial dischargers are based on pollutants of concern discharged by industry; the degree of 

control that can be attained using pollution control technology; consideration of various 

economic tests appropriate to each level of control; and other factors identified in sections 304 

and 306 of the CWA (such as non-water quality environmental impacts including energy 

impacts) (F76 FR 22174-22288). These effluent limitations have been credited for helping 

reduce the amount of pollutants like toxic metals entering the aquatic environment (Smail et al 

2012). While provisions of the CWA have helped significantly improve the quality of aquatic 

ecosystems, nonpoint sources of water pollution, which are believed to be responsible for the 

majority of modern water quality problems in the United States, are not subject to CWA permits 

or regulatory requirements. Instead, nonpoint sources of pollution are regulated by programs 

overseen by the States. 

Water quality is important to all of the listed resources identified above in Tables 2 and 3. In 

some cases, the deterioration of water quality has led to the endangerment of aquatic species; in 

all cases, activities that threaten water quality also threaten these listed resources. Endangered 

and threatened species have experienced population declines that leave them vulnerable to a 

multitude of threats. Because of reduced abundance, low or highly variable growth capacity, and 

the loss of essential habitat, these species are less resilient to additional disturbances. In larger 

populations, stressors that affect only a limited number of individuals could once be tolerated by 

the species without resulting in population level impacts, whereas in smaller populations, the 

same stressors are more likely to reduce the likelihood of survival. It is with this understanding 

of the environmental baseline that we consider the effects of the proposed action, including the 

likely effect that CWIS’s will have on endangered and threatened species and their designated 

critical habitat.
35

7.0 Effects of the Action

The effects of the action refer to the direct and indirect effects of an action on the species or 

critical habitat, together with the effects of other activities that are interrelated and 

interdependent with that action. Interrelated actions are those that are part of a larger action and 

depend on the larger action for their justification. Interdependent actions are those that have no 

independent utility apart from the action under consideration. Indirect effects are those that are 

caused by the proposed action and are later in time, but are still reasonably certain to occur. 

Therefore, the issuance of State NPDES permits and any ensuing adverse effects to ESA-listed 

species or critical habitat caused by operation of CWISs is considered to be an indirect effect of 

EPA’s 316(b) Rule promulgation.

In determining whether an action is likely to jeopardize listed species, the Services consider the 

effects of the action are in conjunction with the environmental baseline. The Services 

understand the effects of this action to include the operation of any facility with a CWIS that is 

permitted, either by EPA or by State or Tribal permitting authorities, pursuant to this regulation. 

We recognize the Rule may result in a net reduction of aquatic organisms lost to impingement 

and entrainment when compared to what has occurred historically. However, our analysis of 

effects is based, in part, on the assumption that all covered facilities must comply with the Rule 

or cease CWIS operations. As such, analysis of the effects of this action includes an evaluation 

of the full extent of impacts to listed species that will occur when facilities operate pursuant to 

the Rule, rather than an evaluation of the expected net decline versus current operations. 

Pursuant to section 7(a)(2) of the ESA, Federal agencies are required to insure their actions are 

not likely to jeopardize the continued existence of any listed species or result in the destruction 

or adverse modification of critical habitat. Using the best available scientific and commercial 

information, we describe in this section: the potential physical, chemical, or biotic stressors 

associated with the proposed actions; the probability of individuals of listed species being 

exposed to these stressors; and the probable responses of those individuals (given exposure). If 

responses are likely to reduce an individual’s fitness (i.e., growth, survival, annual reproductive 

success, and lifetime reproductive success), we evaluate the risk posed to the viability of the 

individuals’ population, and ultimately of the species. The ultimate purpose of this assessment is 

to determine whether the proposed action is expected to reduce the species’ likelihood of 

survival and recovery in the wild. 

Our “destruction or adverse modification” determinations must be based on an action’s effects 

on the conservation value of habitat that has been designated as critical to threatened or 

endangered species. If an area encompassed in a critical habitat designation is likely to be 

exposed to the direct or indirect effects of the proposed action on the natural environment, we 

ask if primary constituent elements included in the designation (if there are any) or physical, 

chemical or biotic components that give the designated area conservation value are likely to 

respond to that exposure. 

7.1 Programmatic Approach

As noted, the scope of the 316(b) Rule is nationwide covering an array of facilities that may 
36

affect a wide variety of listed species. The specific State CWA NPDES programs differ in 

regulatory approaches and the individual facilities vary in their size, scope, control technology, 

and operation. It is also uncertain which facilities may ultimately apply for CWA 316(b) 

permits. Under these circumstances, it is not feasible to conduct a meaningful site specific and 

species specific effects analysis, nor is such analysis required given the programmatic nature of 

the Rule and the fact that the Rule is not self-effecting (i.e. it is implemented only through future 

permits). Rather, the Services determined that a programmatic consultation is appropriate to 

address the regulatory process as it is outlined in the Rule and supporting documentation. The 

316(b) Rule outlines the process and responsibilities for both facility owners and State Directors 

and those measures that will be implemented in the future. In our Programmatic approach, we 

examine whether and to what degree EPA has structured their 316(b) Rule to ensure that 

implementation of the final Rule is not likely to jeopardize the continued existence of 

endangered or threatened species or result in the destruction or adverse modification of critical 

habitat. In this evaluation, we assess whether EPA has structured the Rule and supporting 

documentation to enable EPA to fulfill the following criteria: (1) understand the scope of its 

action; (2) reliably estimate the physical, chemical, or biotic stressors that are likely to be 

produced as a direct or indirect result of their action; (3) minimize adverse effects of such 

activities on ESA-listed species and designated critical habitat; (4) identify, inform, encourage, 

and screen applicants for potential eligibility under or participation in the permitting activity; (5) 

continuously monitor and evaluate likely adverse effects on listed species and critical habitat; (6) 

monitor and enforce permit compliance; and (7) modify its action if new information (including 

inadequate protection for species or low levels of compliance) becomes available.

We assess EPA’s compliance with the provisions of section 7(a)(2) of the ESA by evaluating the 

extent to which the Rule and supporting documentation establishes processes to require EPA, the 

owner or operator, and the Director, to collectively implement the provisions of section 316(b) of 

the CWA in a manner that ensures effects to ESA-listed species and critical habitat will be 

minimized and thereby avoid likely jeopardy and likely destruction or adverse modification of 

critical habitat, consistent with section 7(a)(2) of the ESA. Therefore, we focus primarily on the 

required aspects of the Rule and EPA’s commitment to overseeing the implementation of the 

Rule when considering whether EPA has fulfilled its responsibilities under section 7(a)(2) of the 

ESA. 

Key Assumptions for the Effects Analysis 

In developing this analysis, we needed to make a number of key assumptions due to the lack of 

information and uncertainties surrounding the location, timing, frequency, and intensity of CWIS 

activities. If these assumptions prove incorrect or warrant changes during implementation of the 

Rule, it could affect the validity of this analysis and trigger re-initiation of ESA section 7 

consultation if it results in effects that were not considered herein. When EPA is the NPDES 

permitting authority, EPA will consult on all NPDES permits it issues. Where EPA is not the 

permitting authority, the Rule requires Directors to provide the Services copies of all permit 

applications for review and comment, and to include in the record for the draft permit any 

species protection measures that the Services recommend. In addition, Directors must provide 

the Services with copies of all draft permits. We view this exchange of information and any 

resulting coordination as falling within the broad scope of "technical assistance" as described in 
37

the Services' Consultation Handbook. Accordingly, we use the phrase technical assistance to 

describe the exchange of information between Directors and the Services as required in the Rule. 

The following assumptions were used in completing this analysis:

 The Services will receive all permit applications upon receipt by the Director for a 60 day

review prior to publication of a draft permit as required per the Rule.

 The Services anticipate that where necessary, State and Tribal Directors will incorporate 

the control measures, monitoring, and reporting recommendations provided by the 

Services through technical assistance facilitated by the exchange of information between 

the Directors and the Services into NPDES permits that contain 316(b) requirements.

 The control measures, monitoring, and reporting developed by the Services through 

technical assistance with the Directors will minimize the adverse effects of CWIS to 

levels that will avoid jeopardy to species and/or destruction and adverse modification of 

critical habitat.

 In the case of State permits that have been administratively continued, if the Services or 

EPA identify a permitted action by a facility that meets the eligibility requirements of the 

rule which is likely to have more than a minor detrimental effect on Federally-listed 

species or critical habitat, then the Services or EPA will contact the State to seek to 

remedy the situation (for instance by requesting new information from the facility when 

necessary). EPA will provide support and assistance to the Services in working with the 

State or Tribe. EPA and States have no authority to require changes to an expired, 

administratively continued permit. Instead, Directors have authority to issue a new 

permit. Therefore, EPA or the Services could request that the State issue a new permit. 

See 66 Fed. Reg. 11202 (Feb. 22, 2001). The Services assume this process will resolve 

any concerns regarding adverse effects to ESA-listed species and designated critical 

habitat; 

 EPA will work with States and Tribes to reduce or remove the detrimental effects of the 

permit, including, in appropriate circumstances, by objecting to and federalizing the 

permit where consistent with EPA’s CWA authority; and

 In States where EPA is the permitting authority for NPDES permits, EPA will consult 

with the Services on the issuance of those permits where required by ESA section 7. 

1.1.1 Scope

The scope of the action includes all aspects of EPA’s issuance and implementation of the 316(b) 

Rule, including issuance of NPDES permits containing 316(b) requirements for existing power 

generating facilities and existing manufacturing and industrial facilities that withdraw more than 

2 million gallons of water per day from Waters of the United States and use at least 25 percent of 

the water they withdraw exclusively for cooling purposes. While the majority of permits issued 

under the new 316(b) Rule will be State issued permits, EPA has an ongoing role in the 

administration and enforcement of NPDES permits in the states that assumed the NPDES 

permitting authority. While the following regulations are not subject to this consultation, under 

CWA section 402(d) and its implementing regulations (40 C.F.R. § 123.44), EPA reviews 

proposed State NPDES permits and, when EPA determines the permit fails to be consistent with 

the requirements of the CWA, then EPA may assume the authority to issue permits to which it 

has raised objections. In addition, under CWA section 309, EPA has the authority to enforce 
38

conditions and limitations in State NPDES permits. The Rule establishes these conditions and 

limitations as they pertain to the operation of CWIS. 

In order to reliably estimate the probable individual or aggregate effects to ESA-listed species or 

designated critical habitat, EPA would need to know or reliably estimate the probable number of 

facilities that will be subject to the final Rule. Therefore, we ask whether EPA has structured 

their Rule to reliably estimate the probable number and location of facilities with CWIS that will 

be authorized by the Rule and their impact on federally listed species and designated critical 

habitat. Previously, the majority of facilities have not been required to provide EPA or the 

appropriate permitting authority specific information regarding the operation of the CWIS and 

impacts to federally-listed species and critical habitat. EPA knows general information about the 

power generating and manufacturing facilities (15 percent of the potentially regulated 

community), but it does not know the number, location, volume, and timing of water 

withdrawals (if any) from the approximate 3,155 manufacturing facilities. To rectify this paucity 

of information, the Rule requires all facilities to submit, as part of their NPDES permit 

application, specific information including; the facility’s location, description of cooling water 

operations, source water biological data, and identification of threatened and endangered species 

that may be susceptible to impingement or entrainment at their facility. Depending on a 

facility’s selected method of compliance for the impingement mortality standard, 2 years of 

biological monitoring data may also be required to be part of their permit application. In 

addition, owners and operators must identify all federally-listed threatened and endangered 

species and/or designated critical habitat that are or may be present in the action area. 

Through the requirements described above, owners and operators will be responsible for 

determining if listed species and designated critical habitat are likely to occur in an area affected 

by their cooling water intake operations and for notifying the relevant permitting authority if they 

determine that such effects are likely to occur. This requirement assumes that owners/operators 

will have sufficient knowledge to determine the presence or absence of ESA-listed species, and 

designated critical habitat near their facility, and have the technical knowledge necessary to 

determine if their activity might have direct or indirect effects on these species or designated 

critical habitat. Some owners/operators may have sufficient knowledge to make these 

judgments. However, the following points highlight why only a fraction of facilities seem likely 

to satisfy the requirement. 

 Within their biological evaluation (pg 60), EPA identified 21,039 instances where 

threatened or endangered species and facilities currently overlap. 

 There is a reasonable expectation that a listed species may be directly or indirectly 

affected by a facility’s CWIS if that structure overlaps with the range of a listed species, 

and those effects may rise to the level of “take” as defined by the ESA. 

 Facilities subject to the 316(b) Rule are already required to seek an exemption through an 

ESA section 10 incidental take permit (16 U.S.C. 1539 (a)) or an ESA section 7 

Incidental Take Statement (16 U.S.C. 1536(b)(4)) for activities that result in the taking of 

federally-listed species. To our knowledge, few facilities have sought or obtained 

incidental take coverage for effects to listed species that may occur as a result of 

operation of their CWIS.
39

Further evidence that not all facilities are likely to self-identify as affecting federally-listed 

species or designated critical habitat is discussed within the biological evaluation. EPA selected 

eight facilities with a high number of identified overlaps with federally-listed species for review 

in the belief that these permits were likely to contain a discussion of considerations made for 

threatened and endangered species. Despite EPA’s selection of these facilities because of 

overlap with the habitat of threatened and endangered species, review of the eight permits 

indicated: 

 None of the eight discharge permits reviewed had special conditions or requirements 

specifically aimed at protection or minimization of impingement or entrainment to 

threatened or endangered species; 

 Where ESA considerations were noted, little detail was provided describing the methods 

used to establish a finding of no adverse risk; 

 Where improvements to reduce impingement and entrainment through technological or 

management options were required, these requirements were due to concern for the 

resident aquatic community and not for specific threatened or endangered species; and 

 Most concerns regarding facility impacts to aquatic organisms were focused on facility 

discharges particularly thermal pollution (which is regulated under CWA section 316(a)) 

and not with the impingement and entrainment effects more commonly associated with 

CWIS.

The above information illustrates the problem associated with relying solely on owners and 

operators to identify if their operations impact threatened and endangered species. To help 

rectify this ongoing issue, additional language was included in the Rule that requires permitting 

authorities (State Directors or EPA Directors) to transmit all permit applications subject to the 

Rule to the appropriate Field Office of the USFWS and/or Regional Office of the NMFS for a 

60-day review prior to public notice of the draft or proposed permit. This information will be 

transmitted to the Services’ Field or Regional offices upon receipt of the application. Directors 

are also required to provide public comment and notice of draft permits per 40 CFR 124.10. 

Permitting authorities are required to submit a copy of the fact sheet or statement of basis (for 

EPA-issued permits), the permit application (if any) and the draft permit (if any) to the 

appropriate Field Office of the USFWS and/or Regional Office of the NMFS. While the 

requirement to provide draft permits and notice of public comment to the Services is not a new 

provision, the requirement for Directors to provide permit application materials to the Services 

prior to issuing a draft permit is a new requirement. The 60-day review provided to the Services 

will allow the Services to inform Directors if an owner or operator has accurately self-identified 

any potential risk to federally-listed species and/or critical habitat. In addition, the Services may 

recommend protective measures prior to the Director issuing public notice of the draft permit. 

The Director would then include those recommended protective measures in the public notice of 

the draft permit.

The new conditions EPA imposes through the 316(b) Rule creates a process where the Services 

will have an opportunity to review the determinations submitted by the owners or operators 

regarding the potential effects of the CWIS to ESA-listed species prior to a draft permit being

issued. If an owner/operator or Director does not include recommendations of the Services, 

EPA’s commitment to exercise their oversight authority as described in the April 8, 2014,

correspondence from EPA (attached as Appendix A) and as described this Opinion allows EPA 
40

to correct any issues with the permit prior to issuance if EPA finds (giving deference to the views 

of the Services) that the permit will likely have more than minor detrimental effect or is likely to 

jeopardize the continued existence of listed species ore result in the destruction or adverse 

modification of designated critical habitat. This process established in the Rule and EPA’s 

commitment to the oversight of the process will allow EPA to better estimate the number of 

facilities that will be subject to the final Rule so potential project impacts to federally listed 

species and designated critical habitat can be addressed. 

1.1.2 Stressors

To determine if EPA has structured the Rule to reliably estimate the physical, chemical, or 

biological stressors that are likely to be produced as a direct or indirect result of their action, we 

review requirements in the Rule that allow EPA or the delegated State permitting authorities to 

identify stressors likely to be produced by permitted CWIS of existing facilities. Additionally, 

the Preamble to the Rule states EPA will use the full extent of its CWA authority to object to a 

State permit where EPA finds (giving deference to the views of the Services) that a State permit 

is likely to jeopardize the existence of ESA-listed species or adversely modify designated critical 

habitat. 

We also evaluate the stressors identified in the biological evaluation. We provide a general 

overview and review in detail the following stressors: impingement and entrainment; thermal 

discharges; flow alterations; chemical discharge; and cumulative impacts (the aggregate effects 

of multiple facilities operating on one water source). We assess to what extent EPA has 

structured the Rule and supporting documentation to identify and estimate the stressors, and we 

identify reasons for uncertainty. 

Regulatory Requirements—Identifying Stressors 

For EPA-issued permits that may affect ESA-listed species or designated critical habitat, section 

7(a)(2) consultation is required. Consultation information (50 CFR §402.14(c)) requirements 

include: description of the action; description of the specific area that may be affected by the 

action; description of ESA-listed species or designated critical habitat that may be affected by the 

action; description of the manner in which the action may affect ESA-listed species or designated 

critical habitat; relevant reports (e.g., the biological evaluation); and any other relevant available 

information on the action, the affected species, or critical habitat. Using this information from 

each permitted facility, EPA, with assistance from the Services, will be able to identify potential 

direct and indirect stressors. Therefore, for EPA-issued permits (approximately 8 percent of 

potentially regulated facilities), EPA is likely to know or reliably estimate the physical, chemical, 

or biotic stressors that are likely to be produced as a direct or indirect result of activities. 

The Rule establishes information requirements that provide the basis for identifying and 

estimating potential stressors (122.21(r)(2)). The Director cannot waive these information 

requirements. However, several other information requirements are determined by the Director 

on a case-by-case basis. This Director determination for permit requirements on a case-by-case 

basis will be more unpredictable and inconsistent, making it difficult to accurately estimate 

potential stressors. Director determined Permit requirements and allowable modifications to 

BTA include:
41

 Three BTA Standards for Impingement Mortality involve Director-determined BTA or 

allows the Director to authorize less stringent standards;

o 0.5 ft/sec through screen actual velocity, (the Director may authorize an 

exceedance of this standard for brief periods);

o Modified traveling screens,; and

o Systems of technologies as the BTA for impingement mortality.

 BTA standards for entrainment;

 Site-specific impingement and entrainment requirements until 42 months after the 

effective date of the Rule, for existing units at existing facilities (i.e., not BTA standards);

 Additional measures for shellfish;

 Site-specific BTA Standards for Impingement Mortality for CWIS used for electric 

generating unit(s), with an annual average capacity utilization rating of less than eight 

percent (averaged over a 24-month period);

 Control measures, monitoring and reporting requirements that are designed to reduce or 

remove more than minor detrimental effects to federally-listed species and designated 

critical habitat, or avoid jeopardizing federally-listed species or destroying or adversely 

modifying designated critical habitat (e.g., prey base). Such control measures, 

monitoring and reporting requirements may include measures that may have been 

identified by the Services during coordination;

 Prior to 42 months after the effective date of the Rule, the Director determines on a caseby-case basis when the facility becomes subject to site-specific entrainment requirements; 

 Schedule of requirements (i.e., after issuance of a final permit that establishes the 

entrainment requirements, EPA requires the owner or operator of an existing facility to 

comply with the entrainment standard as soon as possible, based on a schedule of 

requirements established by the Director); and

 Alternative requirements or additional BTA standards for entrainment for new units at 

existing facilities.

The biological evaluation states that a detailed evaluation of each of the potential effects of 

facilities subject to the proposed action is not possible because, 

“...driven by vast uncertainty in the universe of regulated facilities, a lack of baseline 

source water biological characterization data, and a dearth of IM&E [impingement 

mortality and entrainment] monitoring data, the scope and magnitude of potential and 

actual effects is unknown for virtually all species and distinct population segments.”

Nonetheless, the biological evaluation provides a qualitative assessment of the stressors 

potentially arising from the proposed action and their possible direct or indirect effects on ESAlisted species and designated critical habitat. These stressors include: impingement and 

entrainment, thermal discharges, chemical discharges, altered flow regimes, and cumulative 

impacts (Table 3 EPA 2013). Further consideration of each stressor is provided in the following 

sections of this Opinion. In Table 3, EPA divides the stressors into those principally associated 

with the CWIS (i.e., impingement, entrainment, and flow alteration) and those associated with 

the discharge of cooling water (flow alteration, thermal discharge, and chemical discharge). 

While discharge of cooling water is regulated 301, 306, or 316(a) of the CWA, and those 

regulations are not subject to this consultation, cooling water discharge is an indirect effect of 
42

cooling water intake as regulated by the Rule and therefore considered in this Opinion. As 

described in the biological evaluation (pg 37), indirect effects of flow alteration, thermal 

discharge, and chemical discharge may include: physiochemical changes in aquatic habitat; 

secondary effects on upper trophic predators (e.g., by reduction in prey) or other species which 

compete for resources with ESA listed species (e.g., spawning habitat loss from flow reduction); 

and other changes in biological communities and/or ecosystem functions (USEPA 2013c). 

These may affect all life stages of ESA-listed species; however, EPA cannot further elaborate on 

these indirect effects because, as stated in the biological evaluation (USEPA 2013c): 

“The exact nature and magnitude of these indirect effects would be species-specific based 

on the relative size and amount of overlap of habitat with facility and CWIS locations, 

dependence of affected prey populations, life cycle considerations, and many other 

factors. Given the lack of direct data available to EPA, indirect effects are difficult if not 

impossible to measure quantitatively. Accordingly, given the lack of data available, EPA 

did not attempt to estimate the relative magnitude or probability of these indirect effects 

on a species-specific scale, but instead acknowledges that these indirect effects are likely 

to occur, and may play a role when the effects of each are summed, or when [ESA-listed] 

species live in areas with a high density of regulated facilities.” 

Table 3: CWIS Effects on Ecosystem Functions/Cumulative Impacts Potentially Affected, Both Directly and 

Indirectly, by 316(b) Regulations (Taken from USEPA 2013c)

Category Direct/Indirect Local/Regional/

National

A. Impingement and Entrainment (direct and indirect effects)

Effects on Individuals

Loss of individuals (direct effects) Direct Local/Regional/National

Phytoplankton Direct Local/Regional/National

Zooplankton (excluding fish larvae/eggs) Direct Local/Regional/National

Invertebrates Direct Local/Regional/National

Fish Direct Local/Regional/National

Non-fish vertebrates Direct Local/Regional/National

Species and Population-Level Effects

Alteration of phenology of system (function of % water 

reduction in stream) Direct Local/Regional/National

Altered distribution of populations Direct Local

Altered niche space Direct Local/Regional

Altered stable age distributions of populations Direct Regional

Loss of keystone species Direct Local

Loss of T&E species Direct Regional

Novel selection pressure (e.g., negatively buoyant or stationary 

eggs) Direct & Indirect Local

Reduced/altered genetic diversity Direct & Indirect Regional/National

Reduced lifetime ecological function of individuals Direct Local/Regional

Community and Trophic Relationships 

Altered competitive interactions Direct & Indirect Local

Disrupted trophic relationships Direct & Indirect Local

Disrupted control of disease-harboring insects (e.g., mosquito 

larvae, etc.) Indirect & Direct Local/Regional

Increased quantity of detritivores Indirect Local

Loss of ecosystem engineers (due to trophic interactions) Indirect & Direct Local

Reduced potential for energy flows (e.g. trophic transfers) Indirect Local/Regional

Species diversity and richness Direct & Indirect Local/Regional/National

Trophic cascades Indirect & Direct Local/Regional

Ecosystem Function
43

Table 3: CWIS Effects on Ecosystem Functions/Cumulative Impacts Potentially Affected, Both Directly and 

Indirectly, by 316(b) Regulations (Taken from USEPA 2013c)

Category Direct/Indirect Local/Regional/

National

Altered ecosystem succession Indirect & Direct Local/Regional

Decreased ability of ecosystem to control nuisance species 

(algae, macrophytes) Indirect Local

Disrupted cross-ecosystem nutrient exchange (e.g., 

up/downstream, aquatic/terrestrial) Indirect Regional

Disrupted nutrient cycling Indirect & Direct Local/Regional

Reduced compensatory ability to deal with environmental 

stress (resilience) Direct & Indirect Regional

Reduced ecosystem resistance Indirect Local/Regional

Reduced ecosystem stability (alternate states) Indirect Local/Regional

Sediment regulation Indirect Local/Regional

Substrate regulation Indirect Local

B. Thermal Effects 

Novel selection pressure (e.g., thermal optima, location of 

breeding, etc.) Direct & Indirect Regional/National

Altered phenology Direct Local/Regional

Links between temperature and metabolism

Dissolved oxygen (physical) Direct Local

Dissolved oxygen (bacterial, respiratory rates) Indirect Local

Ecological energetic demands Indirect Local/Regional

Ecological nutrient demands Indirect Local/Regional

Altered algal productivity Direct & Indirect Local/Regional

Shifted nutrient cycling Indirect & Direct Local/Regional

C. Chemical Effects (anti-foulants, etc.)

Altered survival/growth/production Indirect & Direct Local

Altered food web dynamics Indirect Local

D. Altered Flow Regimes (local and system-wide)

Altered flow velocity Direct & Indirect Local/Regional

Altered turbulence regime Direct & Indirect Local/Regional

E. Cumulative Impacts (as a concentrated number of facilities)

May push systems over the edge of nonlinearities in the system Direct/Indirect Local/Regional

Intensified CWIS effects (as above, Section B.) Direct/Indirect Local/Regional

Intensified thermal effects (as above, Section B.) Direct/Indirect Local/Regional

EPA’s qualitative assessment included an analysis of the overlap between potentially regulated 

facilities (approximately 3,730) and the ranges or designated critical habitat of ESA-listed 

species (USEPA 2013). EPA estimates that a total of 3,490 facilities (94 percent) overlap with 

species’ ranges, and 153 facilities (four percent) overlap with designated critical habitat (note: 

these estimates include ESA-listed species and designated critical habitat under the jurisdiction 

of both Services). Of the 805 positively identified power generating and manufacturing 

facilities, 768 (95 percent) overlap with one or more species, with 258 (37 percent) of such 

facilities withdrawing more than 125 mgd actual intake flow. Therefore, we interpret these data 

as follows:

 Most facilities overlap with at least one ESA-listed species; therefore, threatened or 

endangered species are likely to be exposed to the stressors potentially produced from 

most facilities; 

 A large proportion of “overlap” facilities withdraw more than 125 mgd actual intake 

flow, indicating that the magnitude of each stressor has the potential to be large; and
44

 Few facilities (four percent) overlap with designated critical habitat, possibly because 

critical habitat has not been designated for most (66 percent) ESA-listed species.

The biological evaluation (page 8), states that some of these facilities are already in compliance 

with the impingement requirements of the Rule, as a result of State regulations; despite such 

regulations and the extent of overlap, EPA concludes that “data do not exist to determine the 

extent to which this geographical overlap impacts individuals or populations of [ESA-listed 

species].” In addition, EPA states that “under the final rule, all regulated facilities are required to 

submit baseline source water biological characterization data.” We agree with EPA that the 

availability and quality of information will increase as facilities collect and submit such data, as 

well as additional impingement and entrainment study results (USEPA 2013c). It is important 

that this data will now be provided to the Services for their review, and the Services will be able 

to provide comment to the Director regarding potential impacts to federally-listed species. This 

will enable the Director and EPA to more reliably estimate the effect of the stressors on ESAlisted species that are likely to be produced as a direct or indirect result of activities.

In the biological evaluation, EPA identifies other sources of uncertainty regarding the effects the 

Rule is likely to have on individual species (USEPA 2013c). These sources of uncertainty 

include:

 Lack of data: EPA was unable to identify the complete universe of facilities regulated by 

the Rule, and EPA found few data to estimate the effects of the Rule on ESA-listed 

species. 

 Location of the facility: the location of the facility (the location of the CWIS was often 

unknown) relative to ESA-listed species or designated critical habitat was determined by 

geographic proximity to the range or habitat designations. It did not consider other 

parameters (i.e., upstream or downstream, nearbank vs. farbank) that may affect species 

and CWIS interactions. 

 Location of the CWIS within the source water: the location and depth of the CWIS 

within the cooling water source can affect the overall impact on ESA-listed species, 

designated critical habitat, and vulnerable life stages.

 CWIS water withdrawal volume of facility: CWIS water withdrawal volume varies 

widely due to the size or generating capacity of the facility. Differences in volume were 

not considered and a single very large facility could have a disproportionate effect on 

ESA-listed species or designated critical habitat, if located nearby.

 Scope of CWIS modifications: EPA states that the nature and degree of required CWIS 

modifications will vary among the non-compliant facilities.

 Accuracy of habitat delineations: There is a wide range of variation in accuracy for 

habitat locations of non-federal identified habitats, including well-defined (GISdelineated), approximate (hydrologic unit codes), and descriptive. 

 Impacts on functional groups: EPA states that implementation of the Rule will result in 

CWIS modifications that will reduce impingement mortality and set facility-specific 

requirements for entrainment, resulting in differential beneficial effects among functional 

groups. EPA expects that “fish or pelagic species vulnerable to impingement would 

benefit to a greater degree than freshwater mussels where entrainment of eggs and 

vulnerable life stages constitute the great proportion of species loss.” 
45

 Proportion of the ESA-listed species: EPA states that, with the exception of Federal 

designated critical habitats, there is no information to indicate the relative size or 

importance of the affected habitat to species or sub-populations, relative to the total 

species range or numbers.

In the BE, EPA states that the Rule expands and better defines the responsibilities of the 

compliant facilities seeking the NPDES permit, as well as the interaction of EPA, States, Tribes 

and Services in evaluating the potential impact to ESA-listed species and designated critical 

habitat. However, EPA acknowledges that initial determinations may be based on little available 

data. As facilities collect and submit source water baseline biological characterization data and 

additional impingement mortality and entrainment study results, EPA believes that data 

availability and quality will increase. It reasons that these data, collected over the period of years 

following NPDES permit renewal, will enable EPA and the Services to better determine the 

potential for any adverse impacts on ESA-listed species on a site specific basis. 

As discussed in Section 7.1.1, the Rule requires the owner or operator to identify all threatened 

and endangered species that might be susceptible to impingement and entrainment at their CWIS 

and identify all federally-listed threatened and endangered species and/or designated critical 

habitat that are or may be present in the action area. In the April 8, 2014, correspondence, 

(Appendix A) EPA verified that whenever the phrase “action area” is used in the Preamble and 

Rule, it is to be interpreted in a manner consistent with the definition as found in the Services’ 

regulations implementing ESA section 7 at 50 CFR 402.02. In other words, “action area” 

includes all areas that may be directly or indirectly affected by the operation of a facility’s CWIS 

(i.e., impingement, entrainment, or other adverse effects caused by resultant environmental 

changes, including but not limited to, loss of prey, changes in water quality, and flow alteration). 

As such, owners/operators should identify all federally listed species and designated critical 

habitat that may be directly or indirectly affected by the result of a facility’s CWIS operation. 

The Rule requires the Director to submit all permit applications to the Services. The Services 

can then verify if the list of ESA-listed species and designated critical habitat affected by CWIS 

operations is accurate. While the Rule does not require biological or environmental monitoring 

of CWIS impacts to ESA-listed species and critical habitat from all facilities; the Director may 

include such monitoring requirements that have been provided by the Services. If a State or 

Tribal Director fails to include the Services’ recommended monitoring requirements and the 

Services believe that the permit may result in more than minor detrimental effects to federallylisted species or designated critical habitat, the permit will be subject to EPA oversight 

provisions as outlined in the Preamble of the Rule, the April 8, 2014 correspondence from EPA

(Appendix A), and in section 2.1 of this Opinion. 

As stated above, the Rule requires that Directors provide permit applications to the Services for a 

60-day review period, during which time, the Services may provide technical assistance and 

develop control measures, monitoring and reporting deemed necessary to minimize impacts on 

ESA-listed species and critical habitat. The Rule does not require the Director to include such 

control measures and monitoring/reporting requirements in the NPDES permit. However, if a 

Director fails to include such measures, monitoring and reporting and the Services believe the 
46

permit will have more than minor detrimental effects on federally-listed species or designated 

critical habitat and contacts EPA, then EPA has committed to the following: 

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply with all 

applicable CWA requirements and will discuss appropriate measures protective of 

federally-listed species and critical habitat;

ii. EPA will work with the State or Tribe to reduce or remove the detrimental impacts of the 

permit, including, in appropriate circumstances, by objecting to and federalizing the 

permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit proposed by 

a State where EPA finds (giving deference to the views of the Services) that a State or 

Tribal permit is likely to jeopardize the continued existence of such species or result in 

the destruction or adverse modification of such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will give 

deference to the views of the Services with regard to effects on federally-listed 

fish and wildlife resources.

Through this process and EPA’s commitment to oversight of the process, the Rule improves the 

availability of data and better defines the responsibilities of relevant parties. In addition, the 

process committed to in the Rule also will ensure that any effects from stressors that have more 

than minor detrimental effects or that rise to the level of jeopardizing a listed species or 

adversely modifying critical habitat will be addressed through State incorporation of appropriate 

measures into State permits, EPA’s work with the State or Tribe to reduce or remove the minor 

detrimental impacts, including in appropriate circumstances by objecting to and federalizing the 

permit consistent with EPA’s CWA authority, or EPA’s commitment to exercise the full extent 

of its CWA authority to object to a permit proposed by a State where EPA finds (giving 

deference to the views of the Services) that a State or Tribal permit is likely to jeopardize the 

continued existence of such species or result in the destruction or adverse modification of such 

critical habitat. 

Impingement and Entrainment

In the biological evaluation (pages 3, 10, 21-36, and others), EPA describes impingement and 

entrainment as potential stressors likely to be produced as a result of its action. Impingement 

affects juvenile (e.g., young-of-year) and adult stages of ESA-listed species, while entrainment 

affects vulnerable early life stages (USEPA 2013c). As stated in the biological evaluation, 

impingement and entrainment from CWIS:

“...may represent a substantial portion of annual reproduction. Consequently, 

[impingement and entrainment] may either lengthen species recovery time, or hasten the 

demise of these species much more so than for species that are abundant. For this reason, 

the population-level and social values of [ESA-listed species] losses are likely to be 

disproportionately higher than the absolute number of losses that occur. Unfortunately, 

available quantitative and qualitative data on the effects of CWIS on [ESA-listed] species 

are extremely limited. However, it is known that adverse effects of CWIS on [ESAlisted] species may occur in several ways:
47

 Individual organisms among [ESA-listed] species may suffer direct mortality as a 

consequence of impingement and entrainment. This direct loss of individuals may be 

particularly important because [ESA-listed] species have severely depressed 

population levels that are approaching local, national, or global extinction.

 Individuals may suffer injury, which may reduce survival probability, reproductive 

potential and fitness.

 [ESA-listed] species may suffer indirect harm if the CWIS substantially alters the 

food web in which these species interact. This might occur as a result of altered 

populations of predator or prey species, the removal of foundation species, or (for 

species with parasitic life history stages) the loss of host species.”

The biological evaluation provided limited data regarding the effect of impingement and 

entrainment on ESA-listed species. However, we were able to accumulate some information 

from a small subset of facilities that have completed section 7 consultations or habitat 

conservation plans regarding the effect of impingement and entrainment to sea turtles. We

analyzed data from 14 facilities representing 7 to 33 years of monitoring per facility. Annual 

entrapment at each facility ranged from 0 to 949 turtles. For all facilities during all years, a total 

of 15,595 turtles were entrapped, an average of 46 turtles per facility per year (standard deviation 

= 165). The annual number of deaths at each facility was between 0 to 28 turtles. Data 

presented by the facilities for all years indicated that a total of 385 entrapped turtles died. This 

data represents a minimized impact on sea turtles that can be expected from impingement and 

entrainment, as the facilities summarized here had worked with NMFS through the ESA section 

7 or the section 10 process to reduce their impacts on sea turtles. For further information on 

potential impacts to sea turtles, see Appendix C.

While quantitative and qualitative data on the effects of CWIS on the suite of ESA-listed species 

that may be affected by implementation of the Rule is limited, effects to more common species 

have been documented through various monitoring studies conducted at individual facilities. 

These studies provide further insight as to the effect impingement and entrainment may have on 

federally-listed species. For example, Bay Shore Power Plant located on Lake Erie near the 

mouth of the Maumee River conducted an impingement and entrainment study in 2005 and 

2006. At the time of the study, the plant took in an estimated 638 million gallons of water/day 

for cooling water purposes (Ager et al 2008). The study estimated over 2.2 billion larval fish 

(approximately 10 percent of the larval population in the river), 208 million fish eggs, and 13 

million juvenile fish were entrained on an annual basis. Additionally, an estimated 46 million 

fish were impinged annually (Ager et al 2008). While four species comprised the majority of 

entrainment and impingement losses, over 50 different species of fish were impinged or 

entrained during the course of the study. 

An ecological assessment prepared by the U.S. Army Corps of Engineers (USACE) for the 

Upper Mississippi River and Illinois Waterways in 2000 provides a summary of the aggregate 

effects of impingement and entrainment from multiple facilities along a watercourse. The 

assessment contained a review of impingement and entrainment rates of fish attributed to 40 

power plants. Eleven of the 40 plants had studies on impingement and/or entrainment rates, with 

most studies being 15 to 20 years old (West 2000). From the data available, the USACE 

estimated six of the power plants accounted for over 64 million fish entrained and over 56 
48

million fish impinged on an annual basis (West 2000). Similar to the Bay Shore study, over 50 

different species of fish were impacted, but a smaller set of species accounted for over 50 percent 

of impingement and entrainment losses (West 2000). In both instances, species considered 

relatively common comprised the majority of individuals impinged or entrained.

These studies illustrate the large number of species and individuals that may be impinged and 

entrained at a single facility, or through the combination of multiple facilities along a 

watercourse. So it is likely that any CWIS operating in the vicinity of listed aquatic organisms 

will cause impingement or entrainment of species protected under the ESA (see Appendix C for 

species under NMFS jurisdiction).

With regard to salmonids, we know that without screens and bypass systems, impingement (and 

resulting mortality) is more likely. Automatically cleaned screens with low approach velocity 

(less than 0.4 ft/s), small screen face openings (3/32" circular or square, or 1.75 mm continuous 

slots or rectangular openings) and bypass systems designed for fish swimming ability and 

behavioral traits, typically avoid most juvenile salmonid fish impingement or entrainment, and 

should be used anywhere juvenile salmonids could be present. With inadequate screen 

submergence, the water velocity directly between the water surface and the top of the screen can 

exceed the juvenile salmon swimming ability, potentially capturing fish above the screens until 

they fatigue or become prey. 

EPA acknowledges the potential for impingement and entrainment to lengthen ESA-listed 

species recovery time, or hasten their demise. Effects to individuals include: death, injury, and 

indirect effects (e.g., resulting from trophic cascades). In the biological evaluation, EPA 

explains that it is unable to quantify the extent of the stressors, as a result of limited data. The 

Services agree with EPA that implementation of the standards set forth in this Rule reduces the 

impingement/entrainment of listed organisms. The Services also acknowledges that the ultimate 

extent of such impingement/entrainment is likely to be reduced by implementation of this Rule 

when compared to the extent that pre-dates the effective date of the Rule (i.e., prior to regulation 

by EPA). Upon taking effect, all facilities covered by the Rule will be required to comply with 

the Rule and therefore the appropriate effects analysis for this Opinion is to ask whether the 

levels of impingement/entrainment that will exist after the Rule takes effect and is implemented 

through NPDES permits are consistent with the obligations of section 7(a)(2) of the ESA. 

The Rule requires owners and operators to provide any previously conducted entrainment 

performance studies as an information requirement of all existing facilities so the Director can 

establish site-specific entrainment standards. Additionally, facilities that withdraw more than

125 million gallons of cooling water/day must submit as part of their permit application, an 

entrainment characterization study that includes a minimum of 2 years of entrainment data 

collection. While the Rule does not require monitoring for impingement or entrainment for 

ESA-listed species at any facilities, the Director may establish additional monitoring for 

impingement, and the Director may also establish monitoring requirements for entrainment on a 

site-specific basis. Director determinations of monitoring may include recommendations 

provided by the Services as a result of their review of permit applications. The Rule also states 

that where the Director requires additional measures to protect federally-listed threatened or

endangered species pursuant to 125.94(g) of the Rule, the Director shall require monitoring 
49

associated with those measures. Allowing the Services to provide the Director impingement and 

entrainment monitoring recommendations tailored to address site-specific and species-specific 

issues will help address the following concerns associated with current monitoring efforts as 

identified in the biological evaluation: 

 Because of the low population densities of ESA-listed species and the small volume of 

water sampled for impingement and entrainment studies, it is likely that many impinged 

or entrained individuals are never recorded;

 Species identification is difficult at early life history stages (e.g., egg, larvae), which 

comprise a large proportion of organisms impinged or entrained; and 

 At facilities using fish return technology, individuals returned to the waterbody may not 

be recorded and the condition of the returned individuals is unknown.

In summary, EPA, in their biological evaluation, acknowledges that impingement and 

entrainment have the potential to either lengthen species recovery time, increase the number of 

deaths/injuries to ESA-listed species, or increase their extinction risk. EPA also acknowledges 

that most facilities overlap with at least one ESA-listed species or designated critical habitat. 

Lastly, EPA stipulates that it cannot quantify the effects of impingement and entrainment at this 

time due to limited data. The Rule does not establish monitoring requirements for the 

impingement or entrainment of ESA-listed species and designated critical habitat. Rather, the 

Rule establishes a process that allows the Director to work with the Services to determine if 

additional measures are necessary to reduce impacts to federally-listed species and designated 

critical habitat and if so, to determine the associated monitoring requirements. If the Director 

chooses to not include the measures and associated monitoring requirements in the permit and 

the Services have concerns that a permit will have more than minor detrimental effects on 

federally-listed species or critical habitat and contact EPA with their concerns, EPA has 

committed to the following:

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply with all 

applicable CWA requirements and will discuss appropriate measures protective of 

federally-listed species and critical habitat;

ii. EPA will work with the State or Tribe to reduce or remove the detrimental impacts of the 

permit, including, in appropriate circumstances, by objecting to and federalizing the 

permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit proposed by 

a State where EPA finds (giving deference to the views of the Services) that a State or 

Tribal permit is likely to jeopardize the continued existence of such species or result in 

the destruction or adverse modification of such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will give 

deference to the views of the Services with regard to effects on federally-listed 

fish and wildlife resources.

To date, EPA has not been able to reliably estimate the impact of impingement and entrainment 

associated with CWIS operations on federally-listed species or critical habitat. However, the 

process of information exchange required in the Rule and EPA’s commitment to the oversight of 
50

that process as described above will allow EPA to more reliably estimate stressors associated 

with impingement and entrainment that are likely to be produced as a direct or indirect result of 

CWIS operations subject to the Rule. In addition, the process committed to in the Rule also will 

ensure that any effects from stressors that have more than minor detrimental effects or that rise to 

the level of jeopardizing a listed species or adversely modifying critical habitat will be addressed 

through State incorporation of appropriate measures into State permits, EPA’s work with the 

State or Tribe to reduce or remove the minor detrimental impacts, including in appropriate 

circumstances by objecting to and federalizing the permit consistent with EPA’s CWA authority, 

or EPA’s commitment to exercise the full extent of its CWA authority to object to a permit 

proposed by a State where EPA finds (giving deference to the views of the Services) that a State 

or Tribal permit is likely to jeopardize the continued existence of such species or result in the 

destruction or adverse modification of such critical habitat.

Thermal discharges

Thermal discharges are regulated under sections 301, 306, or 316(a) of the CWA to protect a 

balanced indigenous population of shellfish, fish and wildlife in and on the water. While those 

sections of the CWA are not subject to this consultation, thermal discharges from facilities 

operating a CWIS regulated under this Rule are an interrelated action and thermal discharges are 

known stressors on aquatic environments. 

As described in the biological evaluation, studies have shown that thermal discharges may 

substantially alter the structure of the aquatic community by modifying photosynthetic (Bulthuis 

1987; Chuang et al. 2009; Martinez-Arroyo et al. 2000; Poornima et al. 2005) metabolic, and 

growth rates (Leffler 1972), and reducing levels of dissolved oxygen. Thermal pollution may 

also alter the location and timing of fish behavior including spawning (Bartholow et al. 2004), 

aggregation, and migration (USEPA 2002), and may result in thermal shock-induced mortality 

for some species (Ash et al 1974; Deacutis 1978; Smythe and Sawyko 2000). Thus, thermal 

pollution is likely to alter the ecological services provided by ecosystems surrounding facilities 

returning heated cooling water into nearby waterbodies.

Thermal discharge limitations vary by State, but typically discharges have to remain below 90°F. 

A study conducted in 2008 found that over 350 power plants across 14 different states reported 

discharges exceeding this threshold (Averyt et al. 2011). Large fish kills attributed to an 

exceedance of thermal discharges at power plants have been documented (NCDWQ 2010, 

Schwarzen, C. 2000 in Averyt et al 2011). Many common species of fish cannot tolerate water 

temperatures that exceed 90°F, and for many species of trout, water temperatures that exceed 

80°F can be fatal (Seaby and Henderson 2007, Skaggs et al 2012). “Heat death” in fish occurs 

when temperatures of fish rise to a level where coordination in the central nervous system begins 

to break down (Seaby and Henderson 2007). 

Dissolved oxygen likely plays a key role in temperature tolerance (Niklitchek 2001). Water 

temperature and dissolved oxygen levels are related, with warmer water generally holding less 

dissolved oxygen. In summer, the coupling of low dissolved oxygen at depth and water 

temperatures greater than 20°C above the thermocline limits non-stressful habitat due to a 

temperature-oxygen habitat squeeze (Coutant 1987). Sturgeon, for example, are more sensitive to 

low level dissolved oxygen conditions than some other fishes and become stressed in hypoxic 

conditions (generally under 5 mg/L), which may limit growth, metabolism, activity, and 
51

swimming (Cech et al. 1984, Secor and Gunderson 1998, Secor and Niklitschek 2001, Secor and 

Niklitschek 2002, Cech and Crocker 2002, Campbell and Goodman 2004). 

In summary, EPA acknowledges in the biological evaluation that temperature is “...a master 

environmental variable for aquatic ecosystems, affecting virtually all biota and biologically 

mediated processes, chemical reactions, as well as structuring the physical environment of the 

water column.” As described above, thermal discharges are regulated under sections 301, 306, 

or 316(a) of the CWA and thus, the Rule does not establish control measures or monitoring 

requirements for habitats of ESA-listed species or designated critical habitat impacted by thermal 

discharges. However, as thermal discharges are an indirect effect of CWIS operations, and the 

Rule allows Directors to base their determination of site specific entrainment requirements on the 

benefits of reducing thermal discharge impacts, Directors may require additional measures, 

monitoring and reporting under 316(b) to conserve federally-listed species or designated critical 

habitat. Measures established by the Director may reflect recommendations made by the 

Services during either the 60-day review or the public comment period. If the owner or operator 

or the Director choose not to incorporate Services’ recommended measures, and the Services

contact EPA with concerns that the permit may cause more than minor detrimental effects to 

federally-listed species or critical habitat, then EPA will exercise its oversight authority, 

consistent with the Preamble to the Rule as clarified in the April 8, 2014 correspondence 

(Appendix A). To date, EPA has not been able to reliably estimate the impact of thermal 

discharge associated with CWIS operations on federally-listed species or designated critical 

habitat. However, more information will now be generated as the Rule promotes the exchange 

of information or technical assistance between the Services and the Directors. EPA now 

commits to the oversight of that process, which will allow EPA to more reliably estimate the 

physical, chemical, or biotic stressors that are likely to be produced as a direct or indirect result 

of thermal discharge activities.

Flow alteration

As described in the biological evaluation, the operation of CWIS, including water withdrawals 

and discharge returns, significantly alters patterns of flow within receiving waters, both in the 

immediate area of the CWIS intake and discharge pipe and in mainstream waterbodies. In 

ecosystems with strongly delineated boundaries (i.e., rivers, lakes, enclosed bays, etc.), CWIS 

may withdraw and subsequently return a substantial proportion of water available to the 

ecosystem. For example, of 521 facilities located on freshwater streams or rivers, 164 (31 

percent) have an average intake greater than 5 percent of the mean annual flow of the source 

waters (USEPA 2013c). Based on the ratio of water demand to water supply, power plants are 

the major drivers of water stress in 44 basins across the United States (Skaggs et al. 2012). As 

EPA describes in the biological evaluation, such withdrawals are likely to have significant 

impact on the aquatic habitat, in general, and on ESA-listed species and designated critical 

habitat, especially in inland riverine environments. 

All withdrawals are likely to alter flow characteristics of the waterbody including turbulence and 

water velocity (USEPA 2013c). As described in the biological evaluation, altered flow velocities 

and turbulence may lead to several changes in the physical environment, including: sediment 

deposition (Hoyal et al. 1995), sediment transport (Bennett and Best 1995), and turbidity (Sumer 

et al. 1996), each of which play a role in the physical structuring of ecosystems. Biologically, 

flow velocity is a dominant controlling factor in aquatic ecosystems. Flow has been shown to 
52

alter feeding rates, settlement and recruitment rates (Abelson and Denny 1997), bioturbation 

activity (Biles et al. 2003), growth rates (Eckman and Duggins 1993), and population dynamics 

(Sanford et al. 1994).

In addition to flow rates, turbulence plays an important role in the ecology of small organisms, 

including fish eggs and larvae, phytoplankton, and zooplankton. In many cases, the turbulence 

of a waterbody directly affects the behavior of aquatic organisms, including fish, with respect to 

swimming speed (Lupandin 2005), location preference with a waterbody (Liao 2007), predatorprey interactions (Caparroy et al. 1998; MacKenzie and Kiorboe 2000), recruitment rates 

(MacKenzie 2000; Mullineaux and Garland 1993), and the metabolic costs of locomotion 

(Enders et al. 2003). The sum of these effects may result in changes to the food web or the 

location of used habitat, and thereby substantially alter the aquatic environment (USEPA 2013).

In the biological evaluation, EPA also acknowledges that flow alteration as a result of CWIS 

operation is likely to change over time as a result of climate change. Climate change is predicted 

to have variable effects on future river discharge in different regions of the United States, with 

some rivers expected to have large increases in flood flows, while other basins will experience 

water stress. For example, Palmer et al. (2008) predict that mean annual river discharge is 

expected to increase by about 20 percent in the Potomac and Hudson River basins, but to 

decrease by about 20 percent in Oregon's Klamath River and California's Sacramento River.

To summarize, in the biological evaluation, EPA states that CWIS may alter habitat that is 

essential to the long-term survival of ESA-listed species as a result of altered flow regimes or 

turbidity. Flow alterations may be caused by all degrees of withdrawals, not just those that 

withdraw a significant proportion of the mean annual flow of source waters. To date, EPA has 

not been able reliably estimate the effects of flow alteration on ESA-listed species and critical 

habitat. While the Rule does not establish control measures or monitoring and reporting 

requirements to reduce the effects of flow alteration on ESA-listed species and designated 

critical habitat, it does establish a process that allows the Director to work with the Services to 

determine the benefits of reducing impacts of flow alteration and in determining appropriate 

controls under section 316(b), including those that conserve ESA-listed species. If additional 

measures are necessary, the Services will be able to provide appropriate monitoring and 

reporting recommendations. The Director may then include these measures, monitoring, and 

reporting in the permit. If a State or Tribal Director chooses to not include the measures and 

associated monitoring requirements in the permit and the Services have concerns that a permit 

will have more than minor detrimental effects on federally-listed species or critical habitat and 

contact EPA with their concerns, EPA has committed to the following:

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply with all 

applicable CWA requirements and will discuss appropriate measures protective of 

federally-listed species and critical habitat;

ii. EPA will work with the State or Tribe to reduce or remove the detrimental impacts of the 

permit, including, in appropriate circumstances, by objecting to and federalizing the 

permit where consistent with EPA’s CWA authority; and 
53

iii. EPA will exercise the full extent of its CWA authority, to object to a permit proposed by 

a State where EPA finds (giving deference to the views of the Services) that a State or 

Tribal permit is likely to jeopardize the continued existence of such species or result in 

the destruction or adverse modification of such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will give 

deference to the views of the Services with regard to effects on federally-listed 

fish and wildlife resources.

The technical assistance process facilitated by the exchange of information as required in the 

Rule and EPA’s commitment to the oversight of that process as described above will allow EPA 

to more reliably estimate stressors associated with flow alterations that are likely to be produced 

as a direct or indirect result of CWIS operations subject to the Rule.

Chemical discharges

As described in the biological evaluation, contaminated effluent is a byproduct of once-through 

cooling water systems. Chemical discharges are addressed in NPDES permits by either water 

quality-based effluent limitations or technology-based effluent limitations of the CWA. We 

consider chemical discharges in this consultation, because in the biological evaluation, EPA 

identifies chemical discharges as a stressor produced by operation of CWIS that fall under the 

purview of this Rule.

In the biological evaluation, EPA explains that toxic pollutants, such as metals, polycyclic 

aromatic hydrocarbons, pesticides, biofouling chemicals, or chlorine may be present in the 

discharge of CWISs. They conclude that such chemical discharges could lead to local 

extirpation of sensitive species, or to greatly altered biological communities due to chronic 

impacts on viability, growth, reproduction, and resistance to other stressors (USEPA 2013). To 

date, EPA has not been able to reliably estimate the effects of chemical discharges on ESA-listed 

species and designated critical habitat, as environmental monitoring and data collection has not 

been required from all facilities. The Rule does not establish specific control measures or 

monitoring and reporting requirements to reduce the effects of chemical discharge on ESA-listed 

species and designated critical habitat; however, it does establish a process that allows the 

Director to work with the Services to determine the benefits of reducing impacts of chemical 

discharge and in determining appropriate controls under section 316(b), including those that 

conserve ESA-listed species. If additional measures are necessary, the Services will be able to 

provide appropriate monitoring and reporting recommendations. The Director may then include 

these measures, monitoring, and reporting in the permit. If the Director chooses to not include 

the measures and associated monitoring requirements in the permit and the Services have 

concerns that a permit will have more than minor detrimental effects on federally-listed species 

or critical habitat and contact EPA with their concerns, EPA has committed to EPA has 

committed to the following:

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply with all

applicable CWA requirements and will discuss appropriate measures protective of 

federally-listed species and critical habitat;
54

ii. EPA will work with the State or Tribe to reduce or remove the detrimental impacts of the 

permit, including, in appropriate circumstances, by objecting to and federalizing the 

permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit proposed by 

a State where EPA finds (giving deference to the views of the Services) that a State or 

Tribal permit is likely to jeopardize the continued existence of such species or result in 

the destruction or adverse modification of such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will give 

deference to the views of the Services with regard to effects on federally-listed 

fish and wildlife resources.

The technical assistance process facilitated by the exchange of information between the Director 

and the Services as required in the Rule, and EPA’s commitment to the oversight of that process 

as described above will allow EPA to more reliably estimate stressors associated with chemical 

discharge that are likely to be produced as a direct or indirect result of CWIS operations subject 

to the Rule.

Aggregate Impacts

As described in the biological evaluation, cumulative impacts are the magnified environmental 

stressors created by regulated CWIS when two or more facilities are located nearby (USEPA 

2013c). To avoid confusion with the regulatory definition of cumulative effects, we use the term 

“aggregate impacts.” Aggregate impacts are likely to occur if multiple facilities are located in 

close proximity, such that they impinge or entrain aquatic organisms within the same source 

waterbody, watershed system, or along a migratory pathway of a specific species (e.g., striped 

bass in the Hudson River) (USEPA 2004). Aggregate impacts include the magnified effects of 

indirect effects associated with the operation of CWISs of two or more facilities. 

EPA estimates that approximately 20 percent of potentially regulated facilities are located on 

waterbodies with multiple CWIS (USEPA 2004). Review of geographic locations of 316(b) 

facilities (approximated by CWIS latitude and longitude) indicates that facilities in inland 

settings are clustered around rivers to a greater extent than marine and estuarine facilities 

(USEPA 2013c). In the biological evaluation, EPA explains that aggregate impacts of clustered 

facilities may be significant, due to concentrated impingement and entrainment mortality, 

combined intake flows, and the potential for other impacts such as thermal or chemical 

discharges and flow alterations. EPA also notes that power generation demand and cooling 

intake water volume is typically at its annual maximum during mid-late summer, which is also a 

period of seasonal low flows and highest in-stream temperatures. Although low flows 

traditionally occur in late summer to early fall, drought conditions and manipulations of water 

levels may lead to low flow during other periods as well. Low flow is problematic when it 

overlaps with seasonal concentrations of eggs, developing young of the years, and migrating 

juveniles or adults (USEPA 2013c). EPA estimates that aggregate impacts may be greater in 

inland waters due to the following factors:

 the majority of national annual intake flow is associated with freshwater CWIS; 

 freshwater plants use a greater relative volume of available fish habitat than marine or 

estuarine counterparts; and 
55

 seasonal variation in power demand and river flow may increase entrainment potential 

during low-flow periods of the year (NETL 2009). 

To summarize, in the biological evaluation, EPA acknowledges that the stressors described 

above are magnified when two or more facilities are located in close proximity; approximately 

20 percent of facilities are located in waterbodies with multiple CWIS; and most facilities 

overlap with at least one ESA-listed species. Because the above stressors have the potential to 

lengthen species recovery time, hasten the demise of these species, or alter habitat that is critical 

to long-term survival, magnification of such stressors has a greater potential to jeopardize the 

continued existence of listed species and adversely modify critical habitat. 

To date, EPA has not been able know or reliably estimate the aggregate impacts of CWIS 

operations on ESA-listed species and critical habitat. While the Rule does not establish control 

measures or monitoring and reporting requirements to reduce aggregate impacts from CWIS on 

ESA-listed species and designated critical habitat; it does establish a process that allows the 

Director to work with the Services to determine if additional measures are necessary to reduce 

aggregate impacts and if so, to determine the associated monitoring reporting requirements. The 

Director may then include these measures, monitoring, and reporting in the permit. If the 

Director chooses to not include the measures and associated monitoring and reporting 

requirements in the permit and the Services have concerns that a permit will have more than 

minor detrimental effects on federally-listed species or critical habitat and contact EPA with their 

concerns, EPA has committed to the following:

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply with all

applicable CWA requirements and will discuss appropriate measures protective of 

federally-listed species and critical habitat;

ii. EPA will work with the State or Tribe to reduce or remove the detrimental impacts of the 

permit, including, in appropriate circumstances, by objecting to and federalizing the 

permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit proposed by 

a State where EPA finds (giving deference to the views of the Services) that a State or 

Tribal permit is likely to jeopardize the continued existence of such species or result in 

the destruction or adverse modification of such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will give 

deference to the views of the Services with regard to effects on federally-listed 

fish and wildlife resources.

Summary

Stressors associated with the operation of CWIS as described above have the potential to 

significantly affect federally-listed species and designated critical habitat. EPA has structured 

the Rule to more reliably estimate these physical, chemical, or biotic stressors as they relate to 

federally-listed species and designated critical habitat. For permits issued by EPA on a facility by 

facility basis, EPA is likely to know or reliably estimate the physical, chemical, or biotic 

stressors that are likely to be produced as a direct or indirect result of activities as they are 

required to consult with the Services through the section 7(a)(2) process if the action may affect 
56

listed species or critical habitat. For State-issued permits, the technical assistance process 

facilitated by the exchange of information between the Director and the Services as required in 

the Rule, and EPA’s commitment to the oversight of that process as described in this Opinion 

and in the April 8, 2014, correspondence from EPA, will allow EPA to more reliably estimate 

stressors that are likely to be produced as a direct or indirect result of activities regulated under 

the Rule. Specifically, the Services will now be able to provide review and comment as to 

whether stressors to ESA-listed species have been correctly identified in permit applications. 

The following are those steps in the Rule and supporting documentation that outline this process: 

 ESA-listed species and/or critical habitat that occurs in the action area for a facility and 

impacted by CWIS will be identified by the owner or operator and provided to the 

Services for verification; 

 The Directors are required to send all permit application information to the Services and 

provide the Services with 60 days to review the information. If the Services provide 

control measures, monitoring or reporting requirements to reduce impacts associated with 

CWIS to the Director, the Director may include those in the permit; 

 If the Director does not include the control measures, monitoring or reporting 

requirements recommended by the Services and the Services have concerns that a permit 

will have more than minor detrimental effects on federally-listed species or critical 

habitat and contact EPA with their concerns:

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply 

with all applicable CWA requirements and will discuss appropriate measures 

protective of federally-listed species and critical habitat;

ii. EPA will work with the State or Tribe to reduce or remove the detrimental 

impacts of the permit, including, in appropriate circumstances, by objecting to and 

federalizing the permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit 

proposed by a State where EPA finds (giving deference to the views of the 

Services) that a State or Tribal permit is likely to jeopardize the continued 

existence of such species or result in the destruction or adverse modification of 

such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will 

give deference to the views of the Services with regard to effects on 

federally-listed fish and wildlife resources.

1.1.3 Minimization of likely adverse effects 

In regulations for new facilities (316(b) Phase I), EPA deemed closed-cycle recirculating 

systems to be the best technology available to minimize adverse environmental impacts resulting 

from the operation of CWIS. In the Rule, EPA requires the owner or operator of a new unit at an 

existing facility to reduce the design intake flow “to a level commensurate with that which can 

be attained by the use of a closed-cycle recirculating system” or to “demonstrate achievement of 

reductions commensurate with closed-cycle recirculating system.” We agree that closed-cycle 

systems are the best technology available and are likely to reduce impingement of ESA-listed 

species and reduce impacts to designated critical habitat; however, it is not clear that closed-
57

cycle systems will minimize, as defined in the Rule, such impacts. In the Rule, minimize means 

“to reduce to the smallest amount, extent, or degree reasonably possible.” Without additional 

devices (e.g., screens or excluder bars), closed-cycle recirculation systems may still impinge 

listed species, which is take (or a more than minor detrimental, effect requiring a permit or 

exemption from the Services).

 

Impingement Standard

The BTA Standards for Impingement Mortality involving demonstrated ≤ 0.5 ft/sec throughscreen velocity (design or actual) exceed velocities recommended by the Services (≤ 0.2, 0.33, or 

0.4 ft/sec, depending on conditions) to protect salmonids and other sensitive fishes (FFTT 2011). 

For example, studies have indicated the federally-threatened delta smelt (Hypomesus 

transpacificus) are slow swimmers that are unable to sustain swimming velocities above 0.33 ft/s 

for more than a few minutes (Swanson et al 2000, Swanson et al 1998). Through screen 

velocities of 0.5 ft/sec would likely not provide adequate protection. Therefore, if facilities 

implement the BTA Standard for Impingement Mortality as found in the Rule, impingement of 

ESA-listed species is still likely to occur. This example demonstrates why the requirement for 

Directors to provide the Services an opportunity to review permit applications prior to issuing a 

draft and final permit per the Rule is a critical aspect of EPA’s action. 

The Rule defines a velocity cap as “an open intake designed to change the direction of water 

withdraw from vertical to horizontal, thereby creating horizontal velocity patterns that result in 

avoidance of the intake by fish and other aquatic organisms. For purposes of this [Rule], the 

velocity cap must use bar screens or otherwise exclude marine mammals, sea turtles, and other 

large aquatic organisms.” Offshore is defined as a minimum of 800 feet from the shoreline and 

outside of the littoral zone. If an offshore velocity cap operates as intended (i.e., avoids intake of 

fish and other aquatic organisms), then this BTA Standard for Impingement Mortality minimizes 

impingement of ESA-listed species and designated critical habitat. While the Rule allows the 

Director to establish alternative procedures for visual or remote inspections that verify the 

effectiveness of the velocity cap, the Services will be provided an opportunity to recommend to 

the Director what inspection procedures should entail and notify EPA of any concerns as they 

relate to federally-listed species 

The Rule defines modified traveling screens as “traveling water screens that incorporate 

measures protective of fish and shellfish, including but not limited to: screens with collection 

buckets or equivalent mechanisms designed to minimize turbulence to aquatic life; addition of a 

guard rail or barrier to prevent loss of fish from the collection system; replacement of screen 

panel materials with smooth woven mesh, drilled mesh, molded mesh, or similar materials that 

protect fish from descaling and other abrasive injury; continuous or near-continuous rotation of 

screens and operation of fish collection equipment to ensure any impinged organisms are 

recovered as soon as practical; a low pressure wash or gentle vacuum to remove fish prior to any 

high pressure spray to remove debris from the screens; and a fish handling and return system 

with sufficient water flow to return the fish directly to the source water in a manner that does not 

promote predation or re-impingement of the fish, or require a large vertical drop.” This BTA 

Standard for Impingement Mortality does not include several of the specifications recommended 

by NMFS and adopted by the USFWS to protect salmonids and other fishes (FFTT 2011), 

including: defined maximum screen face openings; spacing of trash racks; maintenance 
58

schedule; debris management requirements; escape routes; sweeping velocities; and 

height/bottom requirements for screens. The Rule states that the Director may approve of fish 

being returned to water sources other than the original source water, which could result in the 

displacement of ESA-listed species or their prey. Additionally, returning fish or other species to 

water sources other than their source water may result in ESA-listed species being impacted due 

to the inadvertent transfer of disease or aquatic invasive species. Based on correspondence 

received from EPA on April 8, 2014, EPA verified that Directors will address any concerns from 

the Services regarding the return of aquatic species to waters other than their source waters. If 

the Services’ concerns are not addressed and the permit would cause more than minor 

detrimental effects, the permit will be subject to the EPA oversight provisions as committed to 

by EPA as a part of their action. While, the modified traveling screen BTA Standard for 

Impingement Mortality as described in the Rule may not be protective enough of federally-listed 

species and designated critical habitat (e.g., prey base), the Services will be provided an 

opportunity to recommend to the Director additional site-specific and species-specific control 

measures during their review of the permit applications as afforded in the Rule. 

The Rule allows an owner or operator to meet the BTA Standard for Impingement Mortality by 

operating a system of technologies, management practices, and operation measures that the 

Director determines is the best technology available, using information from the impingement 

technology performance optimization study. The range of possible systems, practices, and 

measures is wide and unspecified, and their efficacy is unknown. Therefore, we cannot conclude 

that this standard on its own is likely to minimize the impingement of ESA-listed species or 

critical habitat. However, as previously described, the Services will be provided an opportunity 

to recommend additional site-specific and species-specific control measures during their review 

of permit applications.

The Rule also allows a12-month impingement mortality performance standard, which requires 

monthly monitoring. The Rule requires that impingement mortality be less than 24 percent: 

# fish killed***

< 24 percent # fish impinged

***After collected or retained in ≤ 0.56 inch sieve and held for 18 to 96 hours, or other time as specified by the 

Director*

The Rule indicates that the number of fish killed includes latent mortality, for all non-fragile 

species together that are collected or retained in a sieve with maximum opening dimension of 

0.56 inches and kept for a holding period of 18 to 96 hours; it allows the Director to provide an 

alternate holding period. This Standard on its own does not appear to minimize the impingement 

of ESA-listed species or critical habitat. Instead it places a limit (24 percent) on the proportion 

of impinged “fish” that may be killed. This raises several concerns. EPA estimates 1.9 billion 

age-one equivalents are impinged and entrained each year (USEPA 2013d). In the Preamble of 

the Rule, EPA indicates this number could be in the hundreds of billions of aquatic organisms 

when plankton, fish eggs, and larvae are included. The authorization of so many mortalities -

some of which may be listed-species - may jeopardize the continued existence of ESA-listed 

species, which often exhibit extremely low abundance. Additionally, the Standard does not 
59

address the non-lethal fitness costs associated with impingement, such as injury or loss of 

reproductive success. These concerns further demonstrate why the review process afforded the 

Services in the Rule and EPA’s commitment to exercise their oversight authority if necessary are 

critical elements of this action, as the impingement mortality performance standard on its own is 

still likely to result in a large amount of lethal and non-lethal take. However, EPA makes clear 

that the Rule does not authorize take, as defined by the ESA. Furthermore, the Rule requires that 

each permit include as a permit condition a statement that: “nothing in the permit authorizes take 

for the purposes of a facility’s compliance with the ESA.” 

The Rule includes provisions for de minimis rates of impingement. The Rule states that in 

limited circumstances, rates of impingement may be so low at a facility that additional 

impingement controls may not be justified. However, EPA verified in their April 8, 2014,

correspondence with the Services, that in circumstances where a Director determines a facility’s 

rate of impingement is so exceptionally low as to not warrant additional impingement controls, 

the operation of CWIS may still have more than minor detrimental effects on federally-listed 

species if listed species are subject to impingement. A proposed permit that would cause more 

than minor detrimental effects to federally-listed species would be subject to EPA’s oversight 

authority as committed to by EPA as a part of this action.

Based on the analysis above, implementation of the BTA Standards for Impingement Mortality 

on their own is unlikely to minimize adverse effects on ESA-listed species and designated 

critical habitat. Though some BTA Standards have the potential to minimize adverse effects

(e.g. closed cycle and velocity cap), biological monitoring is needed to verify their effectiveness. 

Through ESA section 7 consultation on EPA issued permits and the technical assistance process

with State or Tribal Directors facilitated by the exchange of information as established in the 

Rule, the Services will be able to provide to EPA or the Director additional site-specific and 

species-specific control measures, monitoring, and reporting recommendations to further 

enhance the protectiveness of these standards as they relate to federally-listed species. Examples 

of species-specific control measures the Services may recommend can be found in Appendix D. 

By including the Services recommendations for control measures, monitoring and reporting in 

the final permit, the State or Tribal Director will further reduce the impacts of CWIS operations 

on federally listed species and designated critical habitat. The Services expect, for purposes of 

this Opinion, that issues related to ESA- listed species will be adequately addressed in light of: 

the two opportunities for the Services to engage in the permitting process (in reviewing the 

permit application and the proposed permit), the obligation of State Directors to consider and 

address any information brought to its attention by the Services and make its permitting 

decisions based on the administrative record before it, the opportunity for public participation in 

the permitting process, and, finally, EPA’s commitment to exercise its oversight authority to 

resolve any issues that arise.

Entrainment Standard

EPA gives discretion to the Director in determination of the entrainment standard. The Rule 

states that entrainment requirements “must reflect the Director’s determination of the maximum 

reduction in entrainment warranted after consideration of factors relevant for determining the 

best technology available for minimizing adverse environmental impact at each facility.” These 

determinations must be based on: 
60

 Numbers and types of organisms entrained, including, specifically, the numbers and 

species (or lowest taxonomic classification possible) of federally-listed threatened or 

endangered species and designated critical habitat (e.g., prey base);

 Impact of changes in particulate emissions or other pollutants associated with 

entrainment technologies;

 Land availability inasmuch as it relates to the feasibility of entrainment technology 

 and remaining useful plant life; and

 Quantified and qualitative social benefits and costs of available entrainment technologies 

of a sufficient quality and rigor for the director to make a decision.

The entrainment standards may also be based on:

 Entrainment impacts on the waterbody

 Thermal discharge impacts

 Credit for unit retirements occurring within the past 10 years

 Impacts on water consumption

 Availability of process water, gray water, waste water, reclaimed water, or other waters 

of appropriate quantity and quality for reuse as cooling water

If all technologies considered have social costs not justified by the social benefits, or have 

unacceptable adverse impacts that cannot be mitigated, the Director may determine that no 

additional control requirements are necessary beyond what the facility is already doing. The 

Director may reject an otherwise available technology as BTA standards for entrainment if the 

social costs are not justified by the social benefits. It is important to note that when making these 

determinations, the ESA and its legislative history indicate the preservation of endangered 

species should be given the highest priority (TVA v. Hill 437 U.S. 153 1978). Additionally, the 

Director may reject an otherwise available technology as a basis for entrainment requirements if 

the Director determines there are unacceptable adverse impacts, including: impingement, 

entrainment, or other adverse effects to ESA-listed species or designated critical habitat. 

The Director-determined entrainment requirements are not required to but “may also reflect any 

control measures, monitoring and reporting requirements that are designed to minimize 

incidental take, reduce or remove more than minor detrimental effects to federally-listed species 

and designated critical habitat, or avoid jeopardizing federally-listed species or destroying or 

adversely modifying designated critical habitat. Such control measures, monitoring and 

reporting requirements may include measures or requirements identified by an appropriate Field 

Office of the USFWS and/or Regional Office of the NMFS Service during the 60 day review 

period pursuant to 125.98(h) of the Rule or the public notice and comment period pursuant to 40 

C.F.R. 124.10. If required by the Director, the owner or operator must implement any additional 

control measures 

EPA’s entrainment standard does not specifically reduce the impacts of entrainment on federallylisted species or designated critical habitat. Director determined entrainment requirements are 

likely to vary from State to State and from permit to permit. For EPA issued permits, EPA will 

consult pursuant to section 7 of the ESA with the Services. For State and Tribal-issued permits, 

per the Rule, the Services will be provided an opportunity to recommend site-specific and 

species-specific entrainment requirements to the Director to minimize incidental take and reduce 
61

or remove more than minor detrimental effects of entrainment on federally-listed species and 

designated critical habitat. By including the Services’ recommendations for control measures, 

monitoring and reporting in the final permit, the Director will further reduce the impacts of 

CWIS operations on federally-listed species and designated critical habitat. It is through this 

process, which the Services assume for this consultation will result in inclusion of control 

measures in State and Tribal-issued permits, and EPA’s commitment as part of their action to 

working with States and Tribes to remove more than minor detrimental effects of permits when 

contacted by the Services that EPA has minimized the adverse effects of entrainment that are 

likely to result from EPA’s action. 

Incidental Take

In the Rule, EPA states, “This regulation does not authorize take, as defined by the Endangered 

Species Act, 16 USC 1532(19). The Fish and Wildlife Service and National Marine Fisheries 

Service have determined that any impingement or entrainment of federally-listed species 

constitute take. Such take may be authorized pursuant to the conditions of a permit issued under 

16 U.S.C. 1539(a) or where consistent with an Incidental Take Statement contained in a 

Biological Opinion pursuant to 16 U.S.C. 1536(o).” In addition, EPA requires the Director to 

include the following language as a permit condition: “Nothing in this permit authorizes take for 

the purposes of a facility’s compliance with the Endangered Species Act.” These are statements 

of fact: incidental take may only be exempted or permitted by the Services. 

Neither the Rule, nor permits issued per the Rule, authorizes the incidental take of ESA-listed 

species. However, if during their review of permits as afforded in the Rule, the Services 

determine that a facility’s CWIS operations may result in incidental take, the Services may 

provide the Director additional control measures designed to minimize incidental take. If the 

Director chooses not to include these measures in the permit and the Services contact EPA with 

their concerns, the permit would be subject to EPA’s oversight authority as committed to by EPA 

as a part of this action. This process, as outlined in the Rule and supporting documentation allow

EPA to address incidental take that is reasonably certain to be caused by implementation of the

Rule. 

Summary

EPA has stated adverse environmental impacts include adverse effects to listed species (USEPA 

2013f), and Section 316(b) of the CWA requires that the location, design, construction, and 

capacity of CWIS reflect the BTA for minimizing adverse environmental impacts. As such, 

when determining if a facility has met the requirements of the Rule, the Director should consider 

if a facility has minimized adverse effects to federally-listed species to the smallest amount, 

extent, or degree reasonably practicable. To aid Directors in their decision, EPA has established 

a requirement in the Rule for Directors to provide the Services with all NPDES permit 

applications subject to the Rule for a 60-day review period. The review period will allow the 

Services to review the impacts a facility may have on federally-listed species and designated 

critical habitat and provide the Director any control measures, monitoring and reporting 

requirements the Services believe are necessary to reduce those impacts. If a Director fails to 

include these recommendations in the permit and the Services contact EPA with their concerns, 

the permit would be subject to EPA’s oversight authority as committed to by EPA as a part of 

this action. This process, as outlined in the Rule and supporting documentation will allow EPA 
62

to minimize adverse effects that are reasonably certain to be caused by implementation of the 

Rule.

1.1.4 Identifies, informs, encourages, and screen applicants for potential 

eligibility under the Rule

In this section, we review requirements in the Rule that allow EPA to identify, inform, 

encourage, and screen applicants for potential eligibility under the Rule. The Rule is clear in that 

it applies to owners and operators of existing facilities with CWIS that withdraw > 2 mgd and 

use at least 25 percent of the water for cooling purposes. EPA was able to positively identify all 

electric facilities (n=575) that will be subject to the Rule; however they were unable to identify 

all manufacturing facilities. EPA will inform the regulated community by publishing the Rule in 

the Federal Register (the final rule will be codified in the Code of Federal Regulations) where it 

previously published the original regulations, the suspension of the original regulations, and the 

proposed regulations. It is likely that owners or operators who had previously been issued 

permits are aware that the Rule is in the process of being amended by EPA. 

The current uncertainty surrounding the true number and location of manufacturing facilities is 

problematic. Adding to the uncertainty are those facilities that currently operate under

administratively continued permits. If an applicant has submitted a complete permit application 

for a new permit and the Director is unable to issue a new permit in time, the previous permit is 

administratively continued without an opportunity for comment or review. Such extensions 

allow the facility to continue operating under the provisions of the old permit until the new 

permit is issued. As of EPA’s latest count (March 2013), approximately 24 percent (n=1,617) of 

all major facilities and 17 percent (n=6,569) of all minor facilities were operating under 

administratively continued NPDES permits (USEPA 2013e). These numbers represent the 

“universe of NPDES facilities” and not just those facilities which may be subject to the Rule.

EPA addresses the uncertainty associated with administratively continued permits and their 

potential effects on federally-listed species with the following measures:

 As stated in the Preamble of the Rule, “given the history of litigation around this section

[316(b)] of the Clean Water Act, states have, in some instances, administratively 

extended permits while awaiting final federal action...” EPA is now taking final action 

through the promulgation of the Rule. Some NPDES permits have been continued for a 

decade or more. For example, the 1991 NPDES permit issued by EPA to the Pilgrim 

Nuclear Power Station has been administratively continued since it expired in 1996 (i.e., 

18 years). 

 The Preamble of the Rule goes on to state that, “the Director should consider if any 

[administratively continued] permits would need additional updated information to 

support the permit issuance decision. The Director may, under 40 CFR 122.21(g)(13), 

request additional information including any application requirements in 122.21(r).” As 

the Rule requires owners and operators to identify all federally-listed threatened and 

endangered species and/or designated critical habitat that are or may be present in the 

action area (the area directly or indirectly affected by the operation of a facility’s CWIS) 

as part of their permit application, this is new information that has not been required in 

the past and provides reason for a Director to request this new information from facilities 

operating under administratively continued permits. 
63

Directors are required to provide the Services with a copy of every NPDES permit application 

pertaining to the Rule, allowing the Services to evaluate if a facility’s CWIS operations 

adversely affect federally-listed species. Directors also have authority to request new 

information and to reopen administratively continued permits based on new information (e.g. 

impacts to federally-listed species not previously considered in previous permit applications). 

Given these provisions and EPA’s commitment to exercise their oversight authorities when 

necessary, the Rule and supporting documentation are structured to allow EPA to identify, 

inform, encourage, and screens applicants of their eligibility under the Rule.

1.1.5 Monitoring and evaluation of adverse effects

EPA has established monitoring requirements for four of seven of the BTA Standards for 

Impingement Mortality. These are mainly non-biological monitoring requirements and include: 

daily flow intake for closed-cycle recirculating systems; daily intake flow for offshore velocity 

caps; and daily through-screen actual velocity (maximum = 0.5 ft/sec). Only the impingement 

mortality performance standard requires biological monitoring, which must be conducted at least 

monthly. The monthly monitoring requirement is not likely to be sufficient to identify the 

impingement of ESA-listed species because such organisms are often found in low abundance 

and/or intermittently, such that their impingement may not be detected by a once/per month

monitoring effort. Such monitoring on its own is not sufficient to identify incidental take of 

impinged ESA-listed species. 

EPA requires the Director to determine monitoring and reporting requirements for entrainment 

on a site-specific basis. For both impingement and entrainment, the Director may establish 

additional monitoring and reporting requirements and those requirements may include 

recommendations provided by the Services. As described in the Rule, where the Director 

requires additional measures to protect federally-listed threatened or endangered species or 

designated critical habitat pursuant to 125.94(g), the Director shall require monitoring associated 

with those measures. Directors are also required to submit facilities’ annual reports submitted 

pursuant to 125.97(g) of the Rule, for compilation and transmittal to the Services.

As described above, the Rule does not establish specific monitoring or reporting requirements to 

evaluate likely adverse effects on ESA-listed species or designated critical habitat. However, 

through technical assistance facilitated by the information exchange and review process required 

per the Rule, the Services will be able to provide monitoring and reporting requirements for 

federally-listed species and designated critical habitat on a site-specific and species-specific 

basis. These recommendations will be provided to the Director for his consideration of inclusion 

in the permit. If a Director chooses not to include the Services’ monitoring and reporting 

recommendations in the permit, and the Services have concerns that a permit will have more than 

minor detrimental effects on federally-listed species or critical habitat and contact EPA with their 

concerns:

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply with all 

applicable CWA requirements and will discuss appropriate measures protective of 

federally-listed species and critical habitat;
64

ii. EPA will work with the State or Tribe to reduce or remove the detrimental impacts of the 

permit, including, in appropriate circumstances, by objecting to and federalizing the 

permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit proposed by 

a State where EPA finds (giving deference to the views of the Services) that a State or 

Tribal permit is likely to jeopardize the continued existence of such species or result in 

the destruction or adverse modification of such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will give 

deference to the views of the Services with regard to effects on federally-listed fish 

and wildlife resources.

1.1.6 Compliance

We expect compliance with regulatory requirements because the Rule is enforceable by law, 

EPA and states may levy fines for non-compliance, and citizens may bring citizen suits. EPA 

expects Directors will comply with this rule and that permittees will comply with their permits 

because of the penalties for noncompliance. Additionally, the Services expect compliance 

because take incidental to operation of CWISs permitted through the implementation process 

described in this Opinion and incorporating the control measures, monitoring, and reporting 

recommended by the Services will be exempted from section 9 and section 4(d) take 

prohibitions. 

To estimate the degree of compliance with the Rule and the extent to which enforcement-related 

activities may be taken, we reviewed EPA’s most recent Annual Noncompliance Report, 2012. 

The report summarizes enforcement and compliance data on the “middle tier of NPDES 

facilities” which comprise 41,688 smaller facilities with individual NPDES permits. Of the 

41,688 facilities, EPA had sufficient data to review the compliance status for 83 percent of the 

facilities (USEPA 2014). Over 8,300 facilities (~24 percent) were identified as having a 

Category I violation (i.e., a more serious violation). Accordingly, the report indicated over 8,600 

informal and formal enforcement actions were taken to correct these violations, resulting in over 

$16 million dollars in penalties and fines assessed (USEPA 2014). The total number of 

enforcement actions is higher than the total number of violations as informal enforcement may 

have required subsequent formal enforcement actions. 

The rate of non-compliance with NPDES permits resulting in Category I violations as described 

above is concerning. When combined with violations of a less serious nature (those below the 

Category I level), this rate may be even higher. However, the number of enforcement actions 

taken indicates Directors and EPA do address non-compliance issues and seek means to remedy 

them. 

Per the Rule, owners and operators are required to identify all federally-listed threatened and 

endangered species and/or designated critical habitat that are or may be present in the action area

of their CWIS. As verified by EPA, the phrase “action area” as used in the Preamble and Rule, 

is to be interpreted in a manner consistent with the definition as found in the Services’ 

regulations implementing ESA Section 7 at 50 CFR 402.02. In other words, “action area” 

includes all areas that may be directly or indirectly affected by the operation of a facility’s 
65

CWIS. Additionally, as described in the biological evaluation and in this Opinion, direct and 

indirect effects may include impingement, entrainment, or other adverse effects caused by 

resultant environmental changes, including but not limited to, loss of prey, changes in water 

quality, and flow alteration. The identification of ESA-listed species and the potential direct and 

indirect effects will now be provided by the Director to the Services for the Services’ review and 

comment prior to publication of a draft and final permit. The exchange of information between 

the Director and the Services will help identify any concerns with CWIS operations as they relate 

to federally-listed species and designated critical habitat. While, this process does not require 

Directors or owners and operators to implement recommendations made by the Service to reduce 

impacts to federally-listed species; EPA, as a part of this action, has committed to exercising 

their oversight authority when requested to do so by the Services if a permit will cause more than 

minor detrimental effects to federally listed species or designated critical habitat. The Services 

expect compliance with their recommended control measures, monitoring and reporting because 

incidental take exemption will be afforded to EPA when the Rule, including its implementation 

process, is carried out as described in this Opinion. In addition, any take incidental to the 

operation of a CWIS permitted under the Rule through the implementation process described in 

this Opinion will be exempt from Section 9 and Section 4(d) prohibitions if the owner/operator 

implements enforceable control measures, monitoring, and reporting as agreed upon by the

owner/operator and the Services, and as reflected in the permit. It is through this process, and 

EPA’s commitment as part of their action to the oversight of the process, that allows EPA to

encourage, monitor/evaluate impacts to ESA-listed species, and enforce compliance with the 

Rule. 

1.1.7 Adaptive management

In this section, we evaluate if EPA structured the Rule to allow them to change it or activities 

authorized under it, if deemed necessary, to minimize unanticipated impacts on listed species and 

critical habitat. The Rule does not require the owner or operator to monitor for unanticipated (or 

anticipated) impacts to ESA-listed species or designated critical habitat; however, the Preamble 

describes the authority the Director has to modify a permit if such unanticipated impacts occur. 

As described in the Preamble, “the NPDES regulations also allow a Director to modify a permit 

during the term of the permit, consistent with the Federal regulations at 40 CFR sections 122.62, 

122.63, 122.64, and 124.5. Among other things, under 40 CFR 122.62, reasons for permit 

modification include new information, not available at the time of permit issuance, including 

information on newly listed threatened or endangered species or federally-designated critical 

habitat (or unanticipated impacts thereto) received that would have justified the application of 

different permit conditions at the time of issuance.” 

The biological evaluation states that the true impact of CWIS may be higher than estimated if 

ESA concerns are not revisited regularly during facility relicensing or permitting activities. For 

example, a review of the potential geographic overlap between ESA-listed species and licensed 

commercial nuclear power facilities in the United States was conducted in 1997 (Sackschewsky 

1997). At that time, approximately 484 ESA-listed species were identified as potentially 

occurring near one or more of the 75 facility sites that were examined. Despite the fact that no 

quantitative take data of ESA-listed species were obtained or analyzed, this review required 

updating in only a few years because: 

 nearly 200 species were added to the ESA list between 1997 and 2003; 
66

 critical habitat were newly designated for many species; and 

 significantly more information became available online, allowing for more accurate and 

efficient evaluations of ESA-listed species’ potential presence near power plants 

(Sackschewsky 2004). 

Sackschewsky reevaluated approximately half of the original facilities identified in 1997 (38 of 

75) six years later and found overlap with 452 ESA-listed species, nearly as many found in all

facilities examined in 1997 (Sackschewsky 2004). Although information about each species was 

gathered to support an assessment of the probability of occurrence at each of the reactor sites, no 

attempt to assess take was completed. Reviewing these issues, the Nuclear Regulatory 

Commission concluded that regular review of ESA compliance at each licensed commercial 

nuclear power generating facility was warranted, particularly due to the periodic updating of 

species and designated critical habitat areas on the ESA lists. In the biological evaluation, EPA 

states, “Similarly, regular reviews of ESA compliance at 316(b) regulated facilities is warranted 

in the future.”

As part of the Rule, all facilities will be required to better characterize the waters in the area of 

influence of their CWIS, including the identification of ESA-listed species. Additionally, 

Directors can require facilities to collect additional information if data is missing, newly-listed 

species or newly-designated critical habitat are located in the vicinity of the facility, or other 

environmental conditions (e.g., water quality, flow) have changed since earlier studies. This 

information can include source water baseline biological characterization data, such as: species 

present (including threatened and endangered), species susceptibility to impingement and 

entrainment, spawning periods, and seasonal patterns of the local presence of species. The 

Services will now have an opportunity to review all information contained within the permit 

application and will be able to provide the Director with monitoring and reporting 

recommendations that are appropriate to assess unanticipated (or anticipated) impacts to ESAlisted species or designated critical habitat. If the Director includes the monitoring 

recommendations provided by the Services in a permit, Directors are required to submit to EPA 

the results of such monitoring on an annual basis. These reports will then be transmitted to the 

Services. If impacts associated with CWIS operations are affecting federally-listed species and 

designated critical habitat in unanticipated ways after a permit has been issued, the Services and 

EPA can request the Director reopen the permit. By including a process where appropriate 

monitoring and reporting for federally-listed species can be developed and implemented on a 

species-specific and site-specific basis, and EPA committing to exercising their oversight 

authority if requested by the Services when a permit will have more than minor detrimental 

effects to federally listed species, the Rule allows EPA to use their authorities to request 

modifications to issued permits in order to minimize unanticipated impacts on listed species and 

critical habitat. 

8.0 Cumulative Effects

Cumulative effects include the effects of future State, tribal, local or private actions that are 

reasonably certain to occur in the action area considered by this Opinion. Future Federal actions 
67

that are unrelated to the proposed action are not considered in this section because they require 

separate consultation pursuant to section 7 of the ESA. 

Declines in the abundance or range of many federally-threatened, endangered, and other special 

status species are attributable to various human activities on Federal, State, and private lands, 

such as human population expansion and associated infrastructure development; construction and 

operation of dams along major waterways; water retention, diversion, or dewatering of springs, 

wetlands, or streams; recreation, including off-road vehicle activity; expansion of agricultural or 

grazing activities, including alteration or clearing of native habitats for domestic animals or 

crops; and introductions of non-native plant, wildlife, or fish or other aquatic species, which can 

alter native habitats or out-compete or prey upon native species. Given the action area has been 

identified as waters over which EPA has jurisdiction , from which existing facilities withdraw 

water for cooling purposes, many of these activities are expected to continue within the range of 

various federally protected wildlife, fish, and plant species, and could contribute to cumulative 

effects to the species within the action area. Species with small population sizes, endemic 

locations, or slow reproductive rates will generally be more susceptible to cumulative effects.

9.0 Integration and Synthesis of Effects

EPA proposes to promulgate regulations under 316(b) of the CWA to establish requirements for 

all existing power generating facilities and existing manufacturing and industrial facilities that 

withdraw more than two million gallons per day (mgd) of water from Waters of the U.S. and use 

at least 25 percent of the water they withdraw exclusively for cooling purposes. The action will 

occur throughout the Waters of the U.S., i.e., the action area. The proposed action is likely to 

adversely affect the species and critical habitats listed in Tables 2 and 3. Here, we integrate 

information presented in this Opinion to summarize stressors and the likely consequences of 

exposing listed resources to these stressors.

A significant portion of the nation’s waters have been impacted by anthropogenic stressors 

described within this Opinion. Based on available information, impingement and entrainment 

has resulted in the death or injury of billions of aquatic organisms, flow regimes have been 

altered, water quality has been degraded by physical and chemical pollutants, and ecosystems

have been altered by a combination of these and other stressors. The operation of CWIS at 

power generating and manufacturing facilities contributes to all of these stressors. 

Power generating facilities are estimated to use between 60 billion and 200 billion gallons of 

water per day (Kenny et al. 2005, Averyt et al. 2011). These withdrawals account for 41 percent 

of all fresh water use in the United States. In some instances, intake from one facility can 

represent more than five percent of the average annual flow of its source water. While much of 

this water is eventually returned to the source, it is returned at temperatures that are as much as

50°F warmer than intake temperatures (Madden 2013). Thermal pollution can have a wide range 

of effects on aquatic communities including altering spawning and migration patterns to altering 

chemical properties of water by reducing dissolved oxygen (Madden 2013). Elevated water 

temperatures in streams, lakes, and rivers as a result of climate changes are projected to further 

exacerbate thermal pollution effects. In addition to thermal pollution, discharges from 316(b) 
68

regulated facilities can include toxic pollutants, such as metals, polycyclic aromatic 

hydrocarbons (PAHs), pesticides, biofouling chemicals, or chlorine (USEPA 2013c)

EPA estimates that hundreds of billions of plankton, fish eggs, and larvae are lost every year as a 

result of impingement or entrainment for cooling water withdrawals (USEPA 2013f). Other 

studies conducted at individual facilities appear to support this estimate (Seaby and Henderson, 

2007, Rossman 1986). When examining the number of ESA-listed species lost as a result of 

impingement and entrainment, EPA extrapolates that more than 65,000 eggs, larvae and adults of 

ESA-listed fish and sea turtles are lost on an annual basis (USEPA 2013c). As stated in the 

biological evaluation, aquatic species are disproportionately imperiled relative to terrestrial 

species; 39 percent of freshwater and diadromous fish species (Jelks et al. 2008), 67 percent of 

freshwater mussels (Williams et al. 1993) and 48 percent of crayfish (Taylor et al. 2007) are 

classified as special concern, threatened, or endangered. Given these numbers, the amount of 

direct loss of ESA-listed species due to impingement and entrainment is probably much higher 

than estimated by EPA, as ESA-listed species are found at low population densities, and the 

volume of water sampled by facility-level impingement and entrainment studies is low.

Our Programmatic Effects Analysis assesses whether, and to what degree, EPA structured the 

Rule to establish processes that require EPA , the owner or operator, and the Directors to

collectively implement the provisions of section 316(b) of the CWA in a manner that addresses

adverse effects to listed species, and ensures the operation of facilities subject to the Rule are not 

likely to jeopardize the continued existence of endangered or threatened species or destroy or 

adversely modify designated critical habitat. We addressed this issue by answering seven 

questions:

First, we concluded that EPA has structured the Rule to better estimate the number of facilities 

that may adversely affect ESA-listed species and designated critical habitat. While EPA is 

currently unable to identify all facilities that will be subject to the Rule and thus quantify impacts 

to listed species associated with CWIS operations, per the Rule, facilities will have to identify

threatened and endangered species and/or designated critical habitat that are or may be within the 

action area. The Services will now have an opportunity to review these determinations prior to a 

draft permit being issued, provide technical assistance to the Directors regarding the species lists,

and the Services may notify the Director or EPA of any inaccuracies or discrepancies that may 

exist. Thereby, facilities whose operations impact listed species or critical habitat will be 

correctly identified. 

Second, we concluded the Rule allows EPA to more reliably estimate the physical, chemical, or 

biotic stressors that are likely to be produced as a direct or indirect result of their action. As 

previously discussed, impingement and entrainment rates of fish at larger facilities can be in the 

billions and smaller facilities may impinge and entrain millions. Other stressors, including flow 

alteration and chemical discharge, can also have significant impacts on the aquatic environment. 

The information exchange between the Director and the Services established in the Rule 

provides a process of technical assistance whereby impacts associated with these stressors will 

be more accurately identified by the Services, as owners, operators, and Directors may not have 

the expertise necessary to do so. For purposes of this consultation, the Services assume that 
69

State and Tribal Directors will include Services’ recommended measures for protection of 

species in final permits. Additionally, EPA’s commitment to the oversight of that process as 

described in the Preamble to the Rule as clarified in the April 8, 2014 correspondence from EPA

(attached as Appendix A), will allow EPA to more reliably estimate stressors that are likely to be 

produced as a direct or indirect result of activities regulated under the Rule. Specifically: 

 Owners’ or operators’ identification and determinations of ESA-listed species and critical 

habitats impacted by their CWIS in their permit application will be provided to the 

Services for verification; 

 The Directors are required to send all permit application information to the Services and 

provide the Services with 60 days to review the information. If the Services provide 

control measures, monitoring or reporting recommendations to reduce impacts associated 

with CWIS to the Director, the Director may include those in the permit; 

 If a Director chooses not to include the Services’ monitoring and reporting 

recommendations in the permit, and the Services have concerns that a permit will have 

more than minor detrimental effects on federally-listed species or critical habitat and 

contact EPA with their concerns:

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply with 

all applicable CWA requirements and will discuss appropriate measures protective of 

federally-listed species and critical habitat;

ii. EPA will work with the State or Tribe to reduce or remove the detrimental impacts of 

the permit, including, in appropriate circumstances, by objecting to and federalizing 

the permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit proposed 

by a State where EPA finds (giving deference to the views of the Services) that a 

State or Tribal permit is likely to jeopardize the continued existence of such species 

or result in the destruction or adverse modification of such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will give 

deference to the views of the Services with regard to effects on federally-listed 

fish and wildlife resources.

Third, we concluded EPA structured the Rule to minimize the adverse effects of impingement, 

entrainment, and other stressors produced by CWIS on ESA-listed species and designated critical 

habitat. As described in our analysis, the Impingement Standards and Director determined 

Entrainment Standard provided in the Rule are not designed to specifically minimize impacts to

ESA-listed species. However, the Services will be able to provide site-specific and speciesspecific control measures, monitoring and reporting recommendations through the review 

process. As EPA was unable to provide specific information on each facility’s CWIS operations 

and associated impacts to federally listed species for purposes of this consultation, the Services’ 

development of control measures is more appropriate during the review of each facility’s permit 

application. EPA’s oversight commitment provides assurance that permits that may result in 

more than minor detrimental effects to listed species or designated critical habitat will be 

corrected before issuing. 
70

Fourth, we concluded that EPA has structured the Rule to identify, inform, and encourage all 

eligible applicants of their eligibility under the Rule. EPA was unable to identify all eligible 

facilities for purposes of this consultation, and eligible facilities may continue to operate under 

administratively continued permits. However, the Rule requires owners and operators provide 

updated information on impacts to ESA-listed species as part of their permit applications. This 

information was not previously required and is information a Director would need to support 

his/her permit issuance decision for facilities with administratively continued permits. A 

Director’s ability to reopen administratively continued permits for new information along with 

EPA’s commitment to exercise their oversight authorities when necessary, allow EPA to 

identify, inform, encourage, and screens applicants of their eligibility under the Rule. 

Fifth, we concluded that EPA has structured the Rule to continuously monitor and evaluate 

adverse effects associated with CWIS on ESA-listed species and designated critical habitat. 

While the Rule does not establish specific monitoring or reporting requirements to evaluate 

adverse effects on ESA-listed species or designated critical habitat, it does allow those 

monitoring and reporting requirements to be developed on a site-specific and species-specific 

basis via technical assistance facilitated by the exchange of information between the Director and

the Services. One of the Services’ assumptions for this consultation is that the Services 

anticipate where necessary, State and Tribal Directors will incorporate the control measures, 

monitoring, and reporting recommendations provided by the Services through technical 

assistance facilitated by the exchange of information between the Directors and the Services into 

NPDES permits that contain 316(b) requirements. If a Director chooses not to include the 

Services’ monitoring and reporting recommendations in the permit, and the Services have 

concerns that a permit will have more than minor detrimental effects on federally-listed species 

or critical habitat and contact EPA with their concerns, EPA has committed to the following 

oversight process described in the Preamble to the Rule and as clarified in the April 8, 2014 

correspondence with the Services (attached as Appendix A):

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply with 

all applicable CWA requirements and will discuss appropriate measures protective of 

federally-listed species and critical habitat;

ii. EPA will work with the State or Tribe to reduce or remove the detrimental impacts of 

the permit, including, in appropriate circumstances, by objecting to and federalizing 

the permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit proposed 

by a State where EPA finds (giving deference to the views of the Services) that a 

State or Tribal permit is likely to jeopardize the continued existence of such species 

or result in the destruction or adverse modification of such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will give 

deference to the views of the Services with regard to effects on federally-listed 

fish and wildlife resources.

Sixth, we concluded EPA has structured the Rule to encourage, monitor/evaluate, and enforce 

compliance regarding ESA issues. We have little data indicating EPA has previously used its 

oversight authority to review and object to State issued permits specifically to reduce the impacts 
71

of NPDES permits on ESA-listed species. However, available data does indicate that EPA and 

Directors do take enforcement actions to correct non-compliant NPDES permits. Additionally, 

EPA expects a high rate of compliance with the Rule and any measures that the Services may 

provide through technical assistance. The exchange of information between the Director and the 

Services required in the Rule will help identify any concerns with CWIS operations as they relate 

to federally-listed species and designated critical habitat. The Directors may address those 

concerns through NPDES permit conditions that implement the Services control measures, 

monitoring, and reporting recommendations. While, the Rule does not stipulate that Directors 

must include recommendations made by the Services to reduce impacts to federally-listed 

species in the permit, one of the Services’ assumptions for this consultation is that the Services 

anticipate where necessary, State and Tribal Directors will incorporate the control measures, 

monitoring, and reporting recommendations provided by the Services through technical 

assistance facilitated by the exchange of information between the Directors and the Services into 

NPDES permits that contain 316(b) requirements. In addition, in the Preamble to the Rule and 

as clarified in the April 8, 2014 correspondence (attached as Appendix A), EPA, as a part of this 

action, has committed to exercising their oversight authority when requested to do so by the 

Services in cases where a permit will cause more than minor detrimental effects to federallylisted species or designated critical habitat. 

Seventh, we concluded the Rule is structured to inform EPA of unanticipated impacts to ESAlisted species and, if necessary, allow EPA to minimize such unanticipated impacts on listed 

species and critical habitat. State Directors have the ability to modify a permit during the term of 

the permit if new information, including information on newly listed threatened or endangered 

species or federally-designated critical habitat (or unanticipated impacts thereto) is received that 

would have justified the application of different permit conditions at the time of issuance. EPA 

also has the authority to object to issuance of permits that will result more than a minor 

detrimental effect on ESA-listed species or critical habitat or result in jeopardy to species and/or 

destruction and adverse modification of critical habitat. In both cases, the Rule establishes a 

process where:

 The Services will have the opportunity to provide Directors with appropriate monitoring 

recommendations designed to detect impacts of CWIS operations on federally-listed 

species and critical habitat. Information provided as a result of this monitoring will allow 

Directors to reopen and modify permits if necessary;

 EPA will work with States and Tribes to remove the detrimental effects of permits if 

requested by the Services to do so.

10.0 Conclusion

After reviewing the current status of the species, the environmental baseline for the action area, 

the effects of the proposed action, and the cumulative effects, it is our biological opinion that 

EPA’s action, as proposed, is not likely to jeopardize the continued existence of ESA-listed 

species listed in Tables 2 and 3 of this Opinion and is not likely to destroy or adversely modify 

designated critical habitat identified in Tables 2 and 3.
72

As described in the Rule and this Opinion, the operation of CWIS can have significant adverse 

effects on the aquatic environment and federally-listed species. EPA’s Rule establishes a process 

(Figure 3) whereby the Services will be provided an opportunity to review permit applications of 

each facility seeking compliance with 316(b) of the CWA, either during a section 7 consultation

with EPA or during review of every permit application submitted to a State or Tribe, and analyze 

impacts to federally-listed species and designated critical habitat that may result from operation 

of the facility’s CWIS. During this review, the Services will have an opportunity to recommend

control measures, monitoring and reporting recommendations on a site specific and species 

specific basis that will minimize adverse effects of CWIS operations. If the Services contact 

EPA with concerns that a State or Tribal permit will have more than minor detrimental effects on 

federally-listed species or critical habitat that cannot be resolved with the State or Tribal 

permitting authority: 

i. EPA will coordinate with the State or Tribe to ensure that the permit will comply with all 

applicable CWA requirements and will discuss appropriate measures protective of 

federally-listed species and critical habitat;

ii. EPA will work with the State or Tribe to reduce or remove the detrimental impacts of the 

permit, including, in appropriate circumstances, by objecting to and federalizing the 

permit where consistent with EPA’s CWA authority; and 

iii. EPA will exercise the full extent of its CWA authority, to object to a permit proposed by 

a State where EPA finds (giving deference to the views of the Services) that a State or 

Tribal permit is likely to jeopardize the continued existence of such species or result in 

the destruction or adverse modification of such critical habitat.

o Based on correspondence received from EPA on April 8, 2014, EPA will give 

deference to the views of the Services with regard to effects on federally-listed 

fish and wildlife resources.

Therefore, it is our opinion that this Rule has built in a sufficient process to insure that it is not 

likely to result in an appreciable reduction in the likelihood of both the survival and recovery of 

any listed species by reducing the reproduction, numbers or distribution of that species. It is also 

our opinion that the process insures that this Rule is not likely to result in destruction or adverse 

modification of critical habitat. The process achieves this through a comprehensive suite of 

requirements, including, but not limited to:

 Ensuring every permit application is provided to and reviewed by the Services ,thereby 

allowing the Services to provide meaningful input to State Directors early in the permit 

application process so that measures to address ESA-listed species may be incorporated 

into State permits; 

 The Services or EPA identifying administratively continued permits which are likely to 

have more than minor detrimental effects on federally-listed species or critical habitat, 

contacting the State to seek to remedy the situation (for instance by requesting new 

information from the facility when necessary) and EPA or the Services requesting that 

the State issue a new permit when appropriate to resolve the concerns of the Services; 

and 
73

 Ultimately ensuring that no permit is issued that is likely to jeopardize the continued 

existence of an ESA-listed species or result in the destruction or adverse modification of 

designated critical habitat by either (a) incorporation into State permits conditions 

necessary to avoid jeopardy to ESA-listed species or adverse modification to critical 

habitat; or (b) if the such conditions are not incorporated, preventing issuance of the State 

permit by exercising the full extent of its CWA authority, to object to a permit proposed 

by a State where EPA finds (giving deference to the views of the Services) that a State or 

Tribal permit is likely to jeopardize the continued existence of such species or result in 

the destruction or adverse modification of such critical habitat jeopardizing permit. 

We base our conclusion, in part, on the following assumptions:

 The Services will receive all permit applications upon receipt by the Director for a 60 day 

review prior to publication of a draft permit as required per the Rule;

 The Services anticipate that where necessary, State and Tribal Directors will incorporate 

the control measures, monitoring, and reporting recommendations provided by the 

Services through technical assistance facilitated by the exchange of information between 

the Directors and the Services into site-specific NPDES permits that contain 316(b) 

requirements;

 The control measures, monitoring, and reporting developed by the Services through 

technical assistance with the Directors will minimize the adverse effects of CWIS to 

levels that will avoid jeopardy to species and/or destruction and adverse modification of 

critical habitat;

 In the case of State permits that have been administratively continued, if the Services or 

EPA identify a permitted action by a facility that meets the eligibility requirements of the 

rule which is likely to have more than a minor detrimental effect on Federally-listed 

species or critical habitat, then the Services or EPA will contact the State to seek to 

remedy the situation (for instance by requesting new information from the facility when 

necessary). EPA will provide support and assistance to the Services in working with the 

State or Tribe. EPA and States have no authority to require changes to an expired, 

administratively continued permit. Instead, Directors have authority to issue a new 

permit. Therefore, EPA or the Services could request that the State issue a new permit. 

See 66 Fed. Reg. 11202 (Feb. 22, 2001). The Services assume this process will resolve 

any concerns regarding adverse effects to ESA-listed species and designated critical 

habitat;

 As discussed in the preamble of the Rule and the April 8, 2014 correspondence 

(Attachment A), EPA will work with States and Tribes to reduce or remove the 

detrimental effects of the permit, including, in appropriate circumstances, by objecting to 

and federalizing the permit where consistent with EPA’s CWA authority; and 

 In States where EPA is the permitting authority for NPDES permits, then EPA will 

consult with the Services on the issuance of those permits where required by ESA section 

7. 
74

Figure 3. General process of Information Exchange and Technical Assistance Between Directors and the 

Services. Ovals represent start and end points; rectangles represent activities required in the Rule; 

diamonds represent discretionary activities described in the Rule. Process may be adjusted when 

warranted for consideration of individual permits.

In permit application, facility identifies 

species or critical habitat present in action 

area?

Director sends permit 

application to 

Services?

Facility implements 

Services 

recommendations? Impacts to species 

and critical habitat 

not minimized, 

take not exempted.

Impacts to species 

and critical habitat 

minimized, incidental 

take exempted

EPA exercises 

oversight 

authority.

Permit subject to 

EPA oversight 

authority.

CWA 316(b) 

violation

CWA 316(b) 

violation

No Yes

Yes or No

no

Permit subject to 

Director and EPA 

oversight authority.

Facility regulated

under CWA 316(b)?

Services 

contact EPA 

with concerns? 

Yes

Yes

Yes

Yes

No

No

No

Director includes 

recommendations from 

Services in final 

permit?

Services provide

recommendations?

Yes

Director may issue 

permit.
75

11.0 Incidental Take Statement

Section 9 of the ESA and Federal regulation pursuant to section 4(d) of the ESA prohibit the 

“take” of endangered and threatened species, respectively, without special exemption. “Take” is 

defined as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt 

to engage in any such conduct. Harm is further defined by the USFWS as an act which actually 

kills or injures wildlife, which may include significant habitat modification or degradation that 

results in death or injury to listed species by significantly impairing essential behavioral patterns, 

including breeding, feeding, or sheltering. Harass is defined by the USFWS as actions that 

create the likelihood of injury to listed species by annoying them to such an extent as to 

significantly disrupt normal behavior patterns which include, but are not limited to, breeding, 

feeding or sheltering. Incidental take is defined as take that is incidental to, and not the purpose 

of, the carrying out of an otherwise lawful activity. Under the terms of sections 7(b)(4) and 

7(o)(2), taking that is incidental and not intended as part of the agency action is not considered to 

be prohibited taking under the ESA provided that such taking is in compliance with the terms 

and conditions of this Incidental Take Statement. 

Section 7(b)(4) and 7(o)(2) of the ESA generally do not apply to listed plant species. However, 

limited protection of listed plants from take is provided to the extent that the ESA prohibits the 

removal and reduction to possession of Federally listed endangered plants or the malicious 

damage of such plants on areas under Federal jurisdiction, or the destruction of endangered 

plants on non-Federal areas in violation of State law or regulation or in the course of any 

violation of a State criminal trespass law.

Amount or Extent of Take Anticipated

While the BE provided an analysis of impacts related to stressors to ESA-listed species, the 

paucity of information submitted by EPA regarding facilities with CWIS does not allow the 

Services to identify facility locations, the specific actions of those facilities that may result in 

take of listed species, the number of individuals that might be taken by those actions, or the 

proportion of populations of endangered or threatened species these might represent. However, 

through implementation of the Rule, this information will be provided to the Services. At the 

appropriate Field Office of the USFWS or Regional Office of NMFS, the Services’ will have the 

opportunity to review all NPDES permit applications for each facility seeking compliance under

316(b) of the CWA, either during section 7 consultation with EPA or during the technical 

assistance process for State and Tribal-issued permits identified in the Rule. This affords the 

Services the opportunity to appropriately evaluate project effects on a site-specific and speciesspecific basis. This review will allow the Services to provide technical assistance to the State or 

Tribal Director and the owner/operator to adjust an action that may result in the take of 

endangered or threatened species. As described in our conclusion, we assume that through

technical assistance with the State or Tribal Directors, appropriate control measures to minimize 

incidental take and detrimental effects associated with the operation of CWIS will be developed

by the Services, and that these measures will ensure that each permit will minimize adverse 

effects and thereby avoid jeopardy to ESA-listed species identified in Tables 2 and 3 and avoid 

destruction or adverse modification of critical habitat. We also assume Directors will 

incorporate the Services’ recommendations into NPDES permits that contain 316(b) 
76

requirements. If it is determined, through section 7 consultation with EPA or through technical 

assistance on individual permits with State or Tribal Directors that take of ESA-listed species is 

still expected to occur after implementation of recommended control measures, the amount or 

extent of incidental take will be quantified, at that time by the appropriate Field Office of the 

USFWS and/or Regional Office of the NMFS. 

Incidental take exemption will be afforded to EPA when the Rule, including its implementation 

process, is carried out as described in this Opinion. In addition, any take incidental to the 

operation of a CWIS permitted under the Rule through the implementation process described in 

this Opinion will be exempt from Section 9 and Section 4(d) prohibitions if the owner/operator 

implements enforceable control measures, monitoring, and reporting as agreed upon by the

owner/operator and the Services, and as reflected in the permit.

In summary, because of the large scale and broad scope of the proposed action, even the best 

scientific and commercial data available are not sufficient to enable the Services to accurately 

estimate the specific amount of potential incidental take associated with the action at this time. 

Incidental take of listed species will be quantified during ESA section 7 consultation process for 

permits issued by EPA or the technical assistance process for State and Tribal-issued permits 

associated with our review of the 316(b) application for a specific facility. This Incidental Take 

Statement does not apply in the absence of any take prohibited under Section 9 or Section 4(d) of 

the ESA.

12.0 Reasonable and Prudent Measures

The following reasonable and prudent measure is necessary and appropriate to minimize impacts 

of incidental take to species identified in Tables 2 and 3.

1. EPA will use its authorities under the CWA to minimize impacts to listed species 

pursuant to the 316(b) Rule and CWA.

13.0 Terms and Conditions

In order to be exempt from the prohibitions of section 9 of the ESA, EPA must comply with the 

following terms and conditions, which implement the reasonable and prudent measure described 

above and outline required reporting/monitoring requirements. These terms and conditions are 

non-discretionary.

1. EPA will ensure the Directors notify both Services and EPA of control measures, 

monitoring, or reporting recommendations provided by the Services that have been 

adopted as permit conditions. A copy of the draft permit provided to the Services per 

40 CFR 124.10(c)(1) prior to finalization of the permit will satisfy this requirement. 

2. EPA will report and provide to the Services: 

a. an annual report summarizing the facility monitoring data submitted by State 

Directors to EPA pursuant to 125.98(k), including data on impacts to ESA-listed 
77

species or critical habitat. If the Director (based on recommendations from the 

Services during their review of permit applications or draft permits) requires

additional reporting per year, then that reporting from the state Director will be 

provided in addition to the annual summary report. The annual report must 

summarize any monitoring reports submitted by facilities to state Directors. EPA 

will provide the compiled raw data to the Services when the State provides such 

data to EPA. EPA will also seek to provide additional raw data from the 

Director’s summarized reports if requested to do so; and 

b. the annual report must include a table that identifies all ESA-listed species taken 

by CWIS along with the total number of organisms taken (deaths and injuries) per 

year at each facility as reported to EPA by the state Director pursuant to 

125.98(k). 

3. In order to review the effectiveness of the technical assistance process between the 

Directors and the Services as outlined in the Rule, EPA will report the following to 

the Services on an annual basis for the first four years following implementation of 

the Rule. As described in the Rule, data requirements for permit applications may 

warrant several years of data collection. Therefore, the number of permits issued may 

increase after the initial four year period. If necessary the Services may subsequently 

request EPA to report on a semi-annual basis:

a. A list of all state permits issued pursuant to 316(b); and

b. Of those permits issued pursuant to 316(b), identification of any that were 

elevated by the Services to an EPA’s Regional Office and how those elevations

were resolved.

4. Within 60 days of finalization of the Rule, EPA will provide each State Director an 

instructional memorandum developed in coordination with the Services detailing the 

technical assistance process that is to occur between the Services and the Directors. 

The memorandum will also further explain how Directors are to interpret the various 

aspects of the Rule, consistent with the April 8, 2014, correspondence from EPA

(attached as Appendix A).

5. Within 60 days of finalization of the Rule, EPA will provide the Services a list of 

those facilities which are currently operating under administratively continued 

permits and may be subject to the Rule.

6. EPA will request Directors reopen any currently administratively continued permit if 

the Services determine the facility’s CWIS operations may have more than minor 

detrimental effects to federally-listed species or critical habitat.

7. If incidental take as quantified for an individual facility through the technical 

assistance process is exceeded, EPA will request the State or Tribal Director reopen 

the permit to analyze if additional control measures, monitoring, and reporting are 

necessary to further minimize adverse effects on ESA-listed species. 

8. EPA will inform Directors that pursuant to the Services Consultation Handbook
78

(1998) if an owner/operator locates dead or injured federally-listed species, 

immediate notification must be made to the appropriate Field Office of the USFWS 

and/or Regional Office of the NMFS. Pertinent information including the date, time, 

location, and possible cause of injury or mortality (e.g. impingement or entrainment) 

of each species shall be recorded and provided to the Services. Instructions for 

proper care, handling, transport, and disposition of such specimens will be issued by 

the Services. Care must be taken in handling sick or injured animals to ensure 

effective treatment and in handling dead specimens to preserve biological material in 

the best possible state.

14.0 Conservation Recommendations

Section 7(a)(1) of the ESA directs Federal agencies to utilize their authorities to further the 

purposes of the Act by carrying out conservation programs for the benefit of endangered and 

threatened species. Conservation recommendations are discretionary agency activities to 

minimize or avoid adverse effects of a proposed action on listed species or critical habitat, to 

help implement recovery plans, or to develop information. We recommend that EPA implement 

the following actions:

1. In consultation with the Service, develop a conservation program for threatened and 

endangered species and, in collaboration with States and Tribes, develop conservation 

plans that specifically addresses threats to listed species and how implementation of 

CWA programs can ameliorate those threats;

2. .EPA should sponsor additional research and development with industry/facilities/States 

to support new technological devices or structures to further reduce impingement and 

entrainment of aquatic organisms. 

In order for the Service to be kept informed of actions minimizing or avoiding adverse effects or 

benefitting listed species or their habitats, the Service requests notification of the implementation 

of any conservation recommendations. 

15.0 Reintiation Notice

This concludes formal consultation on the action. As described in 50 CFR §402.16, reinitiation 

of formal consultation is required where discretionary Federal agency involvement or control 

over the action has been retained (or is authorized by law) and if: (1) the amount or extent of 

incidental take is exceeded-for this programmatic consultation, exceedance of take at individual 

facilities will be addressed as described in term and condition number 7; (2) new information 

reveals effects of the agency action that may affect listed species or critical habitat in a manner 

or to an extent not considered in this opinion; (3) the agency action is subsequently modified in a 

manner that causes an effect to the listed species or critical habitat not considered in this opinion; 

or (4) a new species is listed or critical habitat designated that may be affected by the action. If 

the assumptions about the process outlined in this Opinion regarding how adverse effects to 

ESA-listed species and critical habitat will be addressed are not being followed, then this lack of 
79

adherence to the process constitutes new information per reinitiation trigger Number 2. This

could be the basis for reinitiating consultation. Examples of how adverse effects will be 

addressed that are described in this Opinion include the Services’ review of permit applications 

and draft permits, the transmittal by the Services of recommendations to the Director, and EPA’s 

commitment to oversight of State permits to ensure that control measures, monitoring, and 

reporting recommendations necessary for the protection of ESA-listed species will be included in 

permits. Through the periodic reviews and reporting required of EPA in terms and conditions 

numbers 2 and 3, the Services and EPA will be able to identify whether there are deficiencies 

with the process as analyzed in this Opinion and determine if reinitiation of this consultation is 

necessary.
80

16.0 Literature Cited

Abt Associates. 2014. Environmental Protection Agency memorandum: Estimates of the number 

of facilities regulated by the 316(b) rule.

Abelson, A. and M. Denny. 1997. Settlement of Marine Organisms in Flow. Annual Review of 

Ecology & Systematics 28: 317.

Albright, R., B. Mason, M. Miller, and C. Langdon. 2010. Ocean acidification compromises 

recruitment success of the threatened Caribbean coral Acropora palmata. Proceedings of 

the National Academy of Science. 107 (47): 20400-20404.

Ager, D., Martilla, D., Eng, P.P. 2008. Bay Shore power plant cooling water intake structure 

information and I&E sampling, Unpublished report. Kinectrics North America. 28pp.

Ash, G. R., N. R. Chymko, et al. 1974. Fish kill due to 'cold shock' in Lake Wabamun, Alberta.

Averyt K, J Fisher, A Huber-Lee, A Lewis, J Macknick, N Madden, J Rogers, and S 

Tellinghuisen. 2011. Freshwater use by U.S. power plants: Electricity’s thirst for a 

precious resource, A report of the energy and Water in a Warming World initiative. 

Union of Concerned Scientists, Cambridge, MA. November. 

Bartholow, J. M., Campbell, S.G., Marshall, F. 2004. Predicting the thermal effects of dam 

removal on the Klamath River. Environmental Management 34(6): 856-874.

Benke, A.C. 1990. A perspecitive on America's vanishing streams. Journal of the North Amercan 

benthological society. 9(1):77-88

Bennett, S. J. and J. L. Best. 1995. "Mean flow and turbulence structure over fixed, twodimensional dunes: implications for sediment transport and bedorm stability." 

Sedimentology 42(3): 491-513.

Biles, C. L., M. Solan, et al. 2003. Flow modifies the effect of biodiversity on ecosystem 

functioning: an in situ study of estuarine sediments. Journal of Experimental Marine 

Biology and Ecology 285-286: 165-177.

Bottom D. L., Jones K. K., Cornwell T. J., Gray A. & Simenstad C. A. (2005) Patterns of 

Chinook salmon migration and residency in the Salmon River estuary (Oregon). 

Estuarine Coastal and Shelf Science 64, 79-93.

Bulthuis, D.A. 1987. Effects of temperature on photosynthesis and growth of seagrasses. Aquatic 

botany. 27:27-40.

Caparroy, P., M. T. Pérez, et al. 1998. Feeding behaviour of Centropages typicus in calm and 

turbulent conditions. Marine Ecology - Progress Series 168: 109-118.

Chuang, L.H., Yang, H.H., Lin, H.J., 2009. Effects of a thermal discharge from a nuclear power 

plant on phytoplankton and periphyton in subtropical coastal waters. Journal of sea 

research. 61(4):197-205

Columbia Basin Trust. 2012. Columbia River Basin: dams and hydroelectricity. Columbia Basin 

Trust information publication. 4pp.

Crowley TJ, Berner RA. 2001. CO2 and climate change. Science 292(5518):870.

Dahl, T.E. 2011. Status and trends of wetlands in the conterminous United States 2004 to 2009. 

U.S. Department of the Interior; Fish and Wildlife Service, Washington, D.C. 108 pp.

Deacon, J. E., J.D. Kobetich, J.D. Williams and S. Contreras.1979. "Fishes of North America 

endangered, threatened, or of special concern: 1979." Fisheries 4(2): 1-69

Deacutis, C. F. (1978). "Effect of Thermal Shock on Predator Avoidance by Larvae of Two Fish 

Species." Transactions of the American Fisheries Society 107(4): 632-635.

Eckman, J. E. and D. O. Duggins. 1993. Effects of Flow Speed on Growth of Benthic 

Suspension Feeders. Biology Bulletin 185(1): 28-41. 
81

Enders, E. C., D. Boisclair, et al. 2003. The effect of turbulence on the cost of swimming for 

juvenile Atlantic salmon (Salmo salar). Canadian Journal of Fisheries & Aquatic 

Sciences 60(9): 1149-1160.

Fish Facilities Technical Team (FFTT). 2011. Technical memorandum: bay delta conservation 

plan and anadromous salmonid passage facility design. 65pp

Flather CH, Knowles MS, Kendall IA. 1998. Threatened and endangered species geography. 

Bioscience 48(5):365-376.

Fresh K. L., Casillas E., Johnson L. L. & Bottom D. L. (2005) Role of the estuary in the recovery 

of Columbia River Basin salmon and steelhead: An evaluation of the effects of selected 

factors on population viability. In: NOAA Technical Memorandum p. 155. U.S. 

Department of Commerce, Seattle, Washington.

Gilliom, R. J., Barbash, J.E., Crawford, C. G., Hamilton, P.A., Martin, J.D., Nakagaki, N., 

Nowell, L.H., Scott, J.C., Stackelberg P.E., Thelin G.P., and David M. Wolock, 2006. 

The Quality of Our Nation’s Waters—Pesticides in the Nation’s Streams and Ground 

Water, 1992–2001: U.S. Geological Survey Circular 1291,172 p

Harley CDG. 2011. Climate change, keystone predation, and biodiversity loss. Science 334: 

1124-1127.

Heinz. 2008. The State of the Nation’s Ecosystems 2008: Measuring the lands, waters, and living 

resources of the United States: Highlights. The H. John Heinz III Center for Science, 

Economics and the Environment.

Houghton R. 1994. The worldwide extent of land-use change. Bioscience 44(5):305-313.

Hoyal, D. C. J. D., J. F. Atkinson, et al. (1995). The effect of turbulence on sediment deposition. 

Journal of Hydraulic Research 33(3): 349-360.

ISAB. 2007. Climate change impacts on Columbia River basin fish and wildlife. Independent 

Scientific Advisory Board, Portland, Oregon.

IPCC, 2013: Summary for Policymakers. In: Climate Change 2013: The Physical Science Basis. 

Contribution of Working Group I to the Fifth Assessment Report of the 

Intergovernmental Panel on Climate Change [Stocker, T.F., D. Qin, G.-K. Plattner, M. 

Tignor, S. K. Allen, J. Boschung, A. Nauels, Y. Xia, V. Bex and P.M. Midgley (eds.)]. 

Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA 

Interagency Wild and Scenic River Coordinating Council (IWSRCC). 2011. A Compendium of 

questions & answers relating to wild & scenic rivers. Technical report of the interagency 

wild and scenic rivers coordinating council. 

Jelks, H.L., S.J. Walsh, N.M. Burkhead, S. Contreras-Balderas, E. Díaz-Pardo, D.A. 

Hendrickson, J. Lyons, N.E. Mandrak, F. McCormick, J.S. Nelson, S.P. Platania, B.A. 

Porter, C.B. Renaud, J.J Schmitter-Soto, E.B. Taylor and M.L. Warren, Jr. 2008. 

"Conservation Status of Imperiled North American Freshwater and Diadromous Fishes." 

Fisheries 33(8): 372-407.

Judy, R. D. Jr.; Seeley, P. N.; Murray T. M.; Svirsky S. C.;Whitworth, M. R.; Ischinger, L. S. 

1984: 1982 National fisheries survey. Volume I. Technical report: initial findings. United 

States Fisheries and Wildlife Service, FWS/OBS-84/06. 140 p.

Karl, T.R., J.M. Melillo, and T.C. Peterson, (eds.). 2009. Global Climate Change Impacts in the 

United States. Cambridge University Press.

Kenny, J.F., Barber, N.L., Hutson, S.S., Linsey, K.S., Lovelace, J.K., and Maupin, M.A. 2009. 

Estimated use of water in the United States in 2005: U.S. Geological Survey circular 

1344, 52 p.
82

LCFRB. (2010) Washington lower Columbia salmon recovery & fish and wildlife subbasin plan. 

Lower Columbia Fish Recovery Board, Olympia, Washington.

LCREP. (2007) Lower Columbia River and estuary ecosystem monitoring: Water quality and 

salmon sampling report. Lower Columbia River Estuary Partnership, Portland, Oregon.

Lockwood, B. L. and G. N. Somero. 2011. Invasive and native blue mussels (genus Mytilus) on 

the California coast: The role of physiology in a biological invasion. Journal of 

Experimental Marine Biology and Ecology.

.Langford, T. E. L. (1990). Ecological effects of thermal discharges. Barking, Essex, Elsevier 

Applied Science Publishers Ltd

Lupandin, A. I. 2005. Effect of Flow Turbulence on Swimming Speed of Fish. Biology Bulletin 

32(5): 461-466.

Leffler, C. W. (1972). "Some effects of temperature on the growth and metabolic rate of juvenile 

blue crabs, Callinectes sapidus, in the laboratory." Marine Biology 14(2): 104-110.

Leidy R. A. and P. B. Moyle. 1998. Conservation Status of the World's Fish Fauna: An 

Overview. pages 182-227. In P.L. Fielder and P.M. Kareiva, editors. Conservation 

Biology for the coming decade. Chapman and Hall, New York.

Liao, J. C. 2007. A review of fish swimming mechanics and behaviour in altered flows. 

Philosophical Transactions of the Royal Society B: Biological Sciences 362: 1973-1993.

Littell JS, Elsner MM, Whitely Binder LC, Snover AK. 2009. The Washington climate change 

impacts assessment: evaluating Washington's future in a changing climate. Seattle, 

Washington: University of Washington, Climate Impacts Group.

MacKenzie, B. R. 2000. Turbulence, larval fish ecology and fisheries recruitment: a review of 

field studies. Oceanologica Acta 23(4): 357-375.

MacKenzie, B. R. and T. Kiorboe. 2000. Larval Fish Feeding and Turbulence: A Case for the 

Downside. Limnology and Oceanography 45(1): 1-10.

Madden, N., Lewis A., and Davis M. 2013. Thermal effluent from the power sector:an analysis of 

once-through cooling system impacts on surface watertemperature. Environmental research 

letters (8):8

Martinez, A., Abundes, S., González,M.E., Rosas, I. 2009. On the influence of hot-water discharges 

on phytoplankton communities from a coastal zone of the Gulf of Mexico. Water, air, and 

soil pollution. 119(1-4):209-230.

Morgan, D. S. and J. L. Jones. 1999. Numerical model analysis of the effects of ground-water 

withdrawals on discharge to streams and springs in small basins typical of the Puget 

Sound Lowland, Washington. US Geological Survey water-supply paper:1-73.

Mullineaux, L. S. and E. D. Garland 1993. Larval Recruitment in Response to Manipulated Field 

Flows. Marine Biology 116(4): 667-683. 

National Energy Testing Laboratory (NETL). 2009. Impact of drought on United States steam 

electric power plant cooling water intakes and related water management issues. 

DOE/NETL-2009/1364. April 2009.

National Oceanic and Atmospheric Administration (NOAA). 2013. Office of Ocean and Coastal 

Resource Management website. http://coastalmanagement.noaa.gov/water_quality.html

North Carolina Division of Water Quality (NCDWQ). 2010. Annual report of fish kill events 

2010. Raleigh, NC: Department of Environment and Natural Resources. 18pp.

Palmer, M. A., C. A. Reidy Liermann, et al. (2008). Climate change and the world's river basins: 

anticipating management options. Frontiers in Ecology and the Environment 6(2): 81-89

Philippart, C. J. M., R. Anadón, R. Danovaro, J. W. Dippner, K. F. Drinkwater, S. J. Hawkins, T. 

Oguz, G. O'Sullivan, and P. C. Reid. 2011. Impacts of climate change on European 
83

marine ecosystems: Observations, expectations and indicators☆. Journal of Experimental 

Marine Biology and Ecology.

Poornima, E. H., M. Rajadurai, et al. (2005). "Impact of thermal discharge from a tropical coastal 

power plant on phytoplankton." Journal of Thermal Biology 30(4): 307-316. 

Rapport, D. J. and W. G. Whitford. 1999. How Ecosystems Respond to Stress. BioScience 49(3): 

193.

Ruiz, G. M., P. Fofonoff, and A. H. Hines. 1999. Non-indigenous species as stressors in 

estuarine and marine communities: Assessing invasion impacts and interactions. 

Limnology and Oceanography 44:950–972.

Sackschewsky, M. R. 1997. Threatened and Endangered Species Evaluation for 75 Licensed 

Commercial Nuclear Power Generating Plants. PNNL-11524. Pacific Northwest National 

Laboratory. Richland, WA.

Sackschewsky, M. R. 2004. Threatened and Endangered Species Evaluation for Operating 

Commercial Nuclear Power Generating Plants. Pacific Northwest National Laboratory, 

U.S. Department of Energy. DE-AC06-76RL01830.

Sanford, E. B., D. Bertness, et al. 1994. Flow, food supply and acorn barnacle population 

dynamics. Marine Ecology - Progress Series 104: 49-62.

Schwarzen, C. 2000. Georgia power to build cooling tower to rectify fish kill problem. Knight 

Ridder Tribune Business News, March 3. in Averyt K, J Fisher, A Huber-Lee, A Lewis, J 

Macknick, N Madden, J Rogers, and S Tellinghuisen. 2011. Freshwater use by U.S. 

power plants: Electricity’s thirst for a precious resource, A report of the energy and 

Water in a Warming World initiative. Union of Concerned Scientists, Cambridge, MA. 

November.

Seaby, R.M.H., and Henderson, P.A. 2007. Entrainment, impingement, and thermal impacts at 

Indian Point nuclear poewr station:Techincal report. Pisces conservation Ltd. 57pp 

Skaggs, R., Hibbard, K., Janetos, A., and Rice, J. 2012. Climate and Energy-Water-Land System 

Interactions: Technical Report to the U.S. Department of Energy in Support of the 

National Climate Assessment. U.S. Department of Energy. 152pp. 

Smail, E.A., Webb, E.A., Franks, R.P., Bruland, K.W., Sanudo-Wilhemy, S.A. 2012. Status of 

metal contamination in suface waters of the coastal ocean off Los Angeles, California 

since the implementation of the Clean Water Act. Environmental Science & Policy. 

46:4304-4311. 

Smythe, A. G. and P. M. Sawyko (2000). "Field and laboratory evaluations of the effects of 'cold 

shock' on fish resident in and around a thermal discharge: an overview." Environmental 

Science & Policy 3(Supplement 1): 225-232.

Sponseller, R.A., Grimm, N.B., Boulton, A.J., and Sabo, J.L., 2010. Responses of 

macroinvertebrate communities ti long-term flow variability in a Sonoran Desert stream. 

Global change biology. 16:2891-2900

Staudinger, M.D., Grimm, N.B., Staudt, A., Carter, S.L., Chapin F.S., Kareiva, P., Ruckelshaus, 

M., Stein, B.A.,. 2012. Impacts of climate change on biodiversity, ecosystems, and 

ecosystem services: Technical input to the 2013 national climate assessment. Cooperative 

report to the 2013 national climate assessment. 296 p. 

Sumer, B. M., A. Kozakiewicz, et al. 1996. Velocity and Concentration Profiles in Sheet-Flow 

Layer of Movable Bed. Journal of Hydraulic Engineering 122(10): 549-558.

Swanson, C., Young, P.S., Cech, J.J. 1998. Swimming performance of delta smelt: maximum 

performance, and behavioral and kinematic limitations on swimming at submaximal 
84

velocities. The Journall of Experimental Biology. 201: 333-345.

Swanson, C.,Reid, T., Young, P.S., Cech, J.J. 2000. Comparative environmental tolerances of 

threatened delta smelt (Hypomeus transpacificus) and introduced ewakasagi (H. 

nipponensis) in an altered Claifornia estuary. Oecologia 123: 384-390.

Taylor, C. A., G. A. Schuster, J.E. Cooper, R.J. DiStefano, A.G. Eversole, P. Hamr, H.H. Hobbs 

III, H.W. Robison, C.E. Skelton and R.F. Thoma. 2007. A Reassessment of the 

Conservation Status of Crayfishes of the United States and Canada after 10+ Years of 

Increased Awareness. Fisheries 32(8): 372-389.

Taylor, C.A., M.L. Warren, J.F. Fitzpatrick, H.H. Hobbs, R.F. Jezerinac, W.L. Pflieger, H.W. 

Robinson. 1996. Conservation Status of Crayfishes of the United States and Canada. 

Fisheries 21(4): 25-38.

Taylor, S.G. 2008. Climate warming causes phenological shift in pink salmon, Oncorhynchus 

gorbuscha, behavior at Auke Creek, Alaska. Global Change Biology 14: 229-235. 

U.S. Environmental Protection Agency (USEPA) (2002). Clean Water Act NPDES permitting 

determination for thermal discharge and cooling water intake from brayton point station 

in Somerset, MA. United States Environmental Protection Agency Region 1: New 

England. NPDES Permit No. MA0003654. 

U.S. Environmental Protection Agency (USEPA) (2004). Technical Development Document for 

the Proposed Section 316(b) Rule for Phase III Facilities. Office of Water. EPA-821-R04-015. November 1

U.S. Environmental Protection Agency (USEPA). (2006a) EPA identifies pharmaceutical 

research facility as source of cyanide-related discharge to Wissahickon Creek. In: EPA 

News Release 6/22/2006. U.S. Environmental Protection Agency.

U.S. Environmental Protection Agency (USEPA). 2006b. National estuary program coastal 

condition report. In: EPA Report www.epa.gov/nccr. EPA, Office of Water, and Office of 

Research and Development, Washington, D.C.

U.S. Environmental Protection Agency (USEPA). 2007. National lake fish tissue study: results. 

US EPA(website).http://www.epa.gov/waterscience/fish/study/results.htm

U.S. Environmental Protection Agency (EPA). (2008) Effects of climate change for aquatic 

invasive species and implications for management and research. National Center for 

Environmental Assessment, Washington, DC; EPA/600/R-08/014.

U.S. Environmental Protection Agency (USEPA). 2010. Bienniela national listing of fish 

advisories technical fact sheet. Office of Science and Technology. 7 pp

U.S. Environmental Protection Agency (USEPA). 2012. National coastal condition report IV. 

334 pp.

U.S. Environmental Protection Agency (USEPA). 2013a. National Summary of Impaired Waters 

and TMDL Information. Retrieved November 18 2013, from 

http://iaspub.epa.gov/waters10/attains_nation_cy.control?p_report_type=T

U.S. Environmental Protection Agency (USEPA). 2013b. Memo: Information Concerning 2014 

Clean Water Act Sections 303(d), 305(b), and 314 Integrated Reporting and Listing 

Decisions.

U.S. Environmental Protection Agency (USEPA). 2013c. Endangered species act biological 

evaluation for clean water act section 316(b) rulemaking. 231 pp

U.S. Environmental Protection Agency (USEPA). 2013d. 316(b) existing facilites final rule: 

presentation for Office of Mangement and Budget and interagency reviewers. 15 slides

U.S. Environmental Protection Agency (USEPA). 2013e. Permit status report for non-tribal 
85

individual major and minor permits. 7pp

U.S. Environmental Protection Agency (USEPA). 2013f. Cooling water intakes final preamble. 

483 pp

U.S. Environmental Protection Agency (USEPA). 2014. Annual noncompliance report (ANCR) 

A summary of reviews, violations, and enforcement response at individually-permitted 

nonmajor dischargers under the National Pollution Discharge Elimination System 

(NPDES) Program Calendar Year 2012. 22 pp.

U.S.Fish and Wildlife Service and National Marine Fisheries Service. 1998. Consultation 

Handbook: Procedures for conducting consultation and conference activities under 

section 7 of the Endangered Species Act.

West Consultants, Inc. 2000. Upper Mississippi River and Illinois Waaterway cumulative effects 

study, volume 2: Ecological assessment. Unpublished report. 

Williams, J.D., M.L. Warren, K.S. Cummings, J.L. Harris and R.J. Neves. 1993. "Conservation 

Status of Freshwater Mussels of the United States and Canada." Fisheries 18(9): 6-22.

Williams, J.E., J.E. Johnson, D.A. Hendrickson, S. Contreras-Balderas, J.D. Williams, M. 

Navarro-Mendoza, D.E. McAllister and J.E. Deacon. 1989. "Fishes of North America

Endangered, Threatened, or of Special Concern: 1989." Fisheries 14(6): 2-20.
Appendix A

April 8, 2014 

Email Correspondence with EPA
4/30/2014 DEPARTMENT OF THE INTERIOR Mail - Description of Action Re: EPA's Final Rulemaking for Cooling water Intake Strcutures for Existing Facilities ...

https://mail.google.com/mail/u/0/?ui=2&ik=6b2eda71fe&view=pt&cat=316B%20Rule&search=cat&msg=1454172ca42f0dbf&siml=1454172ca42f0dbf 1/1

Crane, Drew <drew_crane@fws.gov>

Description of Action Re: EPA's Final Rulemaking for Cooling water Intake

Strcutures for Existing Facilities under Clean Water Act Section 316(b)

Wood, Robert <Wood.Robert@epa.gov> Tue, Apr 8, 2014 at 9:06 AM

To: "Frazer, Gary" <gary_frazer@fws.gov>

Cc: "Neugeboren, Steven" <Neugeboren.Steven@epa.gov>, Paul Souza <Paul_Souza@fws.gov>, Patrice Ashfield

<patrice_ashfield@fws.gov>, Drew Crane <drew_crane@fws.gov>, "donna.wieting@noaa.gov"

<donna.wieting@noaa.gov>, "cathy.tortorici@noaa.gov" <cathy.tortorici@noaa.gov>, Edward Boling

<ted.boling@sol.doi.gov>, Pamela Lawrence - NOAA Federal <pamela.lawrence@noaa.gov>, "Southerland,

Elizabeth" <Southerland.Elizabeth@epa.gov>, "Born, Tom" <Born.Tom@epa.gov>, "Hewitt, Julie"

<Hewitt.Julie@epa.gov>, "Shriner, Paul" <Shriner.Paul@epa.gov>

Gary,

EPA has reviewed the attached FWS and NMFS description EPA’s action in the final rulemaking for cooling

water intake structures for existing facilities under Clean Water Act Section 316(b). I confirm that your

description and understanding of the key elements of our action as reflected in this document are

correct. Thanks,

Rob

______________________________

Robert K. Wood, Director

Engineering and Analysis Division

U.S. EPA Office of Water

202-566-1822

Final FWS NMFS Summary of Action 316b 04072014.docx

32K
Final FWS/NMFS Summary of Action 7 April 2014

1

Important Provisions of the Action for Purposes of ESA Consultation: The Services regard 

the following as significant provisions of the pending final regulation with regard to potential 

effects to Federally-listed threatened and endangered species and designated critical habitat and 

request confirmation from EPA that we are understanding and interpreting these provisions 

appropriately.

Impingement, Entrainment, and Entrapment

The regulation requires that the location, design, construction, and capacity of CWIS reflect the 

best technology available for minimizing adverse environmental impacts, primarily by reducing 

the amount of fish and shellfish that are impinged (including entrapped) or entrained at a CWIS. 

The regulation also provides that the Director may establish in the permit additional control 

measures, monitoring requirements and reporting requirements that are designed to minimize 

incidental take, reduce or remove more than minor detrimental effects to Federally-listed species 

and designated critical habitat, or avoid jeopardizing federally-listed species or destroying or 

modifying designated critical habitat. For purposes of this consultation, the Service is 

interpreting the regulation’s application to “fish and shellfish” and the Director’s authority to 

establish additional measures to protect listed species and habitat as broadly encompassing all 

taxa of listed species, including their critical habitat. The Services also interpret the rule 

requirements – impingement (including entrapment) and entrainment reduction actions (e.g., 

BTA standards), including additional measures established by the Director to protect listed 

species and habitat – as applying to all taxa of listed species, including their designated critical 

habitats. 

The Services interpret the BTA standards, including additional measures established by the 

Director to protect listed species and habitat, as applying to, and protecting the aquatic 

environment from, the direct and indirect effects of a CWIS, including effects to a listed species’

prey base. 

As part of the definition of “modified traveling screen” at §125.92, the regulations state that the 

Director may approve of fish being returned to water sources other than the original source 

water, taking into account any recommendations from the Services with respect to endangered or 

threatened species. The Services interpret this limitation to mean that when making permitting 

decisions concerning the return of impinged aquatic species to waters other than the source 

water, the Director will address any concerns from the Services. If the Services’ concerns are 

not addressed and the permit would cause more than minor detrimental effects, the permit will be 

subject to the EPA oversight provisions of section IX.A of the 2001 MOA.

Action Area

Within the preamble and section 125.95(f), EPA uses the term “action area” to indicate the 

extent of potential effects to listed species and designated critical habitat. For the purposes of 

this consultation, the Services interpret the term “action area” whenever it is used in the 

preamble and rule in a manner consistent with the definition of this term in the Services’ 

regulations implementing ESA Section 7 at 50 CFR 402.02.
Final FWS/NMFS Summary of Action 7 April 2014

2

Notification

Section 125.98(h) requires the Director to transmit all permit applications received from existing 

facilities to the appropriate Field Office of the U.S. Fish and Wildlife Service and/or Regional 

Office of the National Marine Fisheries Service upon receipt for a 60 day review prior to public 

notice of the draft or proposed permit. Directors may not propose/publish the draft permit until 

the 60 day review period has ended. Directors are also required to provide public notice and a 

public comment period (40 CFR 124.10) and to submit a copy of the fact sheet or statement of 

basis (for EPA-issued permits), the permit application (if any), and the draft permit (if any) to the 

Service. This includes notice of specific CWIS requirements and notice of the draft permit. 

When the Director submits this information to the Service, the Director should include any 

specific information the Director has about ESA-listed species and designated critical habitat that 

are or may be present in the action area, including any proposed control measures and 

monitoring and reporting requirements for such species and habitat. 

Section 125.95(f) requires owners/operators to identify all endangered/threatened species and 

designated critical habitat in the action area.

Information

Section 125.95(f) requires that the owner or operator of an existing facility or new unit at an 

existing facility must, based on readily available information at the time of the permit application 

instead of the information required at 122.2(r)(4)(vi), identify all Federally-listed threatened and 

endangered species and/or designated critical habitat that are or may be present in the action 

area. The Services interpret “readily available information” to mean information that is publicly 

available information. “Readily available information” includes information obtained from the 

Services. “Readily available information” is not limited to information that is in the facility’s 

possession; however, facilities are not required to create new information (e.g. new studies or 

surveys) in order to identify Federally-listed threatened and endangered species and/or 

designated critical habitat. 

Take

Section 125.98(b)(1) specifies that the Director must include the following language as a permit 

condition “Nothing in this permit authorizes take for the purposes of a facility’s compliance with 

the Endangered Species Act.”

MOA

The Services interpret the statements in the preamble to mean that, consistent with subsection 

IX.A of the 2001 MOA, in situations where the Services contact EPA with concerns that a State 

or Tribal permit will have more than minor detrimental effect on Federally-listed species or 

critical habitat that cannot be resolved with the State or Tribal permitting authority: 

i) EPA will coordinate with the State or Tribe to ensure that the permit will comply with 

all applicable CWA requirements and will discuss appropriate measures protective of Federallylisted species and critical habitat; and
Final FWS/NMFS Summary of Action 7 April 2014

3

ii) EPA will work with the State or Tribe to reduce or remove the detrimental impacts of 

the permit, including, in appropriate circumstances, by objecting to and Federalizing the permit 

where consistent with EPA’s CWA authority.

The Services also interpret the preamble, consistent with subsection IX.A of the 2001 MOA, to 

mean that if EPA determines (after taking into account all available information, including any 

analysis conducted by the Services) that a State or Tribal permit is likely to jeopardize the 

continued existence of any listed species or result in the destruction or adverse modification of 

designated critical habitat, EPA will use the full extent of its CWA authority to object to the 

permit, including Federalizing the permit where consistent with EPA’s CWA authority. 

The Services interpret “giving, as appropriate, substantial weight to the views of the Services” 

and “taking into account . . . any analysis conducted by the Services” to include giving deference

to the views of the Services with regard to effects on Federally-listed fish and wildlife resources.

In those situations where a Director determines, pursuant to §125.94(c)(11), that a facility’s rate 

of impingement is so exceptionally low as to not warrant additional impingement controls, the 

Services may still consider the detrimental effects of the facility operation to be more than minor 

if Federally-listed threatened or endangered species are subject to impingement.

Discretionary Actions

Section 125.94(g) provides that State Directors may include as conditions of a CWIS permit 

control measures to avoid or minimize adverse effects to listed species or designated critical 

habitat, including such measures that are recommended by the Services. 

Monitoring and Reporting

Section 125.94(g) provides that the Director may establish in the permit additional control 

measures, monitoring requirements, and reporting requirements that are designed to minimize 

incidental take, reduce or remove more than minor detrimental effects to Federally-listed species 

and designated critical habitat, or avoid jeopardizing Federally-listed species or destroying or 

adversely modifying designated critical habitat. We interpret this to mean that State or Tribal 

permitting authorities will include any monitoring and reporting recommendations provided by 

the Services. Failure to include these recommendations will subject the permit to the EPA 

oversight provisions of section IX.A of the 2001 MOA in circumstances where the Services are 

concerned about more than minor detrimental effects. This includes, but is not limited to,

monitoring and reporting requirements related to impingement (including entrapment), 

entrainment, flow alteration, and indirect effects (e.g., effects to prey base). 
Appendix B

Status Information for Species 

Under Jurisdiction of NMFS
1

APPENDIX B

Status of Species Under National Marine Fisheries Service’s Jurisdiction

1 Cetaceans ................................................................................................................................ 3

1.1 Cook Inlet Beluga Whale ................................................................................................. 3

1.1.1 Life History............................................................................................................... 3

1.1.2 Population Dynamics................................................................................................ 3

1.1.3 Status......................................................................................................................... 3

1.1.4 Critical Habitat.......................................................................................................... 4

1.2 Southern Resident Killer Whale....................................................................................... 4

1.2.1 Life History............................................................................................................... 4

1.2.2 Population Dynamics................................................................................................ 5

1.2.3 Status......................................................................................................................... 5

1.2.4 Critical Habitat.......................................................................................................... 5

1.3 Main Hawaiian Island Insular False Killer Whale ........................................................... 5

1.3.1 Life History............................................................................................................... 6

1.3.2 Population Dynamics................................................................................................ 6

1.3.3 Status......................................................................................................................... 6

1.3.4 Critical Habitat.......................................................................................................... 7

1.4 Blue Whale....................................................................................................................... 7

1.4.1 Life History............................................................................................................... 7

1.4.2 Population Dynamics................................................................................................ 7

1.4.3 Status......................................................................................................................... 7

1.4.4 Critical Habitat.......................................................................................................... 7

1.5 Fin Whale ......................................................................................................................... 8

1.5.1 Life History............................................................................................................... 8

1.5.2 Population Dynamics................................................................................................ 8

1.5.3 Status......................................................................................................................... 8

1.5.4 Critical Habitat.......................................................................................................... 8

1.6 Sei Whale ......................................................................................................................... 8

1.6.1 Life History............................................................................................................... 9

1.6.2 Population Dynamics................................................................................................ 9

1.6.3 Status......................................................................................................................... 9

1.6.4 Critical Habitat.......................................................................................................... 9

1.7 Humpback Whale............................................................................................................. 9

1.7.1 Life History............................................................................................................... 9

1.7.2 Population Dynamics.............................................................................................. 10

1.7.3 Status....................................................................................................................... 10

1.7.4 Critical Habitat........................................................................................................ 10

1.8 North Atlantic Right Whale ........................................................................................... 10

1.8.1 Life History............................................................................................................. 10

1.8.2 Population Dynamics.............................................................................................. 10

1.8.3 Status....................................................................................................................... 11
2

1.8.4 Critical Habitat........................................................................................................ 11

1.9 North Pacific Right Whale ............................................................................................. 11

1.9.1 Life History............................................................................................................. 11

1.9.2 Population Dynamics.............................................................................................. 11

1.9.3 Status....................................................................................................................... 11

1.9.4 Critical Habitat........................................................................................................ 12

2 Pinnipeds............................................................................................................................... 12

2.1 Steller Sea Lion (Western DPS)..................................................................................... 12

2.1.1 Life History............................................................................................................. 12

2.1.2 Population Dynamics.............................................................................................. 12

2.1.3 Status....................................................................................................................... 13

2.1.4 Critical Habitat........................................................................................................ 13

2.2 Hawaiian Monk Seal ...................................................................................................... 13

2.2.1 Life History............................................................................................................. 13

2.2.2 Population Dynamics.............................................................................................. 14

2.2.3 Status....................................................................................................................... 14

2.2.4 Critical Habitat........................................................................................................ 15

3 Sea Turtles ............................................................................................................................ 15

3.1 Leatherback Sea Turtle................................................................................................... 15

3.1.1 Life History............................................................................................................. 15

3.1.2 Population Dynamics.............................................................................................. 16

3.1.3 Status....................................................................................................................... 16

3.1.4 Critical Habitat........................................................................................................ 16

3.2 Hawksbill Sea Turtle...................................................................................................... 17

3.2.1 Life History............................................................................................................. 17

3.2.2 Population Dynamics.............................................................................................. 17

3.2.3 Status....................................................................................................................... 17

3.2.4 Critical Habitat........................................................................................................ 17

3.3 Kemp’s Ridley Sea Turtle .............................................................................................. 17

3.3.1 Life History............................................................................................................. 18

3.3.2 Population Dynamics.............................................................................................. 18

3.3.3 Status....................................................................................................................... 18

3.3.4 Critical Habitat........................................................................................................ 18

3.4 Olive Ridley Sea Turtle (Mexico’s Pacific Coast Breeding Colonies).......................... 19

3.4.1 Life History............................................................................................................. 19

3.4.2 Population Dynamics.............................................................................................. 19

3.4.3 Status....................................................................................................................... 19

3.4.4 Critical Habitat........................................................................................................ 19

3.5 Olive Ridley Sea Turtle (All Other Areas)..................................................................... 19

3.5.1 Life History............................................................................................................. 19

3.5.2 Population Dynamics.............................................................................................. 19

3.5.3 Status....................................................................................................................... 20

3.5.4 Critical Habitat........................................................................................................ 20

3.6 Loggerhead Sea Turtle (North Pacific Ocean)............................................................... 20

3.6.1 Life History............................................................................................................. 20

3.6.2 Population Dynamics.............................................................................................. 20
3

3.6.3 Status....................................................................................................................... 20

3.6.4 Critical Habitat........................................................................................................ 21

3.7 Loggerhead Sea Turtle (Northwest Atlantic Ocean)...................................................... 21

3.7.1 Life History............................................................................................................. 21

3.7.2 Population Dynamics.............................................................................................. 21

3.7.3 Status....................................................................................................................... 22

3.7.4 Critical Habitat........................................................................................................ 22

3.8 Green Sea Turtle (All Other Areas) ............................................................................... 22

3.8.1 Life History............................................................................................................. 22

3.8.2 Population Dynamics.............................................................................................. 23

3.8.3 Status....................................................................................................................... 23

3.8.4 Critical Habitat........................................................................................................ 23

3.9 Green Sea Turtle (Florida and Mexico’s Pacific Coast Breeding Colonies) ................. 23

3.9.1 Life History............................................................................................................. 23

3.9.2 Population Dynamics.............................................................................................. 24

3.9.3 Status....................................................................................................................... 24

3.9.4 Critical Habitat........................................................................................................ 24

4 Salmonids.............................................................................................................................. 24

4.1 Atlantic Salmon (Gulf of Maine DPS)........................................................................... 24

4.1.1 Life History............................................................................................................. 25

4.1.2 Population Dynamics.............................................................................................. 25

4.1.3 Status....................................................................................................................... 25

4.1.4 Critical Habitat........................................................................................................ 25

4.2 Chinook Salmon (General Overview)............................................................................ 26

4.2.1 Life History............................................................................................................. 26

4.2.2 Population Dynamics.............................................................................................. 27

4.2.3 Status....................................................................................................................... 27

4.2.4 Critical Habitat........................................................................................................ 27

4.3 Chinook Salmon (California Coastal ESU) ................................................................... 27

4.3.1 Life History............................................................................................................. 28

4.3.2 Population Dynamics.............................................................................................. 28

4.3.3 Status....................................................................................................................... 28

4.3.4 Critical Habitat........................................................................................................ 28

4.4 Chinook Salmon (Central Valley Spring-run ESU)....................................................... 29

4.4.1 Life History............................................................................................................. 29

4.4.2 Population Dynamics.............................................................................................. 29

4.4.3 Status....................................................................................................................... 30

4.4.4 Critical Habitat........................................................................................................ 30

4.5 Chinook Salmon (Lower Columbia River ESU)............................................................ 30

4.5.1 Life History............................................................................................................. 31

4.5.2 Population Dynamics.............................................................................................. 31

4.5.3 Status....................................................................................................................... 32

4.5.4 Critical Habitat........................................................................................................ 32

4.6 Chinook Salmon (Upper Columbia River Spring-run ESU).......................................... 32

4.6.1 Life History............................................................................................................. 33

4.6.2 Population Dynamics.............................................................................................. 33
4

4.6.3 Status....................................................................................................................... 33

4.6.4 Critical Habitat........................................................................................................ 33

4.7 Chinook Salmon (Puget Sound ESU) ............................................................................ 34

4.7.1 Life History............................................................................................................. 34

4.7.2 Population Dynamics.............................................................................................. 34

4.7.3 Status....................................................................................................................... 35

4.7.4 Critical Habitat........................................................................................................ 35

4.8 Chinook Salmon (Sacramento River Winter-run ESU)................................................. 35

4.8.1 Life History............................................................................................................. 36

4.8.2 Population Dynamics.............................................................................................. 36

4.8.3 Status....................................................................................................................... 36

4.8.4 Critical Habitat........................................................................................................ 37

4.9 Chinook Salmon (Snake River Fall-run ESU)............................................................... 37

4.9.1 Life History............................................................................................................. 37

4.9.2 Population Dynamics.............................................................................................. 38

4.9.3 Status....................................................................................................................... 38

4.9.4 Critical Habitat........................................................................................................ 38

4.10 Chinook Salmon (Snake River Spring/Summer-run ESU) ........................................ 39

4.10.1 Life History............................................................................................................. 39

4.10.2 Population Dynamics.............................................................................................. 39

4.10.3 Status....................................................................................................................... 40

4.10.4 Critical Habitat........................................................................................................ 40

4.11 Chinook Salmon (Upper Willamette River ESU) ...................................................... 40

4.11.1 Life History............................................................................................................. 41

4.11.2 Population Dynamics.............................................................................................. 41

4.11.3 Status....................................................................................................................... 41

4.11.4 Critical Habitat........................................................................................................ 42

4.12 Chum Salmon (General Overview)............................................................................ 42

4.12.1 Life History............................................................................................................. 42

4.12.2 Population Dynamics.............................................................................................. 43

4.12.3 Status....................................................................................................................... 43

4.12.4 Critical Habitat........................................................................................................ 43

4.13 Chum Salmon (Columbia River ESU) ....................................................................... 43

4.13.1 Life History............................................................................................................. 44

4.13.2 Population Dynamics.............................................................................................. 44

4.13.3 Status....................................................................................................................... 44

4.13.4 Critical Habitat........................................................................................................ 45

4.14 Chum Salmon (Hood Canal Summer-run ESU)......................................................... 45

4.14.1 Life History............................................................................................................. 45

4.14.2 Population Dynamics.............................................................................................. 45

4.14.3 Status....................................................................................................................... 46

4.14.4 Critical Habitat........................................................................................................ 46

4.15 Coho Salmon (General Overview) ............................................................................. 47

4.15.1 Life History............................................................................................................. 47

4.15.2 Population Dynamics.............................................................................................. 48

4.15.3 Status....................................................................................................................... 48
5

4.15.4 Critical Habitat........................................................................................................ 48

4.16 Coho Salmon (Central California Coast ESU)........................................................... 48

4.16.1 Life History............................................................................................................. 48

4.16.2 Population Dynamics.............................................................................................. 48

4.16.3 Status....................................................................................................................... 49

4.16.4 Critical Habitat........................................................................................................ 49

4.17 Coho Salmon (Lower Columbia River ESU)............................................................. 50

4.17.1 Life History............................................................................................................. 50

4.17.2 Population Dynamics.............................................................................................. 50

4.17.3 Status....................................................................................................................... 51

4.17.4 Critical Habitat........................................................................................................ 51

4.18 Coho Salmon (Oregon Coast ESU)............................................................................ 51

4.18.1 Life History............................................................................................................. 52

4.18.2 Population Dynamics.............................................................................................. 52

4.18.3 Status....................................................................................................................... 52

4.18.4 Critical Habitat........................................................................................................ 53

4.19 Coho Salmon (Southern Oregon/Northern California Coast ESU)............................ 53

4.19.1 Life History............................................................................................................. 54

4.19.2 Population Dynamics.............................................................................................. 54

4.19.3 Status....................................................................................................................... 54

4.19.4 Critical Habitat........................................................................................................ 55

4.20 Sockeye Salmon (General Overview) ........................................................................ 55

4.20.1 Life History............................................................................................................. 55

4.20.2 Population Dynamics.............................................................................................. 56

4.20.3 Status....................................................................................................................... 56

4.20.4 Critical Habitat........................................................................................................ 56

4.21 Sockeye Salmon (Ozette Lake ESU).......................................................................... 56

4.21.1 Life History............................................................................................................. 57

4.21.2 Population Dynamics.............................................................................................. 57

4.21.3 Status....................................................................................................................... 57

4.21.4 Critical Habitat........................................................................................................ 58

4.22 Sockeye Salmon (Snake River ESU).......................................................................... 58

4.22.1 Life History............................................................................................................. 58

4.22.2 Population Dynamics.............................................................................................. 59

4.22.3 Status....................................................................................................................... 59

4.22.4 Critical Habitat........................................................................................................ 59

4.23 Steelhead Trout (General Overview).......................................................................... 60

4.23.1 Life History............................................................................................................. 60

4.23.2 Status....................................................................................................................... 61

4.23.3 Population Dynamics.............................................................................................. 61

4.23.4 Critical Habitat........................................................................................................ 61

4.24 Steelhead (California Central Valley DPS)................................................................ 62

4.24.1 Life History............................................................................................................. 62

4.24.2 Population Dynamics.............................................................................................. 62

4.24.3 Status....................................................................................................................... 62

4.24.4 Critical Habitat........................................................................................................ 63
6

4.25 Steelhead (Central California Coast DPS).................................................................. 63

4.25.1 Life History............................................................................................................. 64

4.25.2 Population Dynamics.............................................................................................. 64

4.25.3 Status....................................................................................................................... 64

4.25.4 Critical Habitat........................................................................................................ 65

4.26 Steelhead (Lower Columbia River DPS).................................................................... 65

4.26.1 Life History............................................................................................................. 65

4.26.2 Population Dynamics.............................................................................................. 65

4.26.3 Status and trends..................................................................................................... 66

4.26.4 Critical Habitat........................................................................................................ 66

4.27 Steelhead (Middle Columbia River DPS) .................................................................. 66

4.27.1 Life History............................................................................................................. 67

4.27.2 Population Dynamics.............................................................................................. 67

4.27.3 Status....................................................................................................................... 67

4.27.4 Critical Habitat........................................................................................................ 67

4.28 Steelhead (Northern California DPS)......................................................................... 68

4.28.1 Life History............................................................................................................. 68

4.28.2 Population Dynamics.............................................................................................. 68

4.28.3 Status....................................................................................................................... 69

4.28.4 Critical Habitat........................................................................................................ 69

4.29 Steelhead (Puget Sound DPS) .................................................................................... 69

4.29.1 Life History............................................................................................................. 70

4.29.2 Population Dynamics.............................................................................................. 70

4.29.3 Status....................................................................................................................... 70

4.29.4 Critical Habitat........................................................................................................ 70

4.30 Steelhead (Snake River DPS)..................................................................................... 71

4.30.1 Life History............................................................................................................. 71

4.30.2 Population Dynamics.............................................................................................. 71

4.30.3 Status....................................................................................................................... 72

4.30.4 Critical Habitat........................................................................................................ 72

4.31 Steelhead (South-central California Coast DPS)........................................................ 72

4.31.1 Life History............................................................................................................. 72

4.31.2 Population Dynamics.............................................................................................. 73

4.31.3 Status....................................................................................................................... 73

4.31.4 Critical Habitat........................................................................................................ 73

4.32 Steelhead (Southern California DPS)......................................................................... 73

4.32.1 Life History............................................................................................................. 74

4.32.2 Population Dynamics.............................................................................................. 74

4.32.3 Status....................................................................................................................... 74

4.32.4 Critical Habitat........................................................................................................ 74

4.33 Steelhead (Upper Columbia River DPS).................................................................... 75

4.33.1 Life History............................................................................................................. 75

4.33.2 Population Dynamics.............................................................................................. 75

4.33.3 Status....................................................................................................................... 75

4.33.4 Critical Habitat........................................................................................................ 76

4.34 Steelhead (Upper Willamette River DPS).................................................................. 76
7

4.34.1 Life History............................................................................................................. 76

4.34.2 Population Dynamics.............................................................................................. 76

4.34.3 Status....................................................................................................................... 77

4.34.4 Critical Habitat........................................................................................................ 77

5 Eulachon ............................................................................................................................... 77

5.1 Eulachon (Southern DPS) .............................................................................................. 77

5.1.1 Life History............................................................................................................. 77

5.1.2 Population Dynamics.............................................................................................. 78

5.1.3 Status....................................................................................................................... 79

5.1.4 Critical Habitat........................................................................................................ 80

6 Sturgeon ................................................................................................................................ 81

6.1 Shortnose Sturgeon ........................................................................................................ 81

6.1.1 Life History............................................................................................................. 81

6.1.2 Population Dynamics.............................................................................................. 82

6.1.3 Status....................................................................................................................... 82

6.1.4 Critical Habitat........................................................................................................ 83

6.2 Atlantic Sturgeon (General Overview) .......................................................................... 83

6.2.1 Life History............................................................................................................. 83

6.2.2 Population Dynamics.............................................................................................. 83

6.2.3 Status....................................................................................................................... 84

6.2.4 Critical Habitat........................................................................................................ 84

6.3 Atlantic Sturgeon (Gulf of Maine DPS)......................................................................... 84

6.3.1 Life History............................................................................................................. 84

6.3.2 Population Dynamics.............................................................................................. 84

6.3.3 Status....................................................................................................................... 84

6.3.4 Critical Habitat........................................................................................................ 85

6.4 Atlantic Sturgeon (New York Bight DPS)..................................................................... 85

6.4.1 Life History............................................................................................................. 85

6.4.2 Population Dynamics.............................................................................................. 85

6.4.3 Status....................................................................................................................... 85

6.4.4 Critical Habitat........................................................................................................ 86

6.5 Atlantic Sturgeon (Chesapeake Bay DPS)..................................................................... 86

6.5.1 Life History............................................................................................................. 86

6.5.2 Population Dynamics.............................................................................................. 86

6.5.3 Status....................................................................................................................... 86

6.5.4 Critical Habitat........................................................................................................ 86

6.6 Atlantic Sturgeon (Carolina DPS).................................................................................. 87

6.6.1 Life History............................................................................................................. 87

6.6.2 Population Dynamics.............................................................................................. 87

6.6.3 Status....................................................................................................................... 87

6.6.4 Critical Habitat........................................................................................................ 87

6.7 Atlantic Sturgeon (South Atlantic DPS) ........................................................................ 87

6.7.1 Life History............................................................................................................. 87

6.7.2 Population Dynamics.............................................................................................. 88

6.7.3 Status....................................................................................................................... 88

6.7.4 Critical Habitat........................................................................................................ 88
8

6.8 Green Sturgeon (Southern DPS).................................................................................... 88

6.8.1 Life History............................................................................................................. 88

6.8.2 Population Dynamics.............................................................................................. 88

6.8.3 Status....................................................................................................................... 89

6.8.4 Critical Habitat........................................................................................................ 89

6.9 Gulf Sturgeon ................................................................................................................. 89

6.9.1 Life History............................................................................................................. 89

6.9.2 Population Dynamics.............................................................................................. 90

6.9.3 Status....................................................................................................................... 90

6.9.4 Critical Habitat........................................................................................................ 90

7 Sawfish.................................................................................................................................. 90

7.1 Smalltooth Sawfish (U.S. DPS) ..................................................................................... 90

7.1.1 Life History............................................................................................................. 91

7.1.2 Population Dynamics.............................................................................................. 91

7.1.3 Status....................................................................................................................... 92

7.1.4 Critical Habitat........................................................................................................ 92

8 Rockfish ................................................................................................................................ 92

8.1 Bocaccio (Puget Sound/Georgia Basin DPS) ................................................................ 92

8.1.1 Life History............................................................................................................. 93

8.1.2 Population Dynamics.............................................................................................. 94

8.1.3 Status....................................................................................................................... 94

8.1.4 Critical Habitat........................................................................................................ 95

8.2 Yelloweye Rockfish (Puget Sound/Georgia Basin DPS)............................................... 95

8.2.1 Life History............................................................................................................. 95

8.2.2 Population Dynamics.............................................................................................. 96

8.2.3 Status....................................................................................................................... 96

8.2.4 Critical Habitat........................................................................................................ 97

8.3 Canary Rockfish (Puget Sound/Georgia Basin DPS) .................................................... 97

8.3.1 Life History............................................................................................................. 97

8.3.2 Population Dynamics.............................................................................................. 98

8.3.3 Status....................................................................................................................... 98

8.3.4 Critical Habitat........................................................................................................ 99

9 Abalone ................................................................................................................................. 99

9.1 White Abalone................................................................................................................ 99

9.1.1 Life History............................................................................................................. 99

9.1.2 Population Dynamics.............................................................................................. 99

9.1.3 Status..................................................................................................................... 100

9.1.4 Critical Habitat...................................................................................................... 100

9.2 Black Abalone .............................................................................................................. 100

9.2.1 Life History........................................................................................................... 100

9.2.2 Population Dynamics............................................................................................ 100

9.2.3 Status..................................................................................................................... 100

9.2.4 Critical Habitat...................................................................................................... 101

10 Corals.................................................................................................................................. 101

10.1 Elkhorn Coral ........................................................................................................... 101
9

10.1.1 Life History........................................................................................................... 101

10.1.2 Population Dynamics............................................................................................ 102

10.1.3 Status..................................................................................................................... 102

10.1.4 Critical Habitat...................................................................................................... 102

10.2 Staghorn Coral.......................................................................................................... 102

10.2.1 Life History........................................................................................................... 102

10.2.2 Population Dynamics............................................................................................ 103

10.2.3 Status..................................................................................................................... 103

10.2.4 Critical Habitat...................................................................................................... 103

11 Johnson’s Seagrass.............................................................................................................. 103

11.1.1 Life History........................................................................................................... 103

11.1.2 Population Dynamics............................................................................................ 103

11.1.3 Status..................................................................................................................... 104

11.1.4 Critical Habitat...................................................................................................... 104
1

Status of Species Under National Marine Fisheries Service Jurisdiction

Section 7(a)(2) of the Endangered Species Act (ESA) (16 U.S.C. 1531 et seq.) requires that each 

federal agency ensure any action authorized, funded, or carried out by such agency is not likely 

to jeopardize the continued existence of any endangered or threatened species or result in the 

destruction or adverse modification of critical habitat of such species. The following species are 

under the jurisdiction of NOAA’s National Marine Fisheries Service (NMFS) and may be 

affected by the EPA’s issuance of regulations pursuant to section 316(b) of the Clean Water Act 

(Table 1). 

Table 1. National Marine Fisheries Service species listed under the Endangered 

Species Act that may be affected by the issuance of regulations pursuant to section 

3016(b) of the Clean Water Act. Designated critical habitat is denoted by an asterisk 

(*); proposed critical habitat is denoted by a double asterisk (**).

Common name (Distinct population segment, 

evolutionarily significant unit, or subspecies) Scientific name Status

Cetaceans

Blue whale Balaenoptera musculus Endangered

Bowhead whale Balaena mysticetes Endangered

Fin whale Balaenoptera physalus Endangered

Humpback whale Megaptera novaeangliae Endangered

Killer whale (Southern Resident*) Orcinus orca Endangered

North Atlantic right whale* Eubalaena glacialis Endangered

Sei whale Balaenoptera borealis Endangered

Sperm whale Physeter macrocephalus Endangered

Beluga whale (Cook Inlet)* Delphinapterus leucas Endangered

False killer whale (Hawaiian insular) Pseudorca crassidens Endangered

Pinnipeds

Guadalupe fur seal Arctocephalus townsendi Threatened

Hawaiian monk seal*,** Monachus schauinslandi Endangered

Steller sea lion (Western*) Eumetopias jubatus Endangered

Bearded seal (Beringia) Erignathus barbatus nauticus Threatened

Ringed seal (Arctic) Phoca hispida hispida Threatened

Sea turtles

Green sea turtle (Florida & Mexico’s Pacific coast 

colonies)

Chelonia mydas Endangered

Green sea turtle (all other areas*) Threatened

Hawksbill sea turtle* Eretmochelys imbricate Endangered

Kemp’s ridley sea turtle Lepidochelys kempii Endangered

Leatherback sea turtle* Dermochelys coriacea Endangered

Loggerhead sea turtle (North Pacific Ocean) Caretta caretta Endangered

Loggerhead sea turtle (Northwest Atlantic Ocean**) Threatened

Olive ridley sea turtle (Mexico’s Pacific coast breeding 

colonies)

Lepidochelys olivacea Endangered

Olive ridley sea turtle (all other areas) Threatened

Sturgeons

Shortnose sturgeon Acipenser brevirostrum Endangered

Green sturgeon (southern*) Acipenser medirostris Threatened

Gulf sturgeon* Acipenser oxyrhynchus desotoi Threatened

Atlantic sturgeon (Gulf of Maine) Acipenser oxyrhynchus Threatened

Atlantic sturgeon (New York Bight) Endangered

Atlantic sturgeon (Chesapeake Bay) Endangered
2

Common name (Distinct population segment, 

evolutionarily significant unit, or subspecies) Scientific name Status

Atlantic sturgeon (Carolina) Endangered

Atlantic sturgeon (South Atlantic) Endangered

Salmonids

Atlantic salmon (Gulf of Maine*) Salmo salar Endangered

Chinook salmon (CA Coastal*) Oncorhynchus tschawytscha Threatened

Chinook salmon (Central Valley Spring-run*) Threatened

Chinook salmon (Lower Columbia River*) Threatened

Chinook salmon (Upper Columbia River Spring-run*) Endangered

Chinook salmon (Puget Sound*) Threatened

Chinook salmon (Sacramento River Winter-run*) Endangered

Chinook salmon (Snake River Fall-run*) Threatened

Chinook salmon (Snake River Spring/Summer-run*) Threatened

Chinook salmon (Upper Willamette River*) Threatened

Chum salmon (Columbia River*) Oncorhynchus keta Threatened

Chum salmon (Hood Canal Summer-run*) Threatened

Coho salmon (Central CA Coast*) Oncorhynchus kisutch Endangered

Coho salmon (Lower Columbia River**) Threatened

Coho salmon (Southern Oregon & Northern California 

Coast*)

Threatened

Coho salmon (Oregon Coast*)

Sockeye salmon (Ozette Lake*) Oncorhynchus nerka Threatened

Sockeye salmon (Snake River*) Endangered

Steelhead (Central California Coast*) Oncorhynchus mykiss Threatened

Steelhead (California Central Valley*) Threatened

Steelhead (Lower Columbia River*) Threatened

Steelhead (Middle Columbia River*) Threatened

Steelhead (Northern California*) Threatened

Steelhead (Puget Sound) Threatened

Steelhead (Snake River*) Threatened

Steelhead (South-Central California Coast*) Threatened

Steelhead (Southern California*) Threatened

Steelhead (Upper Columbia River*) Threatened

Steelhead (Upper Willamette River*) Threatened

Other fishes

Pacific eulachon* Thaleichthys pacificus Threatened

Bocaccio (Georgia Basin**) Sebastes paucispinis Endangered

Yelloweye rockfish (Georgia Basin**) Sebastes pinniger Threatened

Canary rockfish (Georgia Basin**) Sebastes ruberrimus Threatened

Smalltooth sawfish* Pristis pectinata Endangered

Marine invertebrates

Elkhorn coral* Acropora palmata Threatened1

Staghorn coral* Acropora cervicornis Threatened1

White abalone Haliotis sorenseni Endangered

Black abalone* Haliotis cracherodii Endangered

Marine plants

Johnson’s seagrass* Halophilia johnsonii Threatened

 

1

Proposed endangered
3

1 Cetaceans

There are about 90 species of cetaceans; all are found in marine environments except for four 

species of freshwater dolphins. The order contains two suborders; mysticeti (baleen whales) and 

odontoceti (toothed whales, which includes dolphins and porpoises). Ten ESA-listed cetacean 

species may be affected by the proposed action and are described below.

1.1 Cook Inlet Beluga Whale

The beluga whale (Delphinapterus leucas) is a small, toothed, white whale. The DPS resides 

year-round within Cook Inlet, in the Gulf of Alaska. It was listed as endangered under the ESA, 

effective December 22, 2008 (73 FR 62919). We used information available in the final rule, the 

2008 Status Reviews (Hobbs and Shelden 2008, Hobbs et al. 2008), and recent stock assessment 

reports (Allen and Angliss 2011) to summarize the status of the DPS, as follows.

1.1.1 Life History

The Cook Inlet DPS is reproductively, genetically, and physically discrete from the four other 

known beluga populations in Alaska (i.e., those north of the Alaska Peninsula). Its unique habitat 

experiences large tidal exchanges, with salinities varying from freshwater to marine at either end 

of the estuary. Belugas occur in mid-Inlet waters in the winter. During spring, summer, and fall, 

they concentrate in the upper Inlet (a contraction of its range), which offers the most abundant 

prey, most favorable feeding topography, best calving areas, and best protection from predation. 

Cook Inlet belugas focus on specific prey species when they are seasonally abundant. During the 

spring, they focus on eulachon; in the summer, as the eulachon runs diminish, their focus shifts 

to salmonids. These fatty, energy-rich prey are critical to pregnant and lactating belugas. Calves 

are born in the summer and remain with their mothers for about 24 months. The calving interval 

ranges from 2 – 4 years. Females reach sexual maturity at 4 to 10 years, and males mature at 8 to 

15 years. Life expectancy exceeds 60 years. 

1.1.2 Population Dynamics

The most recent abundance estimate for the Cook Inlet DPS is 345 (CV = 0.13) belugas, based 

on an average of population estimates from 2008 to 2010 (Allen and Angliss 2011). There were 

an estimated 1,300 whales in 1979. Subsistence removals led to a 47 percent decline from 1994 

to 1998 (from 653 to 347 whales). From 1999 to 2008, the population has declined an average of 

1.5 percent per year, despite restriction on subsistence harvest since 1999 (0 – 2 whales 

harvested annually; 5 total). 

1.1.3 Status

The Cook Inlet beluga whale DPS is endangered as a result of over-exploitation. A brief 

commercial whaling operation in the 1920s harvested 151 Cook Inlet belugas in 5 years. Cook 

Inlet belugas were harvested by Alaska Natives and for sport prior to the enactment of the 

Marine Mammal Protection Act (MMPA) in 1972. Annual subsistence take by Alaska Natives 

during 1995 - 1998 averaged 77 whales, with 20 percent of the population harvested in 1996. 

Subsistence removals through the 1990s are sufficient to account for past declines in abundance, 

but are now restricted. The current decline is attributed to other factors. Since the early 1990s, 

over 200 belugas have stranded along the mudflats in upper Cook Inlet, often resulting in death; 

the cause is uncertain but may be linked with the extreme tidal fluctuations, predator avoidance, 

or pursuit of prey. Additional threats include: coastal development, oil and gas development, 

seismic exploration, point and non- point source discharge of contaminants, contaminated waste 
4

disposal, water quality standards, activities that involve the release of chemical contaminant 

and/or noise, vessel operations, and research (73 FR 62919). Its resilience to future perturbation 

is low because of the following factors: the population is small (N = 345) and has not grown as 

expected with the cessation of harvest; as a result of the range contraction, the population is more 

vulnerable to catastrophic events; and if the current DPS is extirpated, it is unlikely other belugas 

would repopulate Cook Inlet (Hobbs et al. 2008).

1.1.4 Critical Habitat

On April 11, 2011, NMFS designated critical habitat for the Cook Inlet beluga whale that 

includes two areas. Area 1 encompasses the upper Inlet, a 1,909 km2 area bounded by the 

Municipality of Anchorage, the Matanuska-Susitna Borough, and the Kenai Peninsula borough. 

This area hosts a high concentration of belugas from spring through fall. It provides shallow tidal 

flats and river mouths or estuarine areas, important to foraging and calving. Mudflats and 

shallow areas adjacent may allow for molting and escape from predators. Area 2 consists of 

5,891 km2 south of Area 1 including: Tuxedni, Chinitna, and Kamishak Bays on the west coast, 

a portion of Kachemak Bay on the east coast, and south of Kalgin Island. During the fall and 

winter, Belugas typically occur in smaller densities or deeper waters of this feeding and transit 

area. Areas 1 and 2 contain the following physical or biological features essential to the 

conservation of this DPS (76 FR 20180):

(1) Intertidal and subtidal waters of Cook Inlet with depths less than 30 feet (9.1 m) and 

within 5 miles (8 km) of high and medium flow anadromous fish streams.

(2) Primary prey species consisting of four species of Pacific salmon (Chinook, sockeye, 

chum, and coho), Pacific eulachon, Pacific cod, walleye pollock, saffron cod, and 

yellowfin sole.

(3) Waters free of toxins or other agents of a type and amount harmful to Cook Inlet 

beluga whales.

(4) Unrestricted passage within or between the critical habitat areas.

(5) Waters with in-water noise below levels resulting in the abandonment of critical 

habitat areas by Cook Inlet beluga whales.

1.2 Southern Resident Killer Whale

Killer whales (or orcas) are distributed worldwide, but populations are isolated by region and 

ecotype (i.e., different morphology, ecology, and behavior). Southern Resident killer whales 

occur in the inland waterways of Puget Sound, Strait of Juan de Fuca, and Southern Georgia 

Strait during the spring, summer and fall. During the winter, they move to coastal waters 

primarily off Oregon, Washington, California, and British Columbia. The DPS was listed as 

endangered under the ESA on November 18, 2005 (70 FR 69903). We used information 

available in the final rule, the 2011 Status Review (NMFS 2011p) and the 2011 Stock 

Assessment Report (http://www.nmfs.noaa.gov/pr/pdfs/sars/po2011whki-pensr.pdf) to 

summarize the status of this species, as follows.

1.2.1 Life History

Southern Resident killer whales are geographically, matrilineally, and behaviorally distinct from 

other killer whale populations (70 FR 69903). The DPS includes three large, stable pods (J, K, 

and L), which occasionally interact (Parsons et al. 2009). Most mating occurs outside natal pods, 
5

during temporary associations of pods, or as a result of the temporary dispersal of males (Pilot et 

al. 2010). Males become sexually mature at 10 – 17 years of age. Females reach maturity at 12 –

16 years of age and produce an average of 5.4 surviving calves during a reproductive life span of 

approximately 25 years. Mothers and offspring maintain highly stable, life-long social bonds, 

and this natal relationship is the basis for a matrilineal social structure. They prey upon 

salmonids, especially Chinook salmon (Hanson et al. 2010). 

1.2.2 Population Dynamics

The most recent abundance estimate for the Southern Resident DPS is 87 whales in 2012. This 

represents an average increase of 0.4 percent annually since 1982 when there were 78 whales. 

Population abundance has fluctuated during this time with a maximum of approximately 100 

whales in 1995 (http://www.nmfs.noaa.gov/pr/pdfs/sars/po2011whki-pensr.pdf). As compared to 

stable or growing populations, the DPS reflects a smaller percentage of juveniles and lower 

fecundity (NMFS 2011p) and has demonstrated weak growth in recent decades.

1.2.3 Status

The Southern Resident killer whale DPS was listed as endangered in 2005 in response to the 

population decline from 1996 – 2001, small population size, and reproductive limitations (i.e., 

few reproductive males and delayed calving). Current threats to its survival and recovery 

include: contaminants, vessel traffic, and reduction in prey availability. Chinook salmon 

populations have declined due to degradation of habitat, hydrology issues, harvest, and hatchery 

introgression; such reductions may require an increase in foraging effort. In addition, these prey 

contain environmental pollutants (e.g., flame retardants; PCBs; and DDT). These contaminants 

become concentrated at higher trophic levels and may lead to immune suppression or 

reproductive impairment (70 FR 69903). The inland waters of Washington and British Columbia 

support a large whale watch industry, commercial shipping, and recreational boating; these 

activities generate underwater noise, which may mask whales’ communication or interrupt 

foraging. The factors that originally endangered the species persist throughout its habitat:

contaminants, vessel traffic, and reduced prey. The DPS’s resilience to future perturbation is 

reduced as a result of its small population size (N = 86); however, it has demonstrated the ability 

to recover from smaller population sizes in the past and has shown an increasing trend over the 

last several years. NOAA Fisheries is currently conducting a status review prompted by a 

petition to delist the DPS based on new information, which indicates that there may be more 

paternal gene flow among populations than originally detected (Pilot et al. 2010).

1.2.4 Critical Habitat

On November 29, 2006, NMFS designated critical habitat for the Southern Resident killer whale 

(71 FR 69054). The critical habitat consists of approximately 6,630 km2in three areas: the 

Summer Core Area in Haro Strait and waters around the San Juan Islands; Puget Sound; and the 

Strait of Juan de Fuca. It provides the following physical and biological features: water quality to 

support growth and development; prey species of sufficient quantity, quality and availability to 

support individual growth, reproduction and development, as well as overall population growth; 

and inter-area passage conditions to allow for migration, resting, and foraging.

1.3 Main Hawaiian Islands Insular False Killer Whale

NMFS currently recognizes three stocks of false killer whale in Hawaiian waters: the Main 

Hawaiian Islands insular, Hawaii pelagic, and the Northwestern Hawaiian Islands (Carretta et al. 
6

2011, Bradford et al. 2012) (77 FR 70915). NMFS considers all false killer whales found within 

40 km (22 nm) of the Main Hawaiian Islands as belonging to the insular stock and all false killer 

whales beyond 140 km (76 nm) as belonging to the Pelagic Stock (77 FR 70915). The animals 

belonging to the Northwest Hawaiian Islands stock are insular to the Northwest Hawaiian Islands

(Bradford et al. 2012), however, this stock was identified by animals encountered off Kaua‘i. It 

has been previously recognized that the ranges for the two stocks (pelagic and insular) overlap 

by 100 km, but there is also overlap among all three stocks in these presently identified ranges

(Carretta et al. 2011, Bradford et al. 2012). 

The Main Hawaiian Islands insular false killer whale DPS is considered resident to the Main 

Hawaiian Islands and is genetically and behaviorally distinct compared to other stocks (77 FR 

70915). Genetic data suggest little immigration into the Main Hawaiian Islands insular false 

killer whale population (Baird et al. 2012). However, because data on ecological relationships 

among false killer whale groups in the region are uncertain,additional data are being collected to 

identify whether other false killer whale groups in the Hawaiian Islands should also be 

considered part of the Main Hawaiian Islands insular false killer whale DPS (77 FR 70915).

1.3.1 Life History

Main Hawaiian Islands insular false killer whales are large members of the dolphin family. False 

killer whales have dark coloration except for some lighter patches near the throat and middle 

chest. Their body shape is more slender than other large delphinids.

1.3.2 Population Dynamics

The minimum population estimate for the Main Hawaiian Islands insular stock of false killer 

whales is the number of distinct individuals identified during the 2008-2011 photo-identification 

studies, which is 129 false killer whales (Baird, Hawaii insular false killer whale catalog; 

(Carretta et al. 2012). No data are available on current or maximum net productivity rate for this 

stock.

1.3.3 Status 

NMFS listed the Main Hawaiian Island insular population of false killer whales as an endangered 

distinct population segment (DPS) on November 28, 2012 (77 FR 70915). Reeves et al. (2009)

summarized information on false killer whale sightings near Hawaii between 1989 and 2007, 

based on various survey methods, and suggested that the Main Hawaiian Islands insular stock of 

false killer whales may have declined during the last two decades. More recently, Baird (Baird 

2009) reviewed trends in sighting rates of false killer whales from aerial surveys conducted using 

consistent methodology around the Main Hawaiian Islands between 1994 and 2003 (Mobley Jr 

2001, Mobley Jr. 2003, 2004, 2005). Sighting rates during these surveys exhibited a statistically 

significant decline that could not be attributed to any weather or methodological changes. 

Reanalysis of previously published abundance estimates for the insular stock has led to them 

generally being discounted (77 FR 70915). 

The recent Status Review of Main Hawaiian Islands insular false killer whales (Oleson et al. 

2010) presented a quantitative analysis of extinction risk using a Population Viability Analysis 

(PVA). The modeling exercise was conducted to evaluate the probability of actual or near 

extinction, defined as fewer than 20 animals, given measured, estimated, or inferred information 

on population size and trends, and varying impacts of catastrophes, environmental stochasticity 

and Allee effects. A variety of alternative scenarios were evaluated, with all plausible models 
7

indicating the probability of decline to fewer than 20 animals within 75 years as greater than 20 

percent. Though causation was not evaluated, all models indicated current declines at an average 

rate of -9 percent since 1989 (95 percent probability intervals -5 to -12.5 percent) (Oleson et al. 

2010).

1.3.4 Critical Habitat

No critical habitat has been designated for the Main Hawaiian Islands insular false killer whale.

1.4 Blue Whale

The blue whale is the largest animal on earth. Three subspecies comprise the species, which 

occurs in coastal and pelagic waters in all oceans. Though often found in coastal waters, blue 

whales generally occur in offshore waters, from subpolar to subtropical latitudes. The species 

was originally listed as endangered on December 2, 1970 (35 FR 18319). We used information 

available in the recovery plan (NMFS 1998b) and recent stock assessments (Waring et al. 2010, 

Carretta et al. 2013), and the status report (COSEWIC 2002) to summarize the status of the 

species, as follows.

1.4.1 Life History

The gestation period of blue whales is approximately 10 – 12 months, and calves are nursed for 6 

– 7 months. The average calving interval is 2 – 3 years. Blue whales reach sexual maturity at 5 –

15 years of age. Parturition and mating occurs in lower latitudes during the winter season, and 

weaning probably occurs in or en route to summer feeding areas in higher, more productive 

latitudes. Blue whales forage almost exclusively on krill (i.e., relatively large euphausiid 

crustaceans) and can eat approximately 3,600 kg daily. Feeding aggregations are often found at 

the continental shelf edge, where upwelling produces concentrations of krill at depths of 90 –

120 m.

1.4.2 Population Dynamics

There are an estimated 5,000 – 12,000 blue whales worldwide. Three stocks occur in U.S. 

waters: the eastern North Pacific, the western North Atlantic, and Hawaii. For the eastern North 

Pacific stock, the best estimate of abundance is 2,497 whales, with an estimated annual growth 

rate of approximately three percent annually. The western North Atlantic stock has a minimum 

population size of 440 individuals, and abundance appears to be increasing, though there are 

insufficient data to provide reliable population trends. Blue whale sightings are rare in Hawaii, 

and no data are available from which to estimate abundance or trends.

1.4.3 Status

The blue whale is endangered as a result of past commercial whaling. In the North Atlantic, at 

least 11,000 blue whales were taken from the late 19th to mid-20th centuries. In the North 

Pacific, at least 9,500 whales were killed between 1910 and 1965. Commercial whaling no 

longer occurs, but blue whales are threatened by ship strikes, entanglement in fishing gear, 

pollution, and noise. Because populations appear to be increasing in size, the species appears to 

be somewhat resilient to current threats; however, it has not recovered to pre-exploitation levels.

1.4.4 Critical Habitat

No critical habitat has been designated for the blue whale.
8

1.5 Fin Whale

The fin whale is a large, widely distributed baleen whale, comprised of two (or possibly three) 

subspecies. Fin whales are found in deep, offshore waters of all major oceans, primarily in 

temperate to polar latitudes. The species was originally listed as endangered on December 2, 

1970 (35 FR 18319). We used information available in the recovery plan (NMFS 2010b), the 

five-year review (NMFS 2011o), and recent stock assessment reports (Allen and Angliss 2012, 

Waring et al. 2012, Carretta et al. 2013)to summarize the status of the species, as follows.

1.5.1 Life History

The gestation period of fin whales is less than one year, and calves are nursed for 6 – 7 months. 

The average calving interval is 2 – 3 years. Fin whales reach sexual maturity at 6 – 10 years of 

age. Parturition and mating occurs in lower latitudes during the winter season. Intense foraging 

occurs at high latitudes during the summer. Fin whales eat pelagic crustaceans (mainly 

euphausiids or krill) and schooling fish such as capelin, herring, and sand lance. The availability 

of sand lance, in particular, is thought to have had a strong influence on the distribution and 

movements of fin whales along the east coast of the United States.

1.5.2 Population Dynamics

There are over 100,000 fin whales worldwide. Though only two subspecies are recognized 

(Northern Hemisphere and Southern Hemisphere), North Atlantic, North Pacific, and Southern 

Hemisphere fin whales appear to be reproductively isolated. Of the 3 – 7 stocks in the North 

Atlantic (N ~ 50,000), one occurs in U.S. waters, where the best estimate of abundance is 3,985 

whales. There are three stocks in U.S. Pacific waters: Alaska (Nmin =5,700), Hawaii (Nmin = 

101), and California/Oregon/Washington (Nmin = 3,269). Abundance appears to be increasing in 

Alaska (4.8 percent annually) and possibly California. Trends are not available for other stocks 

due to insufficient data. Abundance data for the Southern Hemisphere stock are limited; 

however, there were an estimated 85,200 whales in 1970. 

1.5.3 Status

The fin whale is endangered as a result of past commercial whaling. In the North Atlantic, at 

least 55,000 fin whales were killed between 1910 and 1989. In the North Pacific, at least 74,000 

whales were killed between 1910 and 1975. Approximately 704,000 whales were killed in the 

Southern Hemisphere from 1904 to 1975. Fin whales are still killed under the International 

Whaling Commission’s “aboriginal subsistence whaling” in Greenland, under Japan’s scientific 

whaling program, and via Iceland’s formal objection to the Commission’s ban on commercial 

whaling. Additional threats include: ship strikes, reduced prey availability due to overfishing or 

climate change, and noise. Though the original cause of endangerment remains, whaling has 

been significantly reduced. Its large population size may provide some resilience to current 

threats, but trends are largely unknown.

1.5.4 Critical Habitat

No critical habitat has been designated for the fin whale.

1.6 Sei Whale

The sei whale is a widely distributed baleen whale. Sei whales prefer subtropical to subpolar 

waters on the continental shelf edge and slope worldwide. They are usually observed in deeper 

waters of oceanic areas far from the coastline. The species was originally listed as endangered on 

December 2, 1970 (35 FR 18319). We used information available in the recovery plan (NMFS 
9

2011q), the five-year review (NMFS 2012e), and recent stock assessment reports (Waring et al. 

2012, Carretta et al. 2013)to summarize the status of the species, as follows.

1.6.1 Life History

The gestation period of sei whales is 10 – 12 months, and calves are nursed for 6 – 9 months. 

The average calving interval is 2 – 3 years. Sei whales reach sexual maturity at 6 – 12 years of 

age. They winter at relatively low latitudes and summer at relatively higher latitudes. Throughout 

their range, sei whales occur predominantly in deep water; they are most common over the 

continental slope. Sei whales in the North Atlantic reportedly feed primarily on calanoid 

copepods, with a secondary preference for euphausiids. In the Pacific, they also feed on fish 

(e.g., anchovies, saury, whiting, lamprey, and herring). 

1.6.2 Population Dynamics

There are ~80,000 sei whales worldwide, in the North Atlantic, North Pacific, and Southern 

Hemispere. Three stocks occur in U.S. waters: Nova Scotia (N = 357), Hawaii (Nmin = 37), and 

Eastern North Pacific (Nmin = 83). Population trends are not available due to insufficient data. It 

is unknown whether the population size is stable or fluctuating.

1.6.3 Status

The sei whale is endangered as a result of past commercial whaling. There are no estimates of 

pre-exploitation abundance for the North Atlantic. Models indicate that total abundance declined 

from 42,000 to 8,600 individuals between 1963 and 1974, in the North Pacific. In the Southern 

Hemisphere, pre-exploitation abundance is estimated at 65,000 whales, with recent abundance 

estimated at 9,700 whales. Now, only a few individuals are taken each year by Japan; however, 

Iceland has expressed an interest in targeting sei whales. Current threats include ship strikes, 

fisheries interactions (including entanglement), climate change (habitat loss and reduced prey 

availability), and noise. Its large population size may provide some resilience to current threats, 

but trends are largely unknown.

1.6.4 Critical Habitat

No critical habitat has been designated for the sei whale.

1.7 Humpback Whale

The humpback whale is a widely distributed baleen whale, distinguishable by its long flippers.

The species inhabits all major oceans from the equator to sub-polar latitudes and generally 

prefers coastal waters. The humpback whale was originally listed as endangered on December 2, 

1970 (35 FR 18319). On August 29, 2013, NMFS initiated a status review of the North Pacific 

population to determine whether to identify the population as DPS and to delist it. We used 

information available in the recovery plan (NMFS 1991) and recent stock assessment reports 

(Allen and Angliss 2013, Carretta et al. 2013, Waring et al. 2013)to summarize the status of the 

species, as follows.

1.7.1 Life History

The gestation period of humpback whales is 11 months, and calves are nursed for 12 months. 

The average calving interval is 2 – 3 years and sexual maturity is reached at 5 – 11 years of age. 

Humpback whales inhabit waters over or along the continental shelf and oceanic islands. They 

winter at low latitudes, where they calf and nurse, and summer at high latitudes, where they feed. 
10

Humpbacks exhibit a wide range of foraging behaviors and feed on a range of prey types, 

including: small schooling fishes, euphausiids, and other large zooplankton. 

1.7.2 Population Dynamics

There are over 60,000 humpback whales worldwide, occurring primarily in the North Atlantic, 

North Pacific, and Southern Hemisphere. Current estimates indicate approximately 20,000 

humpback whales in the North Pacific, with an annual growth rate of 4.9 percent (Calambokidis 

2010). Stocks in U.S. waters include: American Samoa, California/Oregon/Washington, and 

Central North Pacific. As of 1993, there was an estimated 11,570 humpback whales in the North 

Atlantic, growing at a rate of three percent annually (Stevick et al. 2003). The Southern 

Hemisphere supports more than 36,000 humpback whales and is growing at a minimum annual 

rate of 4.6 percent (Reilly et al. 2008). 

1.7.3 Status

The humpback whale is endangered as a result of past commercial whaling. Prior to commercial 

whaling, hundreds of thousands of humpback whales existed. Global abundance declined to the 

low thousands by 1968, the last year of substantial catches (Reilly et al. 2008). Humpback 

whales may be killed under “aboriginal subsistence whaling” and “scientific permit whaling” 

provisions of the International Whaling Commission. Additional threats include ship strikes and 

fisheries interactions (including entanglement), and noise. The species’ large population size and 

increasing trends indicate that it is resilient to current threats, and one population (North Pacific) 

is currently being considered for delisting.

1.7.4 Critical Habitat

No critical habitat has been designated for the humpback whale.

1.8 North Atlantic Right Whale

The North Atlantic right whale is a narrowly distributed baleen whale, distinguished by its 

stocky body and lack of a dorsal fin. North Atlantic right whales inhabit coastal waters of the 

Atlantic Ocean, particularly between 20° and 60° latitude. For much of the year, their 

distribution is strongly correlated to the distribution of their prey. The species was originally 

listed as endangered on December 2, 1970 (35 FR 18319). We used information available in the 

5-year review (NMFS 2012a) and the recent stock assessment report (Waring et al. 2013)to 

summarize the status of the species, as follows.

1.8.1 Life History

The gestation period of North Atlantic right whales is 12 – 13 months, and calves are nursed for 

8 – 17 months. The average calving interval is 3 – 5 years. Right whales reach sexual maturity at 

9 years of age. They migrate to low latitudes during the winter to give birth in shallow, coastal 

waters. In the summer, they feed on large concentrations of copepods in the high latitudes. 

1.8.2 Population Dynamics

Right whales occur in the eastern and western North Atlantic; however, less than 20 individuals 

exist in the eastern North Atlantic, and the population may be functionally extinct. There are at 

least 396 individuals in the western North Atlantic population. Despite two periods of increased 

mortality, the species has demonstrated overall growth rates of two percent over 17 years (1990 –

2007). This variability may indicate loss of resilience and susceptibility to population collapse 

(Dai et al. 2012, Scheffer et al. 2012). 
11

1.8.3 Status

The North Atlantic right whale is endangered as a result of past commercial whaling. Preexploitation abundance has been estimated at more than 1,000 individuals, distributed throughout 

temperate, subarctic, coastal and continental shelf waters of the North Atlantic Ocean. 

Commercial whaling reduced the population size to ~50 individuals and truncated the range of 

the species; however, whaling is now prohibited. The two major threats to the survival of the 

species are ship strike and fisheries interactions (including entanglement). While population 

trends are positive, the species’ resilience to future perturbations is low due to its small 

population size and continued threats of ship strike and entanglement. 

1.8.4 Critical Habitat

On June 3, 1994, NMFS designated critical habitat for the North Atlantic right whale (59 FR 

28805). Northern designated areas (Great South Channel, Massachusetts Bay, Cape Cod Bay, 

and Stellwagen Bank) include complex oceanographic features that drive prey density and 

distribution. Southern areas (waters from the coast out 15 nautical miles between the latitudes of 

31°15’ N and 30°15’ N and from the coast out five nautical miles between 30°15’ N and 28°00’ 

N) were designated to protected calving and breeding grounds.

1.9 North Pacific Right Whale

The North Pacific right whale is a baleen whale, distinguished by its stocky body and lack of a 

dorsal fin. It inhabits the Pacific Ocean, particularly between 20° and 60° latitude. The species 

was originally listed with the North Atlantic right whale (i.e., “Northern” right whale) as 

endangered on December 2, 1970 (35 FR 18319). It was listed separately as endangered on 

March 6, 2008 (73 FR 12024). We used information available in the 5-year review (NMFS 

2012c) and the recent stock assessment report (Allen and Angliss 2013) to summarize the status 

of the species, as follows.

1.9.1 Life History

The gestation period of North Pacific right whales is approximately 1 year, and calves are nursed 

for approximately 1 year. Right whales reach sexual maturity at 9 – 10 years of age. Little is 

known about migrating patterns, but whales have been observed in lower latitudes in the winter 

(Japan, California, and Mexico). In the summer, they feed on large concentrations of copepods in 

the Alaskan waters. 

1.9.2 Population Dynamics

The North Pacific right whale remains one of the most endangered whale species in the world, 

likely numbering fewer than 1,000 individuals. There are no reliable estimates of current 

abundance or trends for right whales in the North Pacific, and we do not know whether the 

population size is stable or fluctuating. 

1.9.3 Status

The North Pacific right whale is endangered as a result of past commercial whaling. Preexploitation abundance has been estimated at more than 11,000 individuals. Current threats to 

the survival include poaching, ship strike, fisheries interactions (including entanglement). The 

species’ resilience to future perturbations is low due to its small population size and continued 

threats of poaching, ship strike, and entanglement. 
12

1.9.4 Critical Habitat

In 2008, NMFS designated critical habitat for the North Pacific right whale, which includes an 

area in the Southeast Bering Sea and an area south of Kodiak Island in the Gulf of Alaska (73 FR 

19000). These areas are influenced by large eddies, submarine canyons, or frontal zones which 

enhance nutrient exchange and act to concentrate prey. These areas are adjacent to major ocean 

currents and are characterized by relatively low circulation and water movement. Both critical 

habitat areas support feeding by North Pacific right whales because they contain the designated 

primary constituent elements, which include: nutrients, physical oceanographic processes, certain 

species of zooplankton, and a long photoperiod due to the high latitude (73 FR 19000). 

Consistent North Pacific right whale sights are a proxy for locating these elements. 

2 Pinnipeds

Pinnipedia is the group of semi-aquatic mammals that includes the families: Phocidae (earless or 

true seals); Otaridae (eared seals); and Odobenidae (walrus). Over thirty species of pinniped 

occur worldwide in a variety of aquatic habitats, though they most commonly occur in coastal, 

marine areas. Two ESA-listed pinniped species under NMFS’s jurisdiction (walrus are under the 

jurisdiction of the USFWS) may be affected by the proposed action and are described below.

2.1 Steller Sea Lion (Western DPS)

The Steller sea lion ranges from Japan, through the Okhotsk and Bering Seas, to central 

California. It consists of two morphologically, ecologically, and behaviorally distinct DPSs: the 

Eastern DPS, which includes sea lions in Southeast Alaska, British Columbia, Washington, 

Oregon and California; and the Western DPS, which includes sea lions in all other regions of 

Alaska, as well as Russia and Japan. On May 5, 1997, NMFS issued a final determination to list 

the western DPS as endangered under the ESA (62 FR 24345). We used information available in 

the final listing (62 FR 24345) and the 2012 stock assessment report (Allen and Angliss 2012) to 

summarize the status of the western DPS, as follows.

2.1.1 Life History

Within the western DPS, pupping and breeding occurs at numerous major rookeries from late 

May to early July. Male Steller sea lions become sexually mature at 3 – 7 years of age. They are 

polygynous, competing for territories and females by age 10 or 11. Female Steller sea lion 

become sexually mature at 3 – 6 years of age and reproduce into their early 20s. Most females 

breed annually, giving birth to a single pup, but nutritional stress may result in reproductive 

failure. About 90% of pups within a given rookery are born within a 25-day period, as such they 

are highly vulnerable to fluctuations in prey availability. Most pups are weaned in 1 – 2 years.

Females and their pups disperse from rookeries by August – October. Juveniles and adults 

disperse widely, especially males. Their large aquatic ranges are used for foraging, resting, and 

traveling. Steller sea lions forage on a wide variety of demersal, semi-demersal, and pelagic prey, 

including fish and cephalopods. Some prey species form large seasonal aggregations, including 

endangered salmon and eulachon species. Others are available year round. 

2.1.2 Population Dynamics

As of 2011, the best estimate of abundance of the western Steller sea lion DPS in Alaska was 

52,209 (Nmin = 45, 916). This represents a large decline since counts in the 1950s (N = 140,000) 

and 1970s (N = 110,000). The potential biological removal is estimated at 275 animals. 
13

2.1.3 Status

Steller sea lion western DPS site counts decreased 40 percent from 1991 to 2000, an average 

annual decline of 5.4 percent; however, counts increased 11 percent from 2000 to 2004 and three 

percent between 2004 and 2008, an average annual increase of 1.5 percent. The species was 

listed as threatened in 1990 because of significant declines in population sizes (55 FR 49204). At 

the time, the major threat to the species was thought to be reduction in prey availability. To 

protect and recovery the species, NMFS established the following measures: prohibition of 

shooting at or near sea lions; prohibition of vessel approach to within 3 nautical miles of specific 

rookeries, within 0.5 miles on land, and within sight of other listed rookeries; and restriction of 

incidental fisheries take to 675 sea lions annually in Alaskan waters. In 1997, the western DPS 

was reclassified as endangered because it had continued to decline since its initial listing in 1990 

(62 FR 24345). Despite the added protection (and an annual incidental fisheries take of 

approximately 26 individuals), the DPS is likely still in decline (though the decline has slowed or 

stopped in some portions of the range). The reasons for the continued decline are unknown but 

may be associated with nutritional stress as a result of environmental change and competition 

with commercial fisheries. The DPS appears to have little resilience to future perturbations.

2.1.4 Critical Habitat

In 1997, NMFS designated critical habitat for the Steller sea lion (58 FR 45269). The critical 

habitat includes specific rookeries, haulouts, and associated areas, as well as three foraging areas 

that are considered to be essential for the health, continued survival, and recovery of the species.

In Alaska, areas include major Steller sea lion rookeries, haulouts and associated terrestrial, air, 

and aquatic zones. Critical habitat includes a terrestrial zone extending 3,000 feet (0.9 km) 

landward from each major rookery and haulout; it also includes air zones extending 3,000 feet 

(0.9 kin) above these terrestrial zones and aquatic zones. Aquatic zones extend 3,000 feet (0.9 

km) seaward from the major rookeries and haulouts east of 144°W. In California and Oregon, 

major Steller sea lion rookeries and associated air and aquatic zones are designated as critical 

habitat. Critical habitat includes an air zone extending 3,000 feet (0.9 km) above rookery areas 

historically occupied by sea lions. Critical habitat also includes an aquatic zone extending 3,000 

feet (0.9 kin) seaward.

In addition, NMFS designated special aquatic foraging areas as critical habitat for the Steller sea 

lion. These areas include the Shelikof Strait (in the Gulf of Alaska), Bogoslof Island, and 

Seguam Pass (the latter two are in the Aleutians). These sites are located near Steller sea lion 

abundance centers and include important foraging areas, large concentrations of prey, and host 

large commercial fisheries that often interact with the species. 

2.2 Hawaiian Monk Seal

The Hawaiian monk seal is a large phocid that inhabits the Northwestern Hawaiian Islands 

(NWHI) and main Hawaiian Islands (MHI). It was listed as endangered under the ESA in 1976 

(41 FR 51611). We used information available in the 2007 5-year review (NMFS 2007d), the 

2012 stock assessment report (Carretta et al. 2013), and unpublished NMFS data to summarize 

the status of this species, as follows.

2.2.1 Life History

Monk seals are generally born between February and August. They nurse for 5 – 6 weeks, during

which time the mother does not forage. Upon weaning, the mothers return to sea, and the pups 
14

are left unattended on the beaches. Females spend approximately 8 – 10weeks foraging at sea 

before returning to beaches to molt. They mature at 5 – 10 years of age. Males likely mature at 

the same age but may not gain access to females until they are older. Males compete in a 

dominance hierarchy to gain access to females (i.e., guarding them on shore). Mating occurs at 

sea, however, providing opportunity for female mate choice. Though some females mate every 

year after first parturition, most do not. Overall reproductive rates are low, especially in the 

NWHI. For example, the pooled birth rate at Laysan and Lisianski was 0.54 pups per adult 

female per year (Johanos et al. 1994). The low birth rates may reflect low prey availability. 

Monk seals are considered foraging generalists that feed primarily on benthic and demersal prey. 

They forage in subphotic zones either because these areas host favorable prey items or because 

these areas are less accessible by competitors (Parrish 2009). Juvenile seals may not have the 

experience, endurance, or diving capacity to make such deep dives, leaving them more 

susceptible to starvation. 

2.2.2 Population Dynamics

As of 2012, ~1,212 Hawaiian monk seals remained in the wild. As of 2011, a total of 152 seals 

were documented in the MHI, where the subpopulation is growing at a rate of seven percent 

annually (Baker et al. 2011). The majority of seals (N = 893) still reside in the NWHI. Hawaiian 

monk seals are found predominantly throughout the NWHI with six of the population’s 

reproductive sites being located at Kure Atoll, Midway Atoll, Pearl and Hermes Reef, Lisianski 

Island, Laysan Island, and the French Frigate Shoals (NMFS 2014 citing Antonelis et al. 2006; 

Reeves et al. 2002). 

Hawaiian monk seals occur on lands (islands, atolls, emergent reefs) throughout the Hawaiian 

Archipelago, from Kure Atoll to Hawai‛i Island, a distance of over 2,500 km (approximately 

1,553 miles). Seals forage (search for food) in and transit the waters surrounding and between all 

land areas. Additionally, intermittent sightings of Hawaiian monk seals have occurred at remote 

Johnston Atoll approximately 800 km (about 500 miles) south of the Hawaiian Archipelago. 

Although seals are perhaps not continuously present at this site, they do occur there naturally so 

Johnston Atoll is considered part of the species range. Historically, most Hawaiian monk seals 

have been located in the remote NWHI, with subpopulations at Kure Atoll, Midway Atoll, Pearl 

and Hermes Reef, Lisianski Island, Laysan Island, French Frigate Shoals, Necker Island and 

Nihoa Island. Seals are also seen at Gardner Pinnacles and Maro Reef in the NWHI; however, 

these sites have limited areas where seals can haul out. A historically small, but currently 

growing portion of the seals occur in the MHI, including the islands of Ni‛ihau, Kaua‛i, O‛ahu, 

Molokai‛i, Lāna‛i, Kaho‛olawe, Maui, and Hawai‛i. Seals also land on smaller islands (for 

example, Kaula Rock, Lehua Rock) and offshore islets that occur throughout the MHI (NMFS 

2014). 

2.2.3 Status

The Hawaiian monk seal is a endangered species that continues to decline in abundance at a rate 

of four percent annually, presumably as a result in changes to their foraging base. The species 

has declined in abundance by over 68% since 1958. Birth rates in the NWHI declined 

dramatically in the 1990s, possibly reflecting unfavorable environmental conditions. 

Concurrently, there was a rapid increase in the number of monk seal sightings and births in the 

MHI. Hawaiian monk seals were once harvested for their meat, oil and skins, leading to 

extirpation in the MHI and near-extinction of the species by the 20th century (Hiruki and Ragen 

1992, Ragen 1999). The species experienced a partial recovery by 1960, when hundreds of seals 
15

were counted on NWHI beaches. Since then, however, the species has declined in abundance. 

Though the ultimate cause(s) for the decline remain unknown, threats include: starvation; 

predation by sharks; competition with fish and fisheries; entanglement in marine debris; male 

aggression; beach erosion; and environmental changes that reduce prey availability. In the MHI, 

additional threats include disturbance of nursing pups and illegal killing, which likely reflects 

conflict over actual or perceived fisheries interactions (Kehaulani Watson et al. 2011, McAvoy 

2012). With only ~1,212 individuals remaining the species’ resilience to further perturbation is 

low. Other species in the same genus have gone extinct (i.e., Caribbean monk seal) or have been 

extirpated from the majority of their previous range (i.e., Mediterranean monk seal). We 

conclude that the Hawaiian monk seal’s resilience to further perturbation is low, and its status is 

precarious. 

2.2.4 Critical Habitat

Hawaiian monk seal critical habitat was originally designated on April 30, 1986 (51 FR 16047) 

and was extended on May 26, 1988 (53 FR 18988). It includes all beach areas, sand spits and 

islets (including all beach crest vegetation to its deepest extent inland), lagoon waters, inner reef 

waters, and ocean waters out to a depth of 20 fathoms (37 m) around the NWHI breeding atolls 

and islands. The marine component of this habitat serves as foraging areas, while terrestrial 

habitat provides resting, pupping and nursing habitat. 

On June 2, 2011, NMFS published a proposed rule to revise critical habitat for Hawaiian monk 

seals (76 FR 32026), extending the current designation in the NWHI out to the 500 m depth 

contour (including Sand Island at Midway Atoll) and designating six new areas in the MHI (i.e., 

terrestrial and marine habitat from 5 m inland from the shoreline extending seaward to the 500 m 

depth contour around Kaula, Niihau, Kauai, Oahu, Maui Nui, and Hawaii Islands). A final rule 

has not yet been published.

3 Sea Turtles

Sea turtles are air-breathing reptiles with streamlined bodies and large flippers. They inhabit 

tropical and subtropical ocean waters throughout the world. Of the seven species of sea turtles 

found worldwide, the six species described below are found in U.S. waters and may be affected 

by the proposed action.

3.1 Leatherback Sea Turtle

The leatherback sea turtle is unique among sea turtles for its large size, wide distribution (due to 

thermoregulatory systems and behavior), and lack of a hard, bony carapace. It ranges from 

tropical to subpolar latitudes, worldwide. The species was first listed under the Endangered 

Species Conservation Act (35 FR 8491) and listed as endangered under the ESA since 1973. We 

used information available in the 5-year review (NMFS and USFWS 2007c) and the critical 

habitat designation (77 FR 61573) to summarize the status of the species, as follows.

3.1.1 Life History

Age at maturity remains elusive, with estimates ranging from 5 to 29 years (Spotila et al. 1996, 

Avens et al. 2009). Females lay up to seven clutches per season, with more than 65 eggs per 

clutch and eggs weighing >80 g (Reina et al. 2002, Wallace et al. 2007). The number of 

leatherback hatchlings that make it out of the nest on to the beach (i.e., emergent success) in 

approximately 50% worldwide (Eckert et al. 2012). Females nest every 1 – 7 years. Natal 
16

homing, at least within an ocean basin, results in reproductive isolation between five broad 

geographic regions: eastern and western Pacific, eastern and western Atlantic, and Indian Ocean. 

Leatherback sea turtles migrate long, transoceanic distances between their tropical nesting 

beaches and the highly productive temperate waters where they forage, primarily on jellyfish and 

tunicates. These gelatinous prey are relatively nutrient-poor, such that leatherbacks must 

consume large quantities to support their body weight. Leatherbacks weigh ~33 percent more on 

their foraging grounds than at nesting, indicating that they probably catabolize fat reserves to 

fuel migration and subsequent reproduction (James et al. 2005, Wallace et al. 2006). Sea turtles 

must meet an energy threshold before returning to nesting beaches (Rivalan et al. 2005, SherrillMix and James 2008, Casey et al. 2010). Therefore, their remigration intervals (the time between 

nesting) are dependent upon foraging success and duration (Hays 2000, Price et al. 2004). 

3.1.2 Population Dynamics

The global population of adult females has declined over 70 percent in less than one generation, 

from an estimated 115,000 adult females in 1980 to 34,500 adult females in 1995 (Pritchard 

1982, Spotila et al. 1996). There may be as many as 34,000 – 94,000 adult leather backs in the 

North Atlantic, alone (Turtle Expert Working Group 2007), but dramatic reductions (> 80 

percent) have occurred in several populations in the Pacific, which was once considered the 

stronghold of the species (Sarti Martinez 2000). 

3.1.3 Status

The leatherback sea turtle is an endangered species whose once large nesting populations have 

experienced steep declines in recent decades. The primary threats to leatherback sea turtles 

include: fisheries bycatch, harvest of nesting females, and egg harvesting. As a result of these 

threats, once large rookeries are now functionally extinct, and there have been range-wide 

reductions in population abundance. Other threats include loss of nesting habitat due to 

development, tourism, and sand extraction. Lights on or adjacent to nesting beaches alter nesting 

adult behavior and are often fatal to emerging hatchlings as they are drawn to light sources and 

away from the sea. Plastic ingestion is common in leatherbacks and can block gastrointestinal 

tracts leading to death. Climate change may alter sex ratios (as temperature determines hatchling 

sex), range (through expansion of foraging habitat), and habitat (through the loss of nesting 

beaches, as a result of sea-level rise. The species’ resilience to additional perturbation is low. 

3.1.4 Critical Habitat

On March 23, 1979, leatherback critical habitat was identified adjacent to Sandy Point, St. Croix, 

Virgin Islands from the 183 m isobath to mean high tide level between 17° 42’12” N and 

65°50’00” W (44 FR 17710). This habitat is essential for nesting, which has been increasingly 

threatened since 1979, when tourism increased significantly, bringing nesting habitat and people 

into close and frequent proximity; however, studies do not support significant critical habitat 

deterioration. 

On January 20, 2012, NMFS issued a final rule to designate additional critical habitat for the 

leatherback sea turtle (50 CFR 226). This designation includes approximately 43,798 km2 

stretching along the California coast from Point Arena to Point Arguello east of the 3000 m 

depth contour; and 64,760 km2 stretching from Cape Flattery, Washington to Cape Blanco, 

Oregon east of the 2,000 m depth contour. The designated areas comprise approximately 108558 

km2 of marine habitat and include waters from the ocean surface down to a maximum depth of 

80 m. They were designated specifically because of the occurrence of prey species, primarily 
17

scyphomedusae of the order Semaeostomeae (i.e., jellyfish), of sufficient condition, distribution, 

diversity, abundance and density necessary to support individual as well as population growth, 

reproduction, and development of leatherbacks.

3.2 Hawksbill Sea Turtle

The hawksbill sea turtle has a sharp, curved, beak-like mouth. It has a circumglobal distribution 

throughout tropical and, to a lesser extent, subtropical oceans. The species was first listed under 

the Endangered Species Conservation Act (35 FR 8491) and listed as endangered under the ESA 

since 1973. We used information available in the 5-year reviews (NMFS and USFWS 2007b, 

NMFS 2013e, NMFS and USFWS 2013) to summarize the status of the species, as follows.

3.2.1 Life History

Hawksbill sea turtles reach sexual maturity at 20 – 40 years of age. Females return to their natal 

beaches every 2 – 5 years to nest (an average of 3 – 5 times per season). Clutch sizes are large 

(up to 250 eggs). Sex determination is temperature dependent, with warmer incubation producing 

more females. Hatchlings migrate to and remain in pelagic habitats until they reach 

approximately 22 – 25 cm in straight carapace length. As juveniles, they take up residency in 

coastal waters to forage and grow. As adults, hawksbills use their sharp beak-like mouths to feed 

on sponges and corals.

3.2.2 Population Dynamics

Surveys at 88 nesting sites worldwide indicate that 22,004 – 29,035 females nest 

annually(NMFS 2013e, NMFS and USFWS 2013). In general, hawksbills are doing better in the 

Atlantic and Indian Ocean than in the Pacific Ocean, where despite greater overall abundance, a 

greater proportion of the nesting sites are declining. 

3.2.3 Status

Long-term data on the hawksbill sea turtle indicate that 63 sites have declined over the past 20 to 

100 years (historic trends are unknown for the remaining 25 sites). Recently, 28 sites (68 

percent) have experienced nesting declines, 10 have experienced increases, three have remained 

stable, and 47 have unknown trends. The greatest threats to hawksbill sea turtles are 

overharvesting of turtles and eggs, degradation of nesting habitat, and fisheries interactions. 

Adult hawksbills are harvested for their meat and carapace, which is sold as tortoiseshell. Eggs 

are taken at high levels, especially in Southeast Asia where collection approaches 100 percent in 

some areas. In addition, lights on or adjacent to nesting beaches are often fatal to emerging 

hatchlings and alters the behavior of nesting adults. The species’ resilience to additional 

perturbation is low. 

3.2.4 Critical Habitat

On September 2, 1998, NMFS established critical habitat for hawksbill sea turtles around Mona 

and Monito Islands, Puerto Rico (63 FR 46693). Aspects of these areas that are important for 

hawksbill sea turtle survival and recovery include important natal development habitat, refuge 

from predation, shelter between foraging periods, and food for hawksbill sea turtle prey.

3.3 Kemp’s Ridley Sea Turtle

The Kemp’s ridley is the smallest of all sea turtle species and considered to be the most 

endangered sea turtle, internationally (Zwinenberg 1977, Groombridge 1982, TEWG 2000). Its 

range extends from the Gulf of Mexico to the Atlantic coast, with nesting beaches limited to a 
18

few sites in Mexico and Texas. The species was first listed under the Endangered Species 

Conservation Act (35 FR 8491) and listed as endangered under the ESA since 1973. We used 

information available in the revised recovery plan (NMFS et al. 2011) to summarize the status of 

the species, as follows.

3.3.1 Life History

Adult Kemp’s ridley sea turtles have an average straight carapace length of 2.1 ft (65 cm). 

Females mature at 12 years of age. The average remigration is 2 years. Nesting occurs from 

April to July in large arribadas, primarily at Rancho Nuevo, Mexico. Females lay an average of 

2.5 clutches per season. The annual average clutch size is 97 – 100 eggs per nest. The nesting 

location may be particularly important because hatchlings can more easily migrate to foraging 

grounds in deeper oceanic waters, where they remain for approximately 2 years before returning 

to nearshore coastal habitats. Juvenile Kemp’s ridley sea turtles use these nearshore coastal 

habitats from April through November, but move towards more suitable overwintering habitat in 

deeper offshore waters (or more southern waters along the Atlantic coast) as water temperature 

drops. Adult habitat largely consists of sandy and muddy areas in shallow, nearshore waters less 

than 120 ft (37 m) deep, although they can also be found in deeper offshore waters. As adults, 

Kemp’s ridleys forage on swimming crabs, fish, jellyfish, mollusks, and tunicates. 

3.3.2 Population Dynamics

Of the seven species of sea turtles in the world, the Kemp's ridley has declined to the lowest 

population level. Nesting aggregations at a single location (Rancho Nuevo, Mexico) were 

estimated at 40,000 females in 1947. By the mid-1980s, the population had declined to an 

estimated 300 nesting females. From 1980 to 2003, the number of nests increased 15 percent 

annually. In 2009, an estimated 8,000 nesting females produced over 20,000 nests. In addition, a 

total of 911 nests were recorded on the Texas coast from 2002 – 2010. 

3.3.3 Status

The Kemp’s ridley was listed as endangered in response to a severe population decline, primarily 

the result of egg collection. In 1973, legal ordinances prohibited the harvest of sea turtles from 

May to August, and in 1990, the harvest of all sea turtles was prohibited by presidential decree. 

In 2002, Rancho Nuevo was declared a Sanctuary. A successful head-start program has resulted 

in the reestablishment of nesting at Texan beaches. While fisheries bycatch remains a threat, the 

use of turtle excluder devices mitigates take. Fishery interactions and strandings, possibly due to 

forced submergence, appear to be the main threats to the species. It is clear that the species is 

steadily increasing; however, the species’ limited range and low global abundance make it 

vulnerable to new sources of mortality as well as demographic and environmental randomness, 

all of which are often difficult to predict with any certainty. Therefore, its resilience to future 

perturbation is low.

3.3.4 Critical Habitat

On February 17, 2010, WildEarth Guardians, Santa Fe, New Mexico, submitted to USFWS and 

NMFS a petition to designate critical habitat for the Kemp’s ridley sea turtle (available online at: 

http://www.nmfs.noaa.gov/pr/pdfs/petitions/kempsridley_criticalhabitat_feb2010.pdf). Critical 

habitat has not been designated for the species.
19

3.4 Olive Ridley Sea Turtle (Mexico’s Pacific Coast Breeding Colonies)

The olive ridley sea turtle is a small, mainly pelagic, sea turtle with a circumtropical distribution. 

The species was listed under the ESA on July 28, 1978 (43 FR 32800). The species was 

separated into two listing designations: endangered for breeding populations on the Pacific coast 

of Mexico, and threatened wherever found except where listed as endangered (i.e., in all other 

areas throughout its range). We used information available in the 5-year review (NMFS and 

USFWS 2007d) to summarize the status of the endangered listing, as follows.

3.4.1 Life History

Olive ridley females mature at 10 – 18 years of age. They lay an average of two clutches per 

season (3-6 months in duration). The annual average clutch size is 100 – 110 eggs per nest. Olive 

ridleys commonly nest in successive years. Females nest in solitary or in arribadas, large 

aggregations coming ashore at the same time and location. As adults, Olive ridleys forage on 

crustaceans, fish, mollusks, and tunicates, primarily in pelagic habitats. 

3.4.2 Population Dynamics

The eastern Pacific lineage is genetically and geographically isolated from other olive ridley 

lineages. 

3.4.3 Status

Prior to 1950, abundance was conservatively estimated to be 10 million adults. Years of adult 

harvest reduced the population to just over one million adults by 1969. Shipboard transects along 

the Mexico and Central American coasts between 1992 and 2006 indicate an estimated 1.39 

million adults. Based on the number of olive ridleys nesting in Mexico, populations appear to be 

increasing in one location (La Escobilla: from 50,000 nests in 1988 to more than one million in 

2000) and stable at all others. Harvest prohibitions and the closure of a nearshore turtle fishery 

resulted in a partial recovery; however, remaining threats include Current bycatch in longline and 

trawl fisheries and the illegal harvest of eggs and turtles. Given its large population size, it is 

somewhat resilient to future perturbation.

3.4.4 Critical Habitat

No critical habitat has been designated for the olive ridley sea turtle.

3.5 Olive Ridley Sea Turtle (All Other Areas)

The olive ridley sea turtle is a small, mainly pelagic, sea turtle with a circumtropical distribution. 

The species was listed under the ESA on July 28, 1978 (43 FR 32800). The species was 

separated into two listing designations: endangered for breeding populations on the Pacific coast 

of Mexico, and threatened wherever found except where listed as endangered (i.e., in all other 

areas throughout its range). We used information available in the 5-year review (NMFS and 

USFWS 2007d) to summarize the status of the threatened listing, as follows.

3.5.1 Life History

See above (Olive ridley sea turtle, Mexico’s Pacific coast breeding colonies). 

3.5.2 Population Dynamics

Threatened olive ridley sea turtles nest in arribadas at a few beaches in the eastern Pacific, 

western Atlantic, and northern Indian Oceans. Solitary nesting is observed on many tropical 

beaches throughout the Atlantic, Pacific, and Indian Oceans. Arribadas now range in size from 
20

335 to 2,000 nests in the western Atlantic, from 1,300 to 200,000 turtles in the eastern Pacific, 

and from 1,000 to 200,000 in the Indian Ocean. 

3.5.3 Status

It is likely that solitary nesting locations once hosted large arribadas; since the 1960s, 

populations have experienced declines in abundance of 50 – 80 %. Many populations continue to 

decline. Olive ridley sea turtles continue to be harvested as eggs and adults, legally in some 

areas, and illegally in others. Incidental capture in fisheries is also a major threat. The olive 

ridley sea turtle is the most abundant sea turtle in the world; however, several populations are 

declining as a result of continued harvest and fisheries bycatch. Its large population size, 

however, allows some resilience to future perturbation.

3.5.4 Critical Habitat

No critical habitat has been designated for the olive ridley sea turtle.

3.6 Loggerhead Sea Turtle (North Pacific Ocean)

The loggerhead sea turtle is distinguished from other turtles by its large head and powerful jaws. 

The North Pacific Ocean DPS ranges throughout tropical to temperate waters in the North 

Pacific. The species was first listed as threatened under the Endangered Species Act in 1978 (43 

FR 32800). In 2011, the North Pacific Ocean DPS was listed as endangered under the ESA (76 

FR 58868). We used information available in the 2009 Status Review (Conant et al. 2009) and 

the final listing rule (76 FR 58868) to summarize the status of the species, as follows.

3.6.1 Life History

Mean age at first reproduction for female loggerhead sea turtles is 30 years (SD = 5). Females 

lay an average of three clutches per season. The annual average clutch size is 112 eggs per nest. 

The average remigration interval is 2.7 years. Nesting occurs primarily on Japanese beaches, 

where warm, humid sand temperatures incubate the eggs. Temperature determines the sex of the 

turtle during the middle of the incubation period. Turtles spend the post-hatchling stage in 

pelagic waters. The juvenile stage is spent first in the oceanic zone (Kuroshio Extension 

Bifurcation Region) and later in the neritic zone (i.e., coastal waters) in the eastern and central 

Pacific. Coastal waters in the eastern and western North Pacific provide important foraging 

habitat, inter-nesting habitat, and migratory habitat for adult loggerheads.

3.6.2 Population Dynamics

There are nine loggerhead DPSs, which are geographically separated and genetically isolated, as 

indicated by genetic, tagging, and telemetry data. The North Pacific DPS has a small nesting 

population. An 18-year time series of nesting data in Japan indicates a decline in the North 

Pacific population from 6,638 nests in 1990 to 2,064 nests in 1997. Since then, nesting has 

gradually increased to 7,000 – 8,000 nests, based on estimates taken in 2009). 

3.6.3 Status

In the loggerhead sea turtle North Pacific Ocean DPS, historical evidence from Kamouda Beach 

indicates a substantial overall decline (50 – 90 percent) since 1950. Furthermore, population 

modeling in 2009 indicated that the North Pacific Ocean DPS appears to be declining, is at risk, 

and is thus likely to decline in the foreseeable future (Conant et al. 2009). The decline is a result 

of incidental capture in fishing gear, directed harvest, coastal development, increased human use 

of nesting beaches, and pollution. Coastal fisheries in Japan, the South China Sea, and Baja 
21

California, Mexico are the biggest threat to the species. Drift gillnet fisheries in California and 

Oregon and the Hawaii-based longline fishery once took large numbers of loggerheads; however, 

seasonal and take-based closures have minimized the impact of these fisheries. The DPS remains 

at risk for extinction and its resilience to future perturbations is low.

3.6.4 Critical Habitat

No critical habitat has been designated for the North Pacific Ocean loggerhead sea turtle DPS.

3.7 Loggerhead Sea Turtle (Northwest Atlantic Ocean)

The loggerhead sea turtle is distinguished from other turtles by its large head and powerful jaws. 

The Northwest Atlantic Ocean DPS inhabits continental shelf and estuarine environments 

throughout tropical and temperate waters in the North Atlantic to 40 ̊ W. The species was first 

listed as threatened under the Endangered Species Act in 1978 (43 FR 32800). In 2011, the 

Northwest Atlantic Ocean DPS was listed as threatened under the ESA (76 FR 58868). We used 

information available in the 2009 Status Review (Conant et al. 2009) and the final listing rule (76 

FR 58868) to summarize the status of the species, as follows.

3.7.1 Life History

Adult loggerhead sea turtles have a mean straight carapace length of 3 ft (92 cm). Mean age at 

first reproduction for female loggerhead sea turtles is 30 years (SD = 5). Mating occurs in the 

spring, and eggs are laid throughout the summer. Northwest Atlantic females lay an average of 

five clutches per season. The annual average clutch size is 115 eggs per nest. The average 

remigration interval is 3.7 years (Tucker 2010). Nesting occurs primarily on beaches along the 

southeastern coast of the United States, from southern Virginia to Alabama. Additional nesting 

occurs on beaches throughout the Gulf of Mexico and Caribbean Sea. Temperature determines 

the sex of the turtle during the middle of the incubation period. Post- hatchling loggerheads from 

southeast U.S. nesting beaches may linger for months in waters just off the nesting beach or 

become transported by ocean currents within the Gulf of Mexico and North Atlantic, where they 

become associated with Sargassum habitats, driftlines, and other convergence zones. The 

juvenile stage is spent first in the oceanic zone (e.g., waters around the Azores, Madeira, 

Morocco, and the Grand Banks off Newfoundland) and later in the neritic zone (i.e., continental 

shelf waters) from Cape Cod Bay, Massachusetts, south through Florida, the Caribbean, and the 

Gulf of Mexico. Neritic stage juveniles often inhabit relatively enclosed, shallow water estuarine 

habitats with limited ocean access. Juveniles are omnivorous and forage on crabs, mollusks, 

jellyfish and vegetation at or near the surface (Dodd 1988). Adults inhabit shallow water habitats 

with large expanses of open ocean access, as well as continental shelf waters. Sub-adult and 

adult loggerheads prey on benthic invertebrates such as mollusks and decapod crustaceans in 

hard bottom, coastal habitats. 

3.7.2 Population Dynamics

There are nine loggerhead DPSs, which are geographically separated and genetically isolated, as 

indicated by genetic, tagging, and telemetry data. The Northwest Atlantic Ocean DPS is further 

divided into five recovery units or nesting subpopulations: Northern, Peninsular Florida, Dry 

Tortugas, Northern Gulf of Mexico, and Greater Caribbean. Using a stage/age demographic 

model, the adult female population size of the DPS is estimated at 20,000 – 40,000 females 

(NMFS 2009a). Peninsular Florida hosts more than 10,000 females nesting annually, which 

constitutes 87 percent of all nesting effort in the DPS. A 23 percent increase in nest counts from 
22

1989 until 1998 was followed by a sharp decline in the subsequent decade 

(http://myfwc.com/research/wildlife/sea-turtles/nesting/loggerhead-trends/); large fluctuations in

population size often indicate the loss of resilience and susceptibility to population collapse (Dai 

et al. 2012, Scheffer et al. 2012). Nesting aggregations from Georgia to North Carolina host 

1,000 to 9,999 females nesting annually. The other recovery units are much smaller but are still 

considered essential to the continued existence of the species. 

3.7.3 Status

The loggerhead sea turtle Northwest Atlantic Ocean DPS was listed as threatened under the ESA 

as a result of bycatch mortality, resulting from domestic and international commercial fishing, 

particularly in gillnet, longline, and trawl fisheries. Turtle excluder devices on shrimp trawlers 

and the use of circle hooks in the longline fishery have reduced bycatch significantly; however 

bycatch remains the most significant threat to the DPS. The rangewide nesting trend of the DPS 

from 1989 until 2010 is slightly negative but not significantly different from zero. We conclude 

that, as a result of its relatively large abundance (20,000 – 40,000 females), the DPS is not 

currently at risk of extinction; however, its large fluctuations in population size indicates loss of 

resilience, such that it is likely to become endangered within the foreseeable future.

3.7.4 Critical Habitat

On July 18, 2013, NMFS proposed critical habitat for the Northwest Atlantic Ocean loggerhead 

DPS within the Atlantic Ocean and the Gulf of Mexico. Specific areas proposed for designation 

include 36 occupied marine areas within the range of the Northwest Atlantic Ocean DPS. These 

areas contain one or a combination of nearshore reproductive habitat, winter area, breeding areas, 

and migratory corridors. They also asked for comments on whether to include as critical habitat 

in the final rule some areas that contain foraging habitat and two large areas that contain 

Sargassum habitat.

3.8 Green Sea Turtle (All Other Areas)

The green sea turtle is the largest of the hardshell marine turtles, growing to a weight of 350 lb 

(159 kg) and a straight carapace length of greater than 3.3 ft (1 m). It has a circumglobal 

distribution, occurring throughout nearshore tropical, subtropical, and, to a lesser extent, 

temperate waters. The species was listed under the ESA on July 28, 1978 (43 FR 32800). The 

species was separated into two listing designations: endangered for breeding populations in 

Florida and the Pacific coast of Mexico, and threatened in all other areas throughout its range. 

On August 1, 2012, NMFS found that a petition to identify the Hawaiian population of green 

turtle as a DPS, and to delist the DPS, may be warranted (77 FR 45571). We used information 

available in the 2007 5-Year Review (NMFS and USFWS 2007a) to summarize the status of the 

species, as follows.

3.8.1 Life History

Age at first reproduction for females is 20 - 40 years. They lay an average of three nests per 

season with an average of 100 eggs per nest. The remigration interval (i.e., return to natal 

beaches) is 2 – 5 years. Nesting occurs primarily on beaches with intact dune structure, native 

vegetation, and appropriate incubation temperatures during summer months. After emerging 

from the nest, hatchlings swim to offshore areas and go through a post-hatchling pelagic stage 

where they are believed to live for several years. During this life stage, green sea turtles feed 

close to the surface on a variety of marine algae and other life associated with drift lines and 
23

debris. Adult turtles exhibit site fidelity and migrate hundreds to thousands of kilometers from 

nesting beaches to foraging areas. Green sea turtles spend the majority of their lives in coastal 

foraging grounds, which include open coastlines and protected bays and lagoons. Adult green 

turtles feed primarily on seagrasses and algae, although they also eat jellyfish, sponges, and other 

invertebrate prey.

3.8.2 Population Dynamics

Nesting data at 46 sites from 1990-2006 indicate that 108,761 to 150,521 females nest each year. 

At the 23 sites for which nesting trend data are available, ten are increasing, nine are stable, and 

four are decreasing. Where long term data (≥ 20 years) are available (nine sites), nesting 

populations are stable or increasing in abundance. Nesting populations are doing relatively well 

in the Pacific, Western Atlantic, and Central Atlantic Ocean; whereas, populations are doing 

poorly in Southeast Asia, Eastern Indian Ocean, and Mediterranean. 

3.8.3 Status

Once abundant in tropical and subtropical waters, globally, green sea turtles exist at a fraction of 

their historical abundance, as a result of over-exploitation. Egg harvest, the harvest of females on 

nesting beaches, and directed hunting of turtles in foraging areas remain the three greatest threats 

to their recovery. In addition, bycatch in drift-net, long-line, set-net, pound-net, and trawl 

fisheries kill thousands of green sea turtles annually. Increasing coastal development (including 

construction, beach erosion and renourishment, and artificial lighting) threatens nesting success 

and hatchling survival. Apparent increases in recent years are optimistic but must be viewed 

cautiously, as the datasets represent a fraction of a green sea turtle generation, up to 50 years. 

While the threats of harvest, coastal development, and fisheries bycatch continue, the species 

appears to be somewhat resilient to future perturbations.

3.8.4 Critical Habitat

On September 2, 1998, NMFS designated critical habitat for green sea turtles (63 FR 46694), 

which include coastal waters surrounding Culebra Island, Puerto Rico. Seagrass beds 

surrounding Culebra provide important foraging resources for juvenile, subadult, and adult green 

sea turtles. Additionally, coral reefs surrounding the island provide resting shelter and protection 

from predators. This area provides important developmental habitat for the species.

3.9 Green Sea Turtle (Florida and Mexico’s Pacific Coast Breeding Colonies)

As described above, the green sea turtle was listed under the ESA on July 28, 1978 (43 FR 

32800). The species was separated into two listing designations: endangered for breeding 

populations in Florida and the Pacific coast of Mexico, and threatened in all other areas 

throughout its range. We used information available in the 2007 5-Year Review (NMFS and 

USFWS 2007a) to summarize the status of the species, as follows.

3.9.1 Life History

See above, except in Florida, nests contain an average of 136 eggs and the average remigration 

interval is 2 years. In addition to nesting on Florida beaches, green sea turtles are found in 

coastal waters throughout the state. Important neritic habitats include: Mosquito and Indian River 

Lagoons, Port Canaveral, St. Lucie Inlet, and Biscayne Bay.
24

3.9.2 Population Dynamics

Along the central and southeast coast of Florida, an estimated 200 – 1,100 females nest each year 

(Meylan et al. 1994, Weishampel et al. 2003). According to data collected from Florida’s index 

nesting beach survey from 1989-2012, green sea turtle nest counts across Florida have increased 

approximately ten-fold from a low of 267 in the early 1990s to a high of 10,701 in 2011. In the 

Pacific Mexico, surveys from 2000 to 2006 indicate an average of 6,050 nests, and a 25-year 

dataset reveals an increasing trend for the largest nesting site (Colola). 

3.9.3 Status

The historic and current threats for the Florida and Mexico’s Pacific coast breeding populations 

are the same as described above for all other areas. Recent increases in nesting on Florida 

beaches are likely a result of a Florida statute prohibiting the killing of green sea turtles, ESA 

listing, the 1994 Florida State ban on gillnets and other entangling nets, CITES Appendix I 

listing, and turtle protections in other nations. Recent increases in the Mexican breeding 

populations are likely the result of nesting beach protection (1979) and a 1990 presidential 

decree protecting all sea turtles. However, the threats of harvest, coastal development, and 

fisheries bycatch continue. The populations’ resilience to future perturbations is low but 

increasing with population size increases. 

3.9.4 Critical Habitat

No critical habitat has been designated for the green sea turtle along Florida and Mexico’s 

Pacific Coast.

4 Salmonids

Since 1997 NMFS promulgated a total of 29 limits to the ESA section 9(a) take prohibitions for 

21 threatened Pacific salmon and steelhead Evolutionarily Significant Units (ESUs) or Distinct 

Population Segments (DPSs) (62 FR 38479, July 18, 1997; 65 FR 42422, July 10, 2000; 65 FR 

42485, July 10, 2000; 67 FR 1116, January 9, 2002; 73 FR 7816, February 11, 2008). On June 

28, 2005, as part of the final listing determinations for 16 ESUs of West Coast salmon, NMFS 

amended and streamlined the 4(d) protective regulations for threatened salmon and steelhead (70 

FR 37160). NMFS took this action to provide appropriate flexibility to ensure that fisheries and

artificial propagation programs are managed consistently with the conservation needs of 

threatened salmon and steelhead. Under this change, the section 4(d) protections apply to natural 

and hatchery fish with an intact adipose fin, but not to listed hatchery fish that have had their 

adipose fin removed prior to release into the wild.

4.1 Atlantic Salmon (Gulf of Maine DPS)

The three generally recognized groups of Atlantic salmon (North American, European, and 

Baltic) range from northeastern North America through portions of the North Atlantic Ocean to 

Europe and northwestern Russia in both fresh and saltwater habitats. The North American group 

historically ranged from northern Quebec southeast to Newfoundland and southwest to Long 

Island Sound. It included Canadian populations and U.S. populations, including the listed Gulf of 

Maine (GOM) DPS. The GOM DPS was first listed as endangered by the USFWS and NMFS on 

November 17, 2000 (65 FR 69459). The listing was refined by the Services on June 19, 2009 (74 

FR 29344) to include all anadromous Atlantic salmon whose freshwater range occurs in the 

watersheds from the Androscoggin River northward along the Maine coast to the Dennys River, 
25

and wherever these fish occur in the estuarine and marine environment. We used information 

available in the 2006 Status Review (Fay et al. 2006) and the Final Rule to List the Expanded 

Gulf of Maine DPS as Endangered Under the ESA (74 FR 29344) to summarize the status of the 

GOM DPS, as follows.

4.1.1 Life History

Adult Atlantic salmon typically spawn in early November and juveniles spend approximately 

two years feeding on small invertebrates and occasionally small vertebrates in freshwater until 

they weigh approximately two ounces and are six inches in length. Smoltification (the 

physiological and behavioral changes required for the transition to salt water) usually occurs at 

age two for the GOM DPS. The GOM DPS migrates more than 4,000 km in the open ocean to 

reach feeding areas in the Davis Strait between Labrador and Greenland. Adult salmon feed 

opportunistically and their diet is composed primarily of other fish. The majority of GOM DPS 

salmon (about 90 percent) spend two winters at sea before reaching maturity and returning to 

their natal rivers, with the remainder spending one or three winters at sea. At maturity, GOM 

DPS salmon typically weigh between eight to 15 pounds and average 30 inches in length.

4.1.2 Population Dynamics

Historically, the GOM DPS population was several orders of magnitude larger than 

contemporary populations. Foster and Atkins (1869) estimated that roughly 100,000 adult 

salmon returned to the Penobscot River alone before the river was dammed, whereas estimates of 

abundance for the entire GOM DPS exceeded 5,000 individuals in only four years from 1967 to 

2007. From 2001 to 2007, abundance has been estimated between 819 (in 2002) and 1,416 (in 

2004) individuals. Abundance was estimated at 1,014 individuals in 2007, the most recent year 

for which abundance records are available.

4.1.3 Status

The GOM DPS of Atlantic salmon was listed as endangered in 2000 in response to population 

decline caused by many factors, including overexploitation, degradation of water quality, and 

damming of rivers, all of which remain persistent threats. Atlantic salmon in the GOM DPS 

currently exhibit critically low spawner abundance, poor marine survival, and are still confronted 

with a variety of threats, including: poor water quality, land and water use practices, habitat loss, 

predation, incidental capture and poaching, genetic threats from hatchery programs, and climate 

change. The abundance of Atlantic salmon in the GOM DPS has been low and, in general, has 

been in decline over the past several decades. The proportion of fish of natural origin to 

hatchery-reared fish is very small (approximately 10 percent) and is continuing to decline. The 

conservation hatchery program has assisted in slowing the decline and helping to stabilize 

populations at low levels, but has not contributed to an increase in the overall abundance of 

salmon and has not been able to halt the decline of the naturally reared component of the GOM 

DPS. The 2006 status review reports an estimated extinction risk of 19 to 75 percent within the 

next 100 years for the GOM DPS, even when current levels of hatchery supplementation are 

considered. Even with current conservation efforts, returns of adult Atlantic salmon to the GOM 

DPS rivers remain extremely low. Based on the information above, the species would likely have 

a low resilience to additional perturbations.

4.1.4 Critical Habitat

On June 19, 2009, NMFS and the USFWS defined critical habitat for Atlantic salmon (74 FR 

29300). The critical habitat includes all anadromous Atlantic salmon streams whose freshwater 
26

range occurs in watersheds from the Androscoggin River northward along the Maine coast 

northeastward to the Dennys River, and wherever these fish occur in the estuarine and marine 

environment. PCEs were identified within freshwater and estuarine habitats of the occupied 

range of the GOM DPS and include sites for spawning and incubation, juvenile rearing, and 

migration. Critical habitat and PCEs were not designated within marine environments because of 

the limited knowledge of the physical and biological features that the species uses during the 

marine phase of its life.

4.2 Chinook Salmon (General Overview)

We discuss the distribution, life history, population dynamics, status, and critical habitats of the 

nine species (here we use the word “species” to apply to distinct population segments, DPSs, and 

evolutionary significant units, ESUs) separately; however, because listed Chinook salmon 

species are virtually indistinguishable in the wild and comprise the same biological species, we 

begin this section describing characteristics common across ESUs. We used information 

available in status reviews (Good et al. 2005, Ford 2011), various salmon ESU listing 

documents, and biological opinions (NMFS 2012b) to summarize the status of the species.

Chinook salmon are the largest of the Pacific salmon and historically ranged from the Ventura 

River in California to Point Hope, Alaska in North America, and in northeastern Asia from 

Hokkaido, Japan to the Anadyr River in Russia in both fresh and saltwater habitats (Healey 

1991). In freshwater, Chinook salmon prefer streams that are deeper and larger than those used 

by other Pacific salmon species.

4.2.1 Life History

Chinook salmon exhibit varied and complex life history strategies and can generally be described 

as one of two types: “stream-type” or “ocean type”. Stream-type Chinook salmon ESUs reside in 

freshwater for a year or more following emergence before migrating to salt water; ocean-type 

Chinook salmon ESUs migrate to the ocean within their first year and typifies populations north 

of 56°N (Healey 1991). Stream-type ESUs usually return in late winter and early spring (springrun) as immature adults and reside in deep pools during summer before spawning in fall. Oceantype ESUs migrate to the ocean within their first year (sub-yearlings) and usually return as full 

mature adults in fall (fall-run) and spawn soon after river entry. Temperature and stream flow 

can significantly influence the timing of migrations and spawning, as well as the selection of 

spawning habitat (Geist et al. 2009, Hatten and Tiffan. 2009). All Chinook salmon are 

semelparous (i.e. they die after spawning).

The timing of return to fresh water, and ultimately spawning, often provides a temporal isolating 

mechanism for populations with different life histories. Return timing is often related to 

spawning location. Thus, differences in the timing of spawning migration also serve as a 

geographic isolating mechanism. Fall-run Chinook salmon generally spawn in the mainstem of 

larger rivers and are less dependent on flow, although early autumn rains and a drop in water 

temperature often provide cues for movements to spawning areas. Spring-run Chinook salmon 

take advantage of high flows from snowmelt to access the upper reaches of rivers.

Generally, Chinook salmon outmigrants (smolts) are about two to five inches long when they 

enter saline (often brackish) waters. The process of smoltification enables salmon to adapt to the 

ocean environment. Several factors can affect smoltification process, not only at the interface 

between fresh water and salt water, but higher in the watershed as the process of transformation 
27

begins long before fish enter salt waters. These factors include exposure to chemicals such as 

heavy metals and elevated water temperatures (Wedemeyer et al. 1980).

Chinook salmon feed on a variety of prey organisms depending upon life stage. In freshwater 

and brackish waters Chinook salmon primarily feed on small invertebrates and vertebrates. The 

diet of juvenile Chinook salmon in the ocean off Oregon and Washington is comprised primarily 

of juvenile fishes (cottids, pleuronectids, rockfishes, sandlance, smelts, anchovies, and sardines) 

as well as euphausiids (Emmett et al. 2006, Daly et al. 2012)). Adult Chinook salmon eat larger 

life stages of the same types of forage fishes during their oceanic life stage.

4.2.2 Population Dynamics

The population dynamics of each Chinook salmon ESU will be discussed separately, below.

4.2.3 Status

On June 28, 2005, as part of the final listing determinations for 16 ESUs of West Coast salmon, 

NMFS amended and streamlined the 4(d) protective regulations for threatened salmon and 

steelhead (70 FR 37160) as described in the Protective Regulations for Threatened Salmonid 

Species section of this document. Under this change, the section 4(d) protections apply to natural 

and hatchery fish with an intact adipose fin, but not to listed hatchery fish that have had their 

adipose fin removed prior to release into the wild.

4.2.4 Critical Habitat

Areas designated as critical habitat are important for the species’ overall conservation by 

protecting quality growth, reproduction, and feeding. At the time of designation, primary 

constituent elements (PCEs) are identified and include sites necessary to support one or more 

Chinook salmon life stage(s). These PCEs will be identified for each ESU below, but in general 

they may include freshwater spawning sites, freshwater rearing sites, freshwater migration 

corridors, nearshore marine habitat, and estuarine areas. Physical or biological features that 

characterize these sites will also be discussed for each ESU separately, but they may include 

water quality and quantity, natural cover, forage, adequate passage conditions, and floodplain 

connectivity. The critical habitat designation identified for each ESU contains additional details 

on the areas included as part of the designation, and the areas that were excluded from 

designation.

4.3 Chinook Salmon (California Coastal ESU)

The California Coastal Chinook salmon ESU includes all naturally spawned populations of 

Chinook salmon from rivers and streams south of the Klamath River to the Russian River, 

California. Seven artificial propagation programs were included in the ESU, however on June 26, 

2013, NMFS proposed to remove the artificial propagation programs from the ESU because the 

artificial propagation programs have been terminated (78 FR 38270). We used information 

available in the status review (Good et al. 2005), “An analysis of historical population structure 

for evolutionarily significant units of Chinook salmon, coho salmon, and steelhead in the NorthCentral California Coast Recovery Domain” (Bjorkstedt et al. 2005), “A framework for assessing 

the viability of Threatened and Endangered Salmon and Steelhead in the North-central California 

Coast Recovery Domain” (Spence et al. 2008), listing documents (64 FR 50393; 70 FR 37160), 

and previously issued biological opinions (NMFS 2008a, 2012b) to summarize the status of the 

species.
28

4.3.1 Life History

California Coastal Chinook salmon are a fall-run, ocean-type salmon. A spring-run (river-type) 

component existed historically, but is now considered extinct (Bjorkstedt et al. 2005). The 

different populations vary in run timing depending on latitude and hydrological differences 

between watersheds. Entry of California Coastal Chinook salmon into the Russian River depends 

on increased flow from fall storms, usually in November to January. Juveniles of this ESU 

migrate downstream from April through June and may reside in the estuary for an extended 

period before entering the ocean.

4.3.2 Population Dynamics

Historical estimates of escapement, based on professional opinion and evaluation of habitat 

conditions, suggest abundance was roughly 73,000 in the early 1960s with the majority of fish 

spawning in the Eel River. Comparison of historical and current abundance information indicates 

that independent populations of Chinook salmon are depressed in many basins (Bennett 2005). 

All spring-run populations once occupying the North Mountain Interior are considered extinct or 

nearly so. Redd counts in Mattole River in the northern portion of the ESU indicate a small but 

consistent population; the cooler northern climate likely provides for favorable conditions for 

these populations. The Eel River interior fall-run populations are severely depressed. Two 

functionally independent populations are believed to have existed along the southern coastal 

portion of the ESU; of these two, only the Russian River currently has a run of any significance. 

This is also the only population with abundance time series. The 2000 to 2007 median observed 

(at Mirabel Dam) Russian River Chinook salmon run size is 2,991 with a maximum of 6,103 

(2003) and a minimum of 1,125 (2008) adults (Cook 2008, Sonoma County Water Agency 

2008). The number of spawners has steadily decreased since its high returns in 2003 with 1,963 

fish observed in 2007 and 1,125 observed by December 22, 2008.

4.3.3 Status

NMFS listed California Coastal Chinook salmon as threatened on September 16, 1999 (64 FR 

50393) and reaffirmed their threatened status on June 28, 2005 (70 FR 37160). California 

Coastal Chinook salmon was listed due to the combined effect of dams that prevent them from 

reaching spawning habitat, logging, agricultural activities, urbanization, and water withdrawals 

in the river drainages that support them. This ESU is at considerable risk from population 

fragmentation and reduced spatial diversity. There is little connectivity between the southern and 

northern portions of their range. At the southern portion of the ESU, only the Russian River 

population has had a constant run that exceeded 1,000 adult spawning fish over the last 10 years. 

This places the ESU at risk from random catastrophic events, chronic stressors, and long-term 

environmental change. Life history diversity has been significantly reduced by loss of the springrun race and reduction in coastal populations. Based on these factors, this ESU would likely have 

a low resilience to additional perturbations.

4.3.4 Critical Habitat

NMFS designated critical habitat for California Coastal Chinook salmon on September 2, 2005 

(70 FR 52488). Specific geographic areas designated include the following CALWATER 

hydrological units: Redwood Creek, Trinidad, Mad River, Eureka Plain, Eel River, Cape 

Mendocino, Mendocino Coast and the Russian River. PCEs include freshwater spawning sites, 

freshwater rearing sites, freshwater migration corridors, nearshore marine habitat and estuarine 

areas. The physical or biological features that characterize these sites include water quality and 
29

quantity, natural cover, forage, adequate passage conditions, and floodplain connectivity. The 

spawning PCE in coastal streams is degraded by years of timber harvest that has produced large 

amounts of sand and silt in spawning gravel and reduced water quality by increased turbidity.

Agriculture and urban areas have impacted rearing and migration PCEs in the Russian River by 

degrading water quality and by disconnecting the river from it floodplains by the construction of 

levees. Water management from dams within the Russian and Eel River watersheds maintain 

high flows and warm water during summer which benefits the introduced predatory Sacramento 

pikeminnow, which has resulted in excessive predation along migration corridors. Breaches of 

the sandbar at the mouth of the Russian River result in periodic mixing of salt water which 

degrades the estuary PCE by altering water quality and salinity conditions that support juvenile 

physiological transitions between fresh- and salt water. The current condition of PCEs for this 

ESU indicates that they are not currently functioning or are degraded; these conditions are likely 

to maintain low population abundances across the ESU.

4.4 Chinook Salmon (Central Valley Spring-run ESU)

The Central Valley spring-run Chinook salmon ESU includes all naturally spawned populations 

of spring-run Chinook salmon in the Sacramento River and its tributaries in California. Central 

Valley spring-run Chinook salmon have been extirpated from the San Joaquin River and its 

tributaries and the American River due to the construction of Friant and Folsom dams, 

respectively. Naturally spawning populations of Central Valley spring-run Chinook salmon 

currently are restricted to accessible reaches of the upper Sacramento River, and its tributaries 

Butte, Deer, and Mill Creeks and limited spawning occurs in the basins of smaller tributaries 

(California Department of Fish and Game 1998). This ESU includes one artificial propagation 

program. We used information available in the status review (Good et al. 2005), listing 

documents (64 FR 50393; 70 FR 37160), the draft recovery plan (NMFS 2009c) and previously 

issued biological opinions (NMFS 2012b) to summarize the status of the species.

4.4.1 Life History

The Chinook Central Valley ESU is a spring-run, ocean-type salmon. This ESU returns to the 

Sacramento River between March and July and spawning occurs from late August to early 

October, with a peak in September. Juveniles of this ESU require cool freshwater while they 

mature over the summer.

4.4.2 Population Dynamics

The Central Valley drainage as a whole is estimated to have supported spring-run Chinook 

salmon runs as large as 700,000 fish between the late 1880s and the 1940s (Fisher 1994), 

although these estimates may reflect an already declining population, in part from the 

commercial gillnet fishery that occurred for this ESU. Median natural production of spring-run 

Chinook salmon from 1970 to 1989 was 30,220 fish. In the 1990s, the population experienced a 

substantial production failure with an estimated natural production ranging between 3,863 and 

7,806 fish (with the exception of 1995 which had a natural production of an estimated 35,640 

adults) during the years between 1991 and 1997. Numbers of naturally produced fish increased 

significantly in 1998 to an estimated 48,755 adults and estimated natural production has 

remained above 10,000 fish since then (USFWS and U.S. Bureau of Reclamation 2007).

The Sacramento River trends show long- and short- term negative trend and negative population 

growth. Meanwhile, the median production of Sacramento River tributary populations increased 

from a low of 4,248 with only one year exceeding 10,000 fish before 1998 to a combined natural 
30

production of more than 10,000 spring-run Chinook in all years after 1998 (USFWS and U.S. 

Bureau of Reclamation 2007). Time series data for Mill, Deer, Butte, and Big Chico Creeks 

spring-run Chinook salmon (through 2006) indicate that all three tributary spring-run Chinook 

populations experienced population growth. Although the populations are small, Central Valley 

spring-run Chinook salmon have some of the highest population growth rates of Chinook salmon 

in the Central Valley.

4.4.3 Status

NMFS originally listed Central Valley spring-run Chinook salmon as threatened on September 

16, 1999 (64 FR 50393), and reaffirmed their status on June 28, 2005 (70 FR 37160). This 

species was listed due to loss of historical spawning habitat, degradation of remaining habitat, 

and threats to genetic diversity from hatchery salmon. Risks persist to the spatial structure and 

diversity of the ESU. Only three extant independent populations exist, and they are especially 

vulnerable to disease or catastrophic events because they are in close proximity. In addition, until 

there are means to spatially separate the spring-run and fall-run populations in the lower basin of 

the Feather River, some level of genetic introgression of the races is expected to continue. Based 

on these factors, this ESU would likely have a low resilience to additional perturbations.

4.4.4 Critical Habitat

NMFS designated critical habitat for Central Valley spring-run Chinook salmon on September 2, 

2005 (70 FR 52488). In total, Central Valley spring-run Chinook salmon occupy 37 watersheds 

(freshwater and estuarine). The total area of habitat designated as critical includes about 1,100 

miles of stream habitat and about 250 square miles of estuarine habitat in the San Francisco-San 

Pablo-Suisun Bay complex. PCEs include freshwater spawning sites, freshwater rearing sites, 

freshwater migration corridors, nearshore marine habitat and estuarine areas. The physical or 

biological features that characterize these sites include water quality and quantity, natural cover, 

forage, adequate passage conditions, and floodplain connectivity. Spawning and rearing PCEs 

are degraded by high water temperature caused by the loss of access to historic spawning areas in 

the upper watersheds which maintained cool and clean water throughout the summer. The 

rearing PCE is degraded by floodplain habitat being disconnected from the mainstem of larger 

rivers throughout the Sacramento River watershed, thereby reducing effective foraging. The 

migration PCE is degraded by lack of natural cover along the migration corridors. Juvenile 

migration is obstructed by water diversions along Sacramento River and by two large state and 

federal water-export facilities in the Sacramento-San Joaquin Delta. Contaminants from 

agriculture and urban areas have degraded rearing and migration PCEs to the extent that they 

have lost their functions necessary to serve their intended role to conserve the species. Water 

quality impairments in the designated critical habitat of this ESU include inputs from fertilizers, 

insecticides, fungicides, herbicides, surfactants, heavy metals, petroleum products, animal and 

human sewage, sediment in the form of turbidity, and other anthropogenic pollutants. Pollutants 

enter the surface waters and riverine sediments as contaminated stormwater runoff, aerial drift 

and deposition, and via point source discharges. The current condition of PCEs for this ESU 

indicates they are not currently functioning or are degraded; these conditions are likely to 

maintain low population abundances across the ESU.

4.5 Chinook Salmon (Lower Columbia River ESU)

This Chinook salmon ESU includes all naturally spawned populations of Chinook salmon from 

the Columbia River and its tributaries from its mouth at the Pacific Ocean upstream to a 
31

transitional point between Washington and Oregon, east of the Hood River and the White 

Salmon River, and includes the Willamette River to Willamette Falls, Oregon, exclusive of 

spring-run Chinook salmon in the Clackamas River. Twenty artificial propagation programs are 

included in the ESU (70 FR 37160; 76 FR 50448). We used information available in status 

reviews (Good et al. 2005, Ford 2011, NMFS 2011d), “Historical population structure of Pacific 

salmonids in the Willamette River and Lower Columbia River Basins” (Myers et al. 2006), the 

recovery plan (NMFS 2013c), listing documents (64 FR 14308; 70 FR 37160), and previously 

issued biological opinions (NMFS 2012b) to summarize the status of the species.

4.5.1 Life History

Lower Columbia River Chinook salmon have three life history types: early fall run, ocean-type 

(“tule” salmon); late fall run, stream-type (“bright” salmon); and spring-run, stream-type.

Presently, the fall-runs are the predominant life history types, though spring-run Lower 

Columbia River Chinook salmon were numerous historically.

Both fall-runs of Lower Columbia River Chinook salmon enter fresh water from August through 

October to spawn in large river mainstems; however, the bright salmon has a delayed entry to 

spawning grounds and resides in the river for a longer time between river entry and spawning.

Tule salmon spawn from late September to November, with peak spawning activity in midOctober and brights spawn from November to January, with peak spawning in mid-November.

Most tule salmon remain at sea from one to five years (more commonly three to five years) and 

return to spawn at two to six years of age. Brights return to fresh water predominately as threeand four-year-olds.

Spring-run Chinook salmon enter fresh water in March through June to spawn in upstream 

tributaries in August and September. The spring-run Chinook salmon migrates to the sea as 

yearlings, typically in spring, though some may over-winter in the mainstem Columbia River 

before outmigrating (Lower Columbia Fish Recovery Board 2010). The natural timing of Lower 

Columbia River spring-run Chinook salmon emigration is obscured by hatchery releases. Most 

remain at sea from one to five years (more commonly two to four years) and return to spawn at 

three to six years of age (Lower Columbia Fish Recovery Board 2010).

4.5.2 Population Dynamics

It is estimated that 31 independent Chinook salmon populations (22 fall- and late fall-runs and 

nine spring- runs) existed historically in the Lower Columbia River. Of those 31 populations, it 

is estimated that that eight to 10 historical populations have been extirpated, most of them 

spring-run populations. Historically, the number of spring-run Chinook salmon returning to the 

Lower Columbia River may have almost equaled that of fall-run Chinook salmon. However, the 

majority of spring-run LCR Chinook salmon populations are now extirpated and total returns are 

substantially lower for the fall-run component in recent years.

Historical records of Chinook salmon abundance are sparse. However, cannery records suggest a 

peak run of 4.6 million fish (43 million lbs) in 1883 (Lichatowich 1999). Recent trend indicators 

for most populations are negative. The majority of populations for which data are available have 

a long-term population growth trend of less than one; indicating the population is not replacing 

itself and is in decline (Bennett 2005). Only the late-fall run population in Lewis River has an 

abundance and population trend that may be considered viable. The Sandy River is the only 

stream system supporting measurable natural production of spring-run Chinook salmon; 
32

however, the population is at risk from low abundance and negative to low population growth 

rates (productivity) (McElhany et al. 2007). 

4.5.3 Status

NMFS listed Lower Columbia River Chinook salmon as threatened on March 24, 1999 (64 FR 

14308) and reaffirmed their threatened status on June 28, 2005 (70 FR 37160). This ESU was 

listed due to the combined effect of dams that reduce access to spawning habitat, logging, 

agricultural activities, urbanization, threats to genetic diversity from hatchery salmon, and 

overexploitation. Though the basin-wide spatial structure has remained generally intact, the loss 

of about 35 percent of historical habitat has affected distribution within several Columbia River 

subbasins. The ESU is at risk from generally low abundances in all but one population, 

combined with most populations having a negative or stagnant long-term population growth.

Though fish from conservation hatcheries do help to sustain several LCR Chinook salmon runs 

in the short-term, hatchery production is unlikely to result in sustainable wild populations in the 

long-term. Further, the genetic diversity of all populations (except the late fall-run) has been 

eroded by large hatchery influences. Having only one population that may be viable puts the 

ESU at considerable risk from environmental stochasticity and random catastrophic events. The 

near-loss of the spring-run life history type limits the ESU’s ability to maintain its fitness in the 

face of environmental change. Based on these factors, this ESU would likely have a moderate 

(late fall-run salmon in Lewis River) to low (all other populations) resilience to additional 

perturbations.

4.5.4 Critical Habitat

NMFS designated critical habitat for LCR Chinook salmon on September 2, 2005 (70 FR 

52630). It includes all Columbia River estuarine areas and river reaches proceeding upstream to 

the confluence with the Hood Rivers as well as specific stream reaches in a number of tributary 

subbasins. PCEs include freshwater spawning sites, freshwater rearing sites, freshwater 

migration corridors, nearshore marine habitat and estuarine areas. The physical or biological 

features that characterize these sites include water quality and quantity, natural cover, forage, 

adequate passage conditions, and floodplain connectivity. Timber harvest, agriculture, and 

urbanization have degraded spawning and rearing PCEs by reducing floodplain connectivity and 

water quality, and by removing natural cover in several rivers. Hydropower development 

projects have reduced timing and magnitude of water flows, thereby altering the water quantity 

needed to form and maintain physical habitat conditions and support juvenile growth and 

mobility. Adult and juvenile migration PCEs are affected by several dams along the migration 

route.

4.6 Chinook Salmon (Upper Columbia River Spring-run ESU)

The Upper Columbia River spring-run Chinook salmon ESU includes all naturally spawned 

populations of Chinook salmon in all river reaches accessible to Chinook salmon in Columbia 

River tributaries upstream of Rock Island Dam and downstream of Chief Joseph Dam in 

Washington, excluding the Okanogan River. Six artificial propagation programs are part of this 

ESU. We used information available in status reviews (Good et al. 2005, Ford 2011, NMFS 

2011m), listing documents (63 FR 11482; 64 FR 14308; 70 FR 37160), the recovery plan (Upper 

Columbia Salmon Recovery Board 2007), and previously issued biological opinions (NMFS 

2012b) to summarize the status of the species.
33

4.6.1 Life History

Upper Columbia River spring-run salmon are a stream-type salmon. Salmon in this ESU return 

to the upper Columbia tributaries from April through July, with the run peaking in mid-May.

Spawning occurs in the late summer, peaking in mid- to late August. Juvenile spring-run 

Chinook salmon spend a year in fresh water before emigrating to salt water in the spring of their 

second year. Most returning adults are four- and five-year-old fish that have spent two and three 

years at sea, respectively.

4.6.2 Population Dynamics

The ESU historically consisted of four populations; of these, one is now extinct. Spawning 

escapements have declined within all extant populations (in Wenatchee, Entiat, and Methow 

rivers) since 1958. In the most recent five-year geometric mean (1997 to 2001), spawning 

escapement for naturally produced fish was 273 for the Wenatchee population, 65 for the Entiat 

population, and 282 for the Methow population, only eight to 15 percent of the minimum 

abundance thresholds, though escapement did increase substantially in 2000 and 2001 in all three 

river systems. Based on 1980 to 2004 returns, the average annual growth rate for this ESU is 

estimated at 0.93 (meaning the population is not replacing itself) (Fisher and Hinrichsen 2006).

Assuming that population growth rates were to continue at 1980 to 2004 levels, Upper Columbia 

River spring-run Chinook salmon populations are projected to have very high probabilities of 

decline within 50 years.

4.6.3 Status

NMFS listed Upper Columbia River Spring-run Chinook salmon as endangered on March 24, 

1999 (64 FR 14308), and reaffirmed their endangered status on June 28, 2005 (70 FR 37160).

The ESU was listed due to the combined effects of dams that prevent them from reaching 

spawning habitat; habitat degradation from irrigation diversions, hydroelectric development, 

livestock grazing, and urbanization; and reduced genetic diversity from artificial propagation 

efforts. The Interior Columbia Basin Technical Review Team characterizes the spatial structure 

risk to Upper Columbia River Spring-run Chinook populations as “low” or “moderate” and the 

diversity risk as “high” (Interior Columbia Technical Review Team 2008a, b, c). The high risk is 

a result of reduced genetic diversity from homogenization of populations that occurred under the 

Grand Coulee Fish Maintenance Project in 1939 to 1943. Abundance data showed an increase in 

spawner returns in 2000 and 2001, though this increase was not sustained in subsequent years.

Population viability analyses for this species (using the Dennis Model) suggest that these 

Chinook salmon face a significant risk of extinction: a 75 to 100 percent probability of extinction 

within 100 years (given return rates for 1980 to present). Based on these factors, this ESU would 

likely have a very low resilience to additional perturbations.

4.6.4 Critical Habitat

NMFS designated critical habitat for Upper Columbia River spring-run Chinook salmon on 

September 2, 2005 (70 FR 52630). The designation includes all Columbia River estuaries and

river reaches upstream to Chief Joseph Dam and several tributary subbasins. PCEs include 

freshwater spawning sites, freshwater rearing sites, freshwater migration corridors, nearshore 

marine habitat and estuarine areas. The physical or biological features that characterize these 

sites include water quality and quantity, natural cover, forage, adequate passage conditions, and 

floodplain connectivity. Spawning and rearing PCEs are somewhat degraded in tributary systems 

by urbanization, grazing, irrigation, and diversion. These activities have resulted in excess 
34

erosion of fine sediment and silt that smother spawning gravel and reduction in flow necessary 

for successful incubation, formation of physical rearing conditions, and juvenile mobility. 

Moreover siltation further affects critical habitat by reducing water quality through contaminated 

agricultural runoff; and removing natural cover. Adult and juvenile migration PCEs are heavily 

degraded by Columbia River Federal dam projects and a number of mid-Columbia River Public 

Utility District dam projects also obstruct the migration corridor.

4.7 Chinook Salmon (Puget Sound ESU)

The Puget Sound Chinook salmon ESU includes all naturally spawned populations of Chinook 

salmon from rivers and streams flowing into Puget Sound from the North Fork Nooksack River 

to the Elwha River on the Olympic Peninsula in Washington. Thirty-six hatchery populations 

were included as part of the ESU and five were considered essential for recovery and listed 

(spring-run salmon from Kendall Creek, North Fork Stillaguamish River, White River, and 

Dungeness River, and fall-run salmon from the Elwha River). On June 26, 2013, NMFS 

proposed to change the number of artificial propagation considered to be part of the ESU to 27 

(78 FR 38270). We used information available in the status review (Good et al. 2005), 

“Independent populations of Chinook salmon in Puget Sound” (Ruckelshaus et al. 2006), listing 

documents (63 FR 11482; 64 FR 14308; 70 FR 37160), and previously issued biological 

opinions (NMFS 2012b) to summarize the status of the species.

4.7.1 Life History

Chinook salmon in this area generally have an “ocean-type” life history. Puget Sound 

populations include both early-returning (August) and late-returning (mid-September to October) 

Chinook salmon spawners (Healey 1991). However, within these generalized life histories, 

significant variation occurs in residence time in fresh water and estuarine environments. For 

example, Hayman et al. (1996) described three juvenile Chinook salmon life histories with 

varying residency times in the Skagit River system in northern Puget Sound. Puget Sound 

Chinook salmon generally return to freshwater habitats as three- to four-year-olds. 

4.7.2 Population Dynamics

This ESU has lost 16 spawning aggregations (nine from the early fall-run type) that were either 

independent historical populations or major components of the remaining 22 existing 

independent historical populations identified. The disproportionate loss of early-run life history 

diversity represents a significant loss of the evolutionary legacy of the historical ESU. Estimates 

of the historic abundance range from 1,700 to 51,000 potential Puget Sound Chinook salmon 

spawners per population. During the period from 1996 to 2001, the geometric mean of natural 

spawners in populations of Puget Sound Chinook salmon ranged from 222 to just over 9,489 

fish. Long-term trends in abundance and median population growth rates for naturally spawning 

populations indicate that approximately half of the populations are declining and the other half 

are increasing in abundance over the length of available time series. However, the median overall 

long-term trend in abundance indicates that most of these populations are barely replacing 

themselves. Eight of 22 populations are declining over the short-term, compared to 11 or 12 

populations that have long-term declines. Populations with the greatest long-term population 

growth rates are the North Fork Nooksack and White rivers.
35

4.7.3 Status

NMFS listed Puget Sound Chinook salmon as threatened in 1999 (64 FR 14308) and reaffirmed 

its status as threatened on June 28, 2005 (70 FR 37160). The ESU was listed due to habitat loss 

and degradation from the combined effects of damming, forest practices, agricultural practices, 

and urbanization; reduced genetic diversity from artificial propagation efforts; and overharvest.

The spatial structure of the ESU is compromised by extinct and weak populations being 

disproportionably distributed to the mid- to southern Puget Sound and the Strait of Juan de Fuca.

A large portion (at least 11) of the extant runs is sustained, in part, through artificial propagation. 

Of the populations with greater than 1,000 natural spawners, only two have a low fraction of 

hatchery fish. This places the ESU at risk from random catastrophic events, chronic stressors, 

and long-term environmental change. Life history diversity has been significantly reduced by the 

disproportionate loss of the early fall-run life history. Based on these factors, this ESU would 

likely have a low resilience to additional perturbations.

4.7.4 Critical Habitat

NMFS designated critical habitat for Puget Sound Chinook salmon on September 2, 2005 (70 FR 

52630). Specific geographic area include portions of the Nooksack River, Skagit River, Sauk 

River, Stillaguamish River, Skykomish River, Snoqualmie River, Lake Washington, Green 

River, Puyallup River, White River, Nisqually River, Hamma Hamma River and other Hood 

Canal watersheds, the Dungeness/Elwha Watersheds, and nearshore marine areas of the Strait of 

Georgia, Puget Sound, Hood Canal and the Strait of Juan de Fuca. PCEs include freshwater 

spawning sites, freshwater rearing sites, freshwater migration corridors, nearshore marine 

habitat, and estuarine areas. The physical or biological features that characterize these sites 

include water quality and quantity, natural cover, forage, adequate passage conditions, and 

floodplain connectivity. Forestry practices have heavily impacted migration, spawning, and 

rearing PCEs in the upper watersheds of most rivers systems within critical habitat designated for 

the Puget Sound Chinook salmon. Degraded PCEs include reduced conditions of substrate 

supporting spawning, incubation and larval development caused by siltation of gravel; and 

degraded rearing habitat by removal of cover and reduction in channel complexity. Urbanization 

and agriculture in the lower alluvial valleys of mid- to southern Puget Sound and the Strait of 

Juan de Fuca have reduced channel function and connectivity, reduced available floodplain 

habitat, and affected water quality. Thus, these areas have degraded spawning, rearing, and 

migration PCEs. Hydroelectric development and flood control also obstruct Puget Sound 

Chinook salmon migration in several basins. The most functional PCEs are found in northwest 

Puget Sound: the Skagit River basin, parts of the Stillaguamish River basin, and the Snohomish

River basin where federal land overlap with critical habitat designated for the Puget Sound 

Chinook salmon. However, estuary PCEs are degraded in these areas by reduction in the water 

quality from contaminants, altered salinity conditions, lack of natural cover, and modification 

and lack of access to tidal marshes and their channels.

4.8 Chinook Salmon (Sacramento River Winter-run ESU)

The Sacramento River winter-run Chinook salmon ESU includes all naturally spawned 

populations of winter-run Chinook salmon entering and using the Sacramento River system in 

the Central Valley, California. The ESU now consists of a single spawning population. Two 

hatchery populations were included as part of the ESU, however on June 26, 2013, NMFS 

proposed that one artificial propagation program be removed from the ESU, as the program has 

been terminated (78 FR 38270). We used information available in status reviews (Good et al. 
36

2005, NMFS 2011h), listing documents (54 FR 32085, 55 FR 10260, 69 FR 33102, 70 FR 

37160), the draft recovery plan (NMFS 2009c), and previously issued biological opinions 

(NMFS 2012b) to summarize the status of the species.

4.8.1 Life History

The winter-run Chinook salmon have characteristics of both stream- and ocean-type life 

histories. Adults enter fresh water in winter or early spring but delay spawning until late spring 

(May to June). Fry emerge from the gravel in late June to early July and continue through 

October (Fisher 1994). Young winter-run Chinook salmon start migrating to sea as early as midJuly with a peak movement over the Red Bluff Diversion Dam in September. Some offspring 

move downstream as fry while other rear in the upper Sacramento River and move down as 

smolt. Normally fry have passed the Red Bluff Diversion Dam by October while smolts may 

pass over the dam until March. Juvenile winter-runs occur in the Delta primarily from November 

through early May. Winter-run juveniles remain in the Delta until they are from five to 10 

months of age, and then begin emigrating to the ocean as early as November and continue 

through May (Fisher 1994). Returning adults can be between two to six years of age, but the 

majority return as three-year olds.

4.8.2 Population Dynamics

Construction of Shasta Dams in the 1940s eliminated access to historic spawning habitat for 

winter-run Chinook salmon. As a result the ESU has been reduced to a single spawning 

population which is entirely dependent upon the provision of suitably cool water from Shasta 

Reservoir during periods of spawning, incubation and rearing. Winter-runs may have been as 

large as 200,000 fish based upon commercial fishery records from the 1870s (Fisher 1994).

During the first three years of operation of the counting facility at the Red Bluff Diversion Dam 

(1967 to 1969), an average of 86,500 winter-run Chinook salmon were counted (California 

Department of Fish and Game 2009). Critically low levels were reached during the drought of 

1987 to 1992 with an absolute bottom of 191 fish counted. The three-year average run size for 

the period of 1989 to 1991 was 388 fish. The population grew rapidly from the early 1990s to 

mid-2005; mean run size increased from 1,363 adults before 2000 to 8,470 adults between 2000 

and 2006 (USFWS and U.S. Bureau of Reclamation 2007). Abundance has declined in 

subsequent years (4,461 adults estimated for 2007 and a preliminary estimate between 2,600 to 

2,950 adults for 2008), and the 10-year trend in abundance is negative.

4.8.3 Status

The SR winter-run Chinook salmon ESU was first listed as threatened on August 4, 1989 under 

an emergency rule (54 FR 32085). On January 4, 1994, NMFS reclassified the ESU as an 

endangered species due to several factors, including: (1) the continued decline and increased 

variability of run sizes since its listing as a threatened species in 1989; (2) the expectation of 

weak returns in coming years as the result of two small year classes (1991 and 1993); and (3) 

continuing threats to the species (59 FR 440). On June 14, 2004, NMFS proposed to reclassify 

the ESU as threatened (69 FR 33102), but its status as endangered was upheld in the final listing 

determination on June 28, 2005 (70 FR 37160). Good et al. (2005) found that the SR winter-run 

Chinook salmon ESU was in danger of extinction. The major concerns of the BRT were that 

there is only one extant population, and it is spawning outside of its historical range in 

artificially-maintained habitat that is vulnerable to drought and other catastrophes. Additionally, 

the ESU is expected to have lost some genetic diversity through bottleneck effects in the late 
37

1980s and early 1990s and hatchery releases may also have affected population genetics.

Abundance data showed an increase in spawner returns from 1990s to mid-2005, though this 

increase was not sustained in subsequent years. The population growth rate for this ESU is 

negative, indicating the population has been declining and is not self-sustaining. Based on these 

factors, this ESU would likely have a very low resilience to additional perturbations.

4.8.4 Critical Habitat

NMFS designated critical habitat for this species on June 16, 1993 (58 FR 33212). The 

designation includes: the Sacramento River from Keswick Dam, Shasta County (river mile 302) 

to Chipps Island (river mile 0) at the westward margin of the Sacramento-San Joaquin Delta, and 

other specified estuarine waters. PCEs include specific water temperature criteria, minimum 

instream flow criteria, and water quality standards. In addition, biological features vital for the 

ESU include unimpeded adult upstream migration routes, spawning habitat, egg incubation and 

fry emergence areas, rearing areas for juveniles, and unimpeded downstream migration routes for 

juveniles. As there is overlap in designated critical habitat for both the Sacramento River Winterrun Chinook salmon and the spring-run Chinook salmon, the conditions of PCEs for both ESUs 

are similar. Spawning and rearing PCEs are degraded by high water temperature caused by the 

loss of access to historic spawning areas in the upper watersheds where water maintain lower 

temperatures. The rearing PCE is further degraded by floodplain habitat disconnected from the 

mainstems of larger rivers throughout the Sacramento River watershed. The migration PCE is 

also degraded by the lack of natural cover along the migration corridors. Rearing and migration 

PCEs are further affected by pollutants entering the surface waters and riverine sediments as 

contaminated stormwater runoff, aerial drift and deposition, and via point source discharges.

Juvenile migration is obstructed by water diversions along Sacramento River and by two large 

state and federal water-export facilities in the Sacramento-San Joaquin Delta. The current 

condition of PCEs for the Sacramento River Winter-run Chinook salmon indicates that they are 

not currently functioning or are degraded. Their conditions are likely to maintain low population 

abundances across the ESU.

4.9 Chinook Salmon (Snake River Fall-run ESU)

The Snake River (SR) Fall-run Chinook salmon ESU includes all naturally spawned populations 

of fall-run Chinook salmon in the mainstem Snake River below Hells Canyon Dam; and in the 

Tucannon River, Grande Ronde River, Imnaha River, Salmon River, and Clearwater River 

subbasins. Four artificial propagation programs are included in the ESU. We used information 

available in status reviews (Good et al. 2005, Ford 2011, NMFS 2011i), listing documents (57 

FR 14653, 70 FR 37160), and previously issued biological opinions (NMFS 2012b) to 

summarize the status of the species.

4.9.1 Life History

Prior to dam construction, fall Chinook salmon were primarily ocean-type; however, today both 

an ocean-type and reservoir-type occur (Connor et al. 2005). Adult ocean-type salmon in the 

ESU enter the Columbia River in July and August and spawn from October to November.

Juveniles emerge from the gravels in March and April of the following year, moving 

downstream from natal spawning and early rearing areas from June through early autumn.

Reservoir-type juveniles overwinter in pools created by dams before migrating to sea; this 

response is likely due to early development in cooler temperatures which prevents rapid growth.
38

Phenotypic characteristics have shifted in apparent response to environmental changes from 

hydroelectric dams (Connor et al. 2005).

4.9.2 Population Dynamics

The SR Fall-run Chinook salmon ESU consists of one extant population that is confined to a 

small fraction (15 percent) of its historical range. Two populations have been extirpated.

Estimated annual returns for the period 1938 to 1949 were at 72,000 fish. By the 1950s, numbers 

had declined to an annual average of 29,000 fish (Bjornn and Horner 1980). Numbers of SR Fallrun Chinook salmon continued to decline during the 1960s and 1970s as approximately 80 

percent of their historic habitat were eliminated or severely degraded by the construction of the 

Hells Canyon complex (1958 to 1967) and the lower Snake River dams (1961 to 1975). The 

abundance of natural-origin spawners of the ESU for 2001 (2,652 adults) exceeded 1,000 fish for 

the first time since counts began at the Lower Granite Dam in 1975. The total spawning 

escapement into natural areas above Lower Granite Dam has remained relatively high since the 

rapid increase in the late 1990s. The current 5-year geometric mean total escapement is above 

10,000, substantially greater than the 1997−2001 geometric mean reported in the previous BRT 

review. A relatively high proportion of the estimated spawners are of hatchery origin (78% for 

the most recent 5-year cycle). However natural-origin returns have also increased substantially 

over the geometric mean estimates for the 2005 BRT review and the cycle just prior to the 1997 

listing decision. 

4.9.3 Status

NMFS listed Snake River fall-run Chinook salmon as endangered in 1992 (57 FR 14653), but 

reclassified their status as threatened on June 28, 2005 (70 FR 37160). The ESU was listed due 

to habitat loss and degradation from the combined effects of damming; forest, agricultural, 

mining and wastewater management practices; and overharvest. Both long- and short-term trends 

in natural returns are positive. Productivity is likely sustained largely by a system of small 

artificial rearing facilities in the lower Snake River Basin. Depending upon the assumptions 

made regarding the reproductive contribution of hatchery fish, long- and short-term trends in 

productivity are at or above replacement. Low abundances in the 1990s combined with a large 

proportion of hatchery derived spawners likely have reduced genetic diversity from historical

levels; however, the salmon in this ESU remain genetically distinct from similar fish in other 

basins. The population remains at a moderate risk of becoming extinct (probability between five 

and 25 percent in 100 years). Based on these factors, this ESU would likely have a moderate 

resilience to additional perturbations.

4.9.4 Critical Habitat

NMFS designated critical habitat for Snake River fall-run Chinook salmon on December 28, 

1993 (58 FR 68543). This critical habitat encompasses the waters, waterway bottoms, and 

adjacent riparian zones of specified lakes and river reaches in the Columbia River that are or 

were accessible to listed Snake River salmon (except reaches above impassable natural falls, and 

Dworshak and Hells Canyon dams. Specific PCEs were not designated in the critical habitat final 

rule; instead four “essential habitat” categories were described: 1) spawning and juvenile rearing 

areas, 2) juvenile migration corridors, 3) areas for growth and development to adulthood, and 4) 

adult migration corridors. The “essential features” that characterize these sites include 

substrate/spawning gravel; water quality, quantity, temperature, velocity; cover/shelter; food; 

riparian vegetation; space; and safe passage conditions. Hydropower operations and flow 
39

management practices have impacted spawning and rearing habitat and migration corridors 

throughout the ESU’s range. The major degraded essential habitat and features include: safe 

passage for juvenile migration; rearing habitat water quality; and spawning areas with gravel, 

water quality, cover/shelter, riparian vegetation, and space to support egg incubation and larval 

growth and development. Water quality impairments in the designated critical habitat are 

common within the range of this ESU. Pollutants such as petroleum products, pesticides, 

fertilizers, and sediment in the form of turbidity enter the surface waters and riverine sediments 

from the headwaters of the Snake, Salmon, and Clearwater Rivers to the Columbia River estuary; 

traveling along with contaminated stormwater runoff, aerial drift and deposition, and via point 

source discharges.

4.10 Chinook Salmon (Snake River Spring/Summer-run ESU)

The SR Spring/Summer-run Chinook ESU includes all naturally spawned populations of 

spring/summer-run Chinook salmon in the mainstem Snake River and the Tucannon River, 

Grande Ronde River, Imnaha River, and Salmon River subbasins. Fifteen artificial propagation 

programs are included in the ESU, however on June 26, 2013, NMFS proposed the number of 

artificial propagation programs included in the ESU be changed to 11 (78 FR 38270). We used 

information available in status reviews (Matthews and Waples 1991, Good et al. 2005, NMFS 

2011i), Interior Columbia Basin Technical Recovery Team reports (Interior Columbia Technical 

Review Team 2003), listing documents (57 FR 14653, 70 FR 37160), and previously issued 

biological opinions (NMFS 2012b) to summarize the status of the species.

4.10.1 Life History

Snake River spring/summer-run Chinook salmon have a stream-type life history. Spring-run 

salmon of this ESU pass Bonneville Dam beginning in early March to mid-June and spawn from 

mid- to late August. Summer-run salmon return to the Columbia River from June through 

August and spawn approximately one month later than spring-run salmon. Summer-run salmon 

tend to spawn lower in the Snake River drainages than spring-run fish; however, an overlap of 

summer-run and spring-run spawning areas does occur. In both run types eggs incubate over the 

winter, and hatch in late winter and early spring of the following year. Juvenile fish mature in 

fresh water for one year before they migrate to the ocean in the spring of their second year of 

life. Depending on the tributary and the specific habitat conditions, juveniles may migrate 

extensively from natal reaches into alternative summer-rearing or overwintering areas. Salmon of 

this ESU return from the ocean to spawn primarily as four and five year-old fish, after two to 

three years in the ocean.

4.10.2 Population Dynamics

The Interior Columbia Basin Technical Recovery Team has identified 32 populations in five 

major population groups (Upper Salmon River, South Fork Salmon River, Middle Fork Salmon 

River, Grande Ronde/Imnaha, Lower Snake Mainstem Tributaries) for this species. Historic 

populations above Hells Canyon Dam are considered extinct. The status review reports that total 

annual salmon production of this ESU may have exceeded 1.5 million adults in the late 1800s.

Total (natural plus hatchery origin) returns fell to roughly 100,000 spawners by the late 1960s 

(Fulton 1968). Abundance of summer run Chinook salmon have increased since low returns in 

the mid-1990s (lowest run size was 692 fish in 1995). The 1997 to 2008 geometric mean total 

return for the summer run component at Lower Granite Dam was slightly more than 8,700 fish, 

compared to the geometric mean of 3,076 fish for the years 1987 to 1996 (Data from the 
40

Columbia Basin Fisheries Agencies and Tribes http://www.fpc.org/). However, over 80 percent 

of the 2001 return and over 60 percent of the 2002 return originated from hatcheries. 

4.10.3 Status

NMFS listed Snake River spring/summer-run Chinook salmon as threatened on April 22, 1992 

(57 FR 14653), and reaffirmed their status on June 28, 2005 (70 FR 37160). The ESU was listed 

due to habitat loss and degradation from the combined effects of damming; forest, agricultural, 

mining, and wastewater management practices; overharvest; and artificial propagation. There is

no obvious long-term positive trend, though recent trends are approaching one, indicating the 

population is nearly replacing itself. Risks to individual populations within the ESU may be 

greater than the extinction risk for the entire ESU due to low levels of annual abundance of 

individual populations. Multiple spawning sites are accessible and natural spawning and rearing 

are well distributed within the ESU. However, many spawning aggregates have also been 

extirpated, which has increased the spatial separation of some populations. The South Fork and 

Middle Fork Salmon Rivers currently support the bulk of natural production in the drainage.

There is no evidence of wide-scale genetic introgression by hatchery populations. The high 

variability in life history traits indicates sufficient genetic variability within the ESU to maintain 

distinct subpopulations adapted to local environments. Based on these factors, this ESU would 

likely have a moderate resilience to additional perturbations.

4.10.4 Critical Habitat

NMFS designated critical habitat for Snake River spring/summer-run Chinook salmon on 

December 28, 1993 (58 FR 68543). This critical habitat encompasses the waters, waterway 

bottoms, and adjacent riparian zones of specified lakes and river reaches in the Columbia River 

that are or were accessible to listed Snake River salmon (except reaches above impassable 

natural falls, and Dworshak and Hells Canyon dams). Specific PCEs were not designated in the 

critical habitat final rule; instead four “essential habitat” categories were described: 1) spawning 

and juvenile rearing areas, 2) juvenile migration corridors, 3) areas for growth and development 

to adulthood, and 4) adult migration corridors. The “essential features” that characterize these 

sites include substrate/spawning gravel; water quality, quantity, temperature, velocity; 

cover/shelter; food; riparian vegetation; space; and safe passage conditions. Hydropower 

operations and flow management practices have impacted spawning and rearing habitat and 

migration corridors in some regions. The Interior Columbia Basin Technical Review Team 

reports that the Panther Creek population was extirpated because of legacy and modern miningrelated pollutants that created a chemical barrier to fish passage. Water quality impairments are 

common in the range of the critical habitat designated for this ESU. Pollutants such as petroleum 

products, pesticides, fertilizers, and sediment in the form of turbidity enter the surface waters and 

riverine bottom substrate from the headwaters of the Snake, Salmon, and Clearwater Rivers to 

the Columbia River estuary as contaminated stormwater runoff, aerial drift and deposition, and 

via point source discharges.

4.11 Chinook Salmon (Upper Willamette River ESU)

The Upper Willamette River Chinook salmon ESU includes all naturally spawned populations of 

spring-run Chinook salmon in the Clackamas River and in the Willamette River, and its 

tributaries, above Willamette Falls, Oregon. Seven artificial propagation programs are included 

in the ESU, however on June 26, 2013, NMFS proposed to change the number of artificial 

propagation programs included in the ESU to six (78 FR 38270). We used information available 
41

in status reviews (Good et al. 2005, NMFS 2011n), the recovery plan (Oregon Department of 

Fish and Wildlife and NMFS 2011), “Historical population structure of Pacific salmonids in the 

Willamette River and Lower Columbia River Basins” (Myers et al. 2006), listing documents (64 

FR 14308, 70 FR 37160), and previously issued biological opinions (NMFS 2012b) to 

summarize the status of the species.

4.11.1 Life History

Upper Willamette River Chinook salmon are a spring-run, stream-type salmon. Adults appear in 

the lower Willamette River in February, but the majority of the run ascends Willamette Falls in 

April and May, with a peak in mid- to late May. Present-day salmon ascend the Willamette Falls 

via a fish ladder. The migration of spring Chinook salmon over Willamette Falls extends into 

July and August and overlaps with the beginning of the introduced fall-run of Chinook salmon.

The adults hold in deep pools over summer and spawn between August to October, with a peak 

in September. Fry emerge from December to March and juvenile migration varies among three 

distinct emigration “runs”: fry migration in late winter and early spring; sub-yearling (less than 

one year old) migration in fall to early winter; and yearlings (greater than one year old) migrating 

in late winter to spring. Sub-yearlings and yearlings rear in the mainstem Willamette River 

where they also use floodplain wetlands in the lower Willamette River during the winter-spring 

floodplain inundation period. Fall-run Chinook salmon spawn in the Upper Willamette but are 

not considered part of the ESU because they are not native. Salmon of this ESU return from the 

ocean to spawn primarily as four and five year-old fish, after two to three years in the ocean.

4.11.2 Population Dynamics

Historically, this ESU included sizable numbers of spawning salmon in the Santiam River, the 

middle fork of the Willamette River, and the McKenzie River, as well as smaller numbers in the 

Molalla River, Calapooia River, and Albiqua Creek. Most natural spring-run Chinook salmon 

populations of this ESU are likely extirpated or nearly so; the spring-run in the McKenzie River 

is the only known remaining naturally reproducing population in this ESU. The total abundance 

of adult spring-run Chinook salmon (hatchery-origin + natural-origin fish) passing Willamette 

Falls has remained relatively steady over the past 50 years (ranging from approximately 20,000 

to 70,000 fish). However, the current abundance is an order of magnitude below the peak 

abundance levels observed in the 1920s (approximately 300,000 adults). Total number of fish 

increased during the period from 1996 to 2004 when it peaked at more than 96,000 adult springrun Chinook salmon passing Willamette Falls. Since then, the run has steadily decreased with 

only about 14,000 fish counted in 2008, the lowest number since 1960. ESU abundance 

increased again to about 25,000 adult spring-run Chinook salmon in 2009. Runs consist of a 

high, but uncertain, fraction of hatchery-produced fish.

4.11.3 Status

NMFS listed Upper Willamette River Chinook salmon as threatened on March 24, 1999 (64 FR 

14308) and reaffirmed their status on June 28, 2005 (70 FR 37160). The ESU was listed due to 

habitat loss and degradation from the combined effects of damming; agricultural practices; 

urbanization; overharvest; and artificial propagation. The McKenzie River population is the only 

remaining self-sustaining naturally reproducing independent population. The other natural-origin 

populations in this ESU have very low current abundances, and long- and short-term population 

trends are negative. The spatial distribution of the species has been reduced by the loss of 30 to 

40 percent of the total historic habitat. This loss has restricted spawning to a few areas below 
42

dams. Access of fall-run Chinook salmon to the upper Willamette River and the mixing of 

hatchery stocks within the ESU have threatened the genetic integrity and diversity of the species. 

Much of the genetic diversity that existed between populations has been homogenized. Based on 

these factors, this ESU would likely have a low resilience to additional perturbations.

4.11.4 Critical Habitat

NMFS designated critical habitat for this species on September 2, 2005 (70 FR 52630).

Designated critical habitat includes all Columbia River estuarine areas and river reaches 

proceeding upstream to the confluence with the Willamette River as well as specific stream 

reaches in a number of subbasins. PCEs include freshwater spawning and rearing sites, 

freshwater migration corridors. The physical or biological features that characterize these sites 

include water quality and quantity, natural cover, forage, adequate passage conditions, and 

floodplain connectivity. The migration PCE is degraded by dams altering migration timing and 

water management altering the water quantity necessary for mobility and survival. Migration, 

rearing, and estuary PCEs are also degraded by loss of riparian vegetation and in-stream cover.

Pollutants such as petroleum products, fertilizers, pesticides, and fine sediment enter the stream 

through runoff, point source discharge, drift during application, and non-point discharge where 

agricultural and urban development occurs. Degraded water quality in the lower Willamette 

River where important floodplain rearing habitat is present affects the ability of this habitat to 

sustain its role to conserve the species. The current condition of PCEs identified in this critical 

habitat indicates that migration and rearing PCEs are not currently functioning or are degraded 

and impact their ability to serve their intended role for species conservation. 

4.12 Chum Salmon (General Overview)

We discuss the distribution, life history, population dynamics, status, and critical habitats of the 

two species (here we use the word “species” to apply to distinct population segments, DPSs, and 

evolutionary significant units, ESUs) separately; however, because listed chum salmon species 

are virtually indistinguishable in the wild and comprise the same biological species, we begin 

this section describing characteristics common across ESUs. We used information available in 

status reviews (Johnson et al. 1997, Good et al. 2005), various listing documents, and biological 

opinions (NMFS 2012b) to summarize the status of the species.

Because their range extends farther along the shores of the Arctic Ocean than other Pacific 

salmonid, chum salmon have the widest natural geographic and spawning distribution of the 

Pacific salmonids. Chum salmon have been documented to spawn from Korea and the Japanese 

island of Honshu, east around the rim of the North Pacific Ocean to Monterey Bay, California.

Historically, chum salmon were distributed throughout the coastal regions of western Canada 

and the U.S. Presently, major spawning populations occur as far south as Tillamook Bay on the 

northern Oregon coast.

4.12.1 Life History

In general, North American chum salmon migrate north along the coast in a narrow coastal band 

that broadens in southeastern Alaska. Chum salmon usually spawn in the lower reaches of rivers 

during summer and fall. Redds are dug in the mainstem or in side channels of rivers from just 

above tidal influence to nearly 100 km from the sea. The time to hatching and emergence from 

the gravel redds are influenced by DO, gravel size, salinity, nutritional conditions, behavior of 

alevins in the gravel, and incubation temperature (Bakkala 1970, Schroder 1977, Salo 1991).
43

Chum salmon juveniles use shallow, low flow habitats for rearing that include inundated 

mudflats, tidal wetlands and their channels, and sloughs. The duration of estuarine residence for 

chum salmon juveniles are known for only a few estuaries. Observed residence time ranged from 

four to 32 days, with about 24 days as the most common.

Immature salmon distribute themselves widely over the North Pacific Ocean and maturing adults 

return to the home streams at various ages, usually at two to five years of age, and in some cases 

up to seven years (Bigler 1985). This ocean-type migratory behavior contrasts with the streamtype behavior of some other species in the genus Oncorhynchus (e.g., steelhead, coho, and most 

types of Chinook and sockeye salmon). Stream-type salmonids usually migrate to sea at a larger 

size, after months or years of freshwater rearing. Thus, survival and growth for juvenile chum 

salmon depend less on freshwater conditions than on favorable estuarine conditions. Another 

behavioral difference between chum salmon and other salmonid species is that chum salmon 

form schools. Presumably, this behavior reduces predation (Pitcher 1986) especially if fish 

movements are synchronized to swamp predators (Miller and Brannon 1982). All chum salmon 

are semelparous (i.e., they die after spawning) and exhibit obligatory anadromy (i.e., there are no 

recorded landlocked or naturalized freshwater populations; they must spend portions of their 

lives in both salt and freshwater habitats).

Chum salmon feed on a variety of prey organisms depending upon life stage and size. In 

freshwater Chum salmon feed primarily on small invertebrates; in saltwater, their diet consists of 

copepods, tunicates, mollusks, and fish.

4.12.2 Population Dynamics

The population dynamics of each chum salmon ESU will be discussed separately, below.

4.12.3 Status

On June 28, 2005, as part of the final listing determinations for 16 ESUs of West Coast salmon, 

NMFS amended and streamlined the 4(d) protective regulations for threatened salmon and 

steelhead (70 FR 37160) as described in the Protective Regulations for Threatened Salmonid 

Species section of this document. Under this change, the section 4(d) protections apply to natural 

and hatchery fish with an intact adipose fin, but not to listed hatchery fish that have had their 

adipose fin removed prior to release into the wild.

4.12.4 Critical Habitat

Areas designated as critical habitat are important for the species’ overall conservation by 

protecting quality growth, reproduction, and feeding. At the time of designation, primary 

constituent elements (PCEs) are identified and include sites necessary to support one or more 

chum salmon life stage(s). For both ESUs discussed below, PCEs include freshwater spawning, 

rearing, and migration areas; estuarine and nearshore marine areas free of obstructions; and 

offshore marine areas with good water quality. The physical or biological features that 

characterize these sites include water quality and quantity, natural cover, forage, adequate 

passage conditions, and floodplain connectivity. The critical habitat designation identified for 

each ESU contains additional details on the areas included as part of the designation, and the 

areas that were excluded from designation.

4.13 Chum Salmon (Columbia River ESU)

The Columbia River chum salmon ESU includes all naturally spawned populations of chum 

salmon in the Columbia River and its tributaries in Washington and Oregon. Three artificial 
44

propagation programs are part of the ESU. We used information available in status reviews 

(Good et al. 2005, Ford 2011, NMFS 2011d), listing documents (63 FR 11774, 64 FR 14508, 70 

FR 37160), recovery plans (Lower Columbia Fish Recovery Board 2010, Oregon Department of 

Fish and Wildlife 2010, NMFS 2013c), “Historical population structure of Pacific salmonids in 

the Willamette River and Lower Columbia River Basins” (Myers et al. 2006), and previously 

issued biological opinions (NMFS 2012b) to summarize the status of the species.

4.13.1 Life History

Salmon of this ESU return to the Columbia River from mid-October to November and spawning 

occurs from early November to late December. Adults generally spawn in the lower reaches of 

rivers, digging redds along the edges of the mainstem and in tributaries or side channels. Some 

spawning sites are located in areas where geothermally-warmed groundwater or mainstem flow 

upwells through the gravel. Chum salmon fry emigrate to estuaries from March through May 

shortly after emergence. Like ocean-type Chinook salmon, juvenile chum salmon rear in 

estuaries for an extended period (weeks to months) before beginning their long distance oceanic 

migration, primarily from February to June. The period of estuarine residence is a critical life 

history phase and plays a major role in determining the size of the subsequent adult run back to 

fresh water. Chum salmon remain in the North Pacific and Bering Sea for two to six years, with 

most adults returning to the Columbia River as four-year-olds.

4.13.2 Population Dynamics

Historically, the ESU was composed of 17 populations in Oregon and Washington between the 

mouth of the Columbia River and the Cascade crest. Of these populations, 15 of them (six in 

Oregon and nine in Washington) are so depleted that either their baseline probability of 

persistence is very low or they are extirpated or nearly so. An extensive 2000 survey in Oregon 

streams supports that chum salmon almost had been extirpated from the Oregon portion of this 

ESU. Over the last century, Columbia River chum salmon returns have collapsed from hundreds 

of thousands to just a few thousand per year. Only two populations (Grays River and the Lower 

Gorge) with any significant spawning remain today, both in Washington. The estimated size of 

the Lower Gorge population is at 400 to 500 individuals, down from a historical level of greater 

than 8,900. A significant increase in spawner abundance occurred in 2001 and 2002 to around 

10,000 adults. However, spawner surveys indicate that the abundance again decreased to low 

levels during 2003 through 2008 though the spawner surveys may underestimate abundance 

since the proportion of tributary and mainstem spawning differ between years and the surveys do 

not include spawners in the Columbia River mainstem. In the 1980s, estimates of the Grays 

River population ranged from 331 to 812 individuals. However, the population increased in 2002 

to as many as 10,000 individuals. Based on data for number of spawners per river mile, this 

increase continued through 2003 and 2004. However, fish abundance fell again to less than 5,000 

fish during the years 2005 through 2008.

4.13.3 Status

NMFS listed Columbia River chum salmon as threatened on March 25, 1999 (64 FR 14508) and 

reaffirmed their status on June 28, 2005 (71 FR 37160). The ESU was listed due to habitat loss 

and degradation from the combined effects of water withdrawal, conveyance, storage, and flood 

control; logging and agriculture; mining; urbanization; and overharvest. Much of the historical 

spatial structure has been lost on both the population and the ESU levels by extirpation (or nearextirpation) of many local stocks and the widespread loss of estuary habitats. Estimates of 
45

abundance and trends are available only for the Grays River and Lower Gorge populations, both 

of which have long- and short-term productivity trends at or below replacement. Limited 

distribution also increases risk to the ESU from local disturbances. Although hatchery production 

of chum salmon has been limited and hatchery effects on diversity are thought to have been 

relatively small, diversity has been greatly reduced at the ESU level because of presumed 

extirpations and the low abundance in the remaining populations (fewer than 100 spawners per 

year for most populations). Based on these factors, this ESU would likely have a low resilience 

to additional perturbations.

4.13.4 Critical Habitat

NMFS originally designated critical habitat for Columbia River chum salmon on February 16, 

2000 (65 FR 7764); critical habitat was re-designated on September 2, 2005 (70 FR 52630).

Designated critical habitat includes areas in the following subbasins: Middle Columbia/Hood, 

Lower Columbia/Sandy, Lewis, Lower Columbia/Clatskanie, Lower Cowlitz, and Lower 

Columbia subbasin and river corridor. PCEs for this ESU and physical or biological features that 

characterize them are described in Section 3.0.4. Limited information exists on the quality of 

essential habitat characteristics for this ESU; however, the migration PCE has been significantly 

impacted by dams obstructing adult migration and access to historic spawning locations and 

water quality and cover for estuary and rearing PCEs have decreased in quality to the extent that 

the PCEs are not likely to maintain their intended function to conserve the species.

4.14 Chum Salmon (Hood Canal Summer-run ESU)

The Hood Canal summer-run chum salmon ESU includes all naturally spawned populations in 

Hood Canal and its tributaries as well as populations in Olympic Peninsula rivers between Hood 

Canal and Dungeness Bay, Washington. Eight artificial propagation programs are included in the 

ESU, however on June 26, 2013, NMFS proposed to change the number of artificial propagation 

programs included in the ESU to four (78 FR 38270). We used information available in status 

reviews (Good et al. 2005, NMFS 2011g), listing documents (63 FR 11774, 64 FR 14508, 70 FR 

37160), and previously issued biological opinions (NMFS 2012b) to summarize the status of the 

species.

4.14.1 Life History

Salmon of this ESU enter natal rivers from late August until October (Washington Department of 

Fisheries et al. 1993) and spawning occurs from mid-September through mid-October. Adults 

generally spawn in low gradient, lower mainstem reaches of natal streams, typically in center 

channel areas due to the low flows encountered in the late summer and early fall and fry emerge 

between January and May. After hatching, fry move rapidly downstream to subestuarine habitats 

where they rear for an average of 23 days before entering the ocean. Summer-run chum salmon 

seem to have a longer incubation time than fall-run chum salmon in the same streams.

Consequently, offspring of summer-run chum salmon have lower average weight and less lipid 

content than offspring of fall-run chum salmon. Thus, prey availability during their early life 

history is important for fry survival. Most adult salmon of this ESU return from the ocean to 

spawn as three- and four-year old fish.

4.14.2 Population Dynamics

Historically, this ESU consisted of two independent populations (the Strait of Juan de Fuca and 

Hood Canal populations) that, together, contained an estimated 16 stocks (Sands et al. 2007). Of 
46

the 16 historic stocks, seven are considered extirpated, primarily from the eastern side of Hood 

Canal. Of the extant Strait of Juan de Fuca stocks, three spawn in rivers and streams entering the 

eastern Strait of Juan de Fuca and Admiralty Inlet. The Hood Canal population consists of six 

extant stocks within the Hood Canal watershed. HC Summer-run chum salmon are part of an 

extensive rebuilding program developed and implemented in 1992 by state and tribal comanagers. The largest supplemental program occurs at the Big Quilcene River fish hatchery.

Reintroduction programs occur in Big Beef (Hood Canal population) and Chimacum (Strait of 

Juan de Fuca population) creeks. Adult returns for some of the HC Summer-run chum salmon 

stocks showed modest improvements in 2000, with upward trends continuing in 2001 and 2002.

The recent five-year mean abundance is variable among stocks, ranging from one fish to nearly 

4,500 fish. Productivity in the last five-year period (2005 to 2009) has been very low, especially 

compared to the relatively high productivity observed during the five to 10 previous years (1994 

to 2004).

4.14.3 Status

NMFS listed Hood Canal summer-run chum salmon as threatened on March 25, 1999 (64 FR 

14508), and reaffirmed their status on June 28, 2005 (70 FR 37160). The ESU was listed due to 

habitat loss and degradation from the combined effects of water withdrawal, conveyance, 

storage, and flood control; logging and agriculture; mining; urbanization; overharvest; and 

artificial propagation. Much of the historical spatial structure and connectivity has been lost on 

both the population and the ESU levels by extirpation of many local stocks and the widespread 

loss of estuary and lower floodplain habitats. Long-term trends in productivity are above 

replacement only for the Quilcene and Union River stocks; however, most stocks remain 

depressed. The overall trend in spawning abundance is generally stable (meaning adults are 

replacing themselves) for the Hood Canal population (all natural spawners and natural-origin 

only spawners) and for the Strait of Juan de Fuca population (all natural spawners). Only the 

Strait of Juan de Fuca population’s natural-origin only spawners shows a significant positive 

trend. Estimates of the fraction of naturally spawning hatchery fish exceed 60 percent for some 

stocks, which indicates that reintroduction programs are supplementing the numbers of total fish 

spawning naturally in streams. There is also concern that the Quilcene hatchery stock has high 

rates of straying, and may represent a risk to historical population structure and diversity. Based 

on these factors, this ESU would likely have a low resilience to additional perturbations.

4.14.4 Critical Habitat

NMFS designated critical habitat for Hood Canal summer-run chum salmon on September 2, 

2005 (70 FR 52630). Designated critical habitat includes the Skokomish River, Hood Canal 

subbasin, which includes the Hamma Hamma and Dosewallips rivers and others, the Puget 

Sound subbasin, Dungeness/Elwha subbasin, and nearshore marine areas of Hood Canal and the 

Strait of Juan de Fuca. This includes a narrow nearshore zone within several Navy 

security/restricted zones and approximately eight miles of habitat that was unoccupied at the 

time of the designation (including Finch, Anderson and Chimacum creeks), but has been reseeded. PCEs for this ESU and physical or biological features that characterize them are 

described in Section 3.0.4. The spawning PCE is degraded by excessive fine sediment in the 

gravel and the rearing PCE is degraded by loss of access to sloughs in the estuary and nearshore 

areas and excessive predation. Low flow in several rivers also adversely affects most PCEs. In 

estuarine areas, both migration and rearing PCEs of juveniles are impaired by loss of functional 
47

floodplain areas necessary for growth and development of juvenile chum salmon. These 

degraded conditions likely maintain low population abundances across the ESU.

4.15 Coho Salmon (General Overview)

We discuss the distribution, life history, population dynamics, status, and critical habitats of the 

four species (here we use the word “species” to apply to distinct population segments, DPSs, and 

evolutionary significant units, ESUs) separately; however, because listed coho salmon species 

are virtually indistinguishable in the wild and comprise the same biological species, we begin 

this section describing characteristics common across ESUs. We used information available in 

status reviews (Good et al. 2005), various listing documents, and biological opinions (NMFS 

2012b) to summarize the status of the species.

The species was historically distributed throughout the North Pacific Ocean from central 

California to Point Hope, Alaska, through the Aleutian Islands, and from the Anadyr River, 

Russia, south to Hokkaido, Japan.

4.15.1 Life History

Coho salmon exhibit a stream-type life history. Most coho salmon enter rivers between 

September and February. In many systems, coho salmon wait to enter until fall rainstorms have 

provided the river with sufficiently strong flows and depth. Coho salmon spawn from November 

to January, and occasionally into February and March. Some spawning occurs in third-order 

streams, but most spawning activity occurs in fourth- and fifth-order streams with gradients of 

three percent or less. After fry emerge in spring, they disperse upstream and downstream to 

establish and defend territories weak water currents such as backwaters and shallow areas near 

stream banks. Juveniles rear in these areas during the spring and summer. In early fall juveniles 

move to river margins, backwater, and pools. During winter juveniles typically reduce feeding 

activity and growth rates slow down or stop. By March of their second spring, juveniles feed 

heavily on insects and crustaceans and grow rapidly before smoltification and outmigration 

(Olegario 2006). Relative to species such as chum salmon, Chinook salmon, and steelhead, coho 

salmon smolts usually spend a short time (one to three days) in the estuary with little feeding 

(Thorpe 1994, Miller and Sadro 2003). After entering the ocean, immature coho salmon initially 

remain in nearshore waters close to the parent stream. North American coho salmon will migrate 

north along the coast in a narrow coastal band that broadens in southeastern Alaska. During this 

migration, juvenile coho salmon tend to occur in both coastal and offshore waters.

Along the Oregon/California coast, coho salmon primarily return to rivers to spawn as three-year 

olds, having spent approximately 18 months rearing in fresh water and 18 months in salt water.

In some streams, a smaller proportion of males may return as two-year olds. The presence of 

two-year old males can allow for substantial genetic exchange between brood years. The 

relatively fixed three-year life cycle exhibited by female coho salmon limits demographic 

interactions between brood years. This makes coho salmon more vulnerable to environmental 

perturbations than other salmonids that exhibit overlapping generations, i.e., the loss of a coho 

salmon brood year in a stream is less likely than for other Pacific salmon to be reestablished by 

females from other brood years. All coho salmon are semelparous and anadromous.

Coho salmon feed on a variety of prey organisms depending upon life stage and size. While at 

sea, coho salmon tend to eat fish including herring, sand lance, sticklebacks, sardines, shrimp 

and surf smelt. While in estuaries and in fresh water coho salmon are significant predators of 

Chinook, pink, and chum salmon, as well as aquatic and terrestrial insects. Smaller fish, such as 
48

fry, eat chironomids, plecoptera and other larval insects, and typically use visual cues to find 

their prey.

4.15.2 Population Dynamics

The population dynamics of each Chinook salmon ESU will be discussed separately, below.

4.15.3 Status

On June 28, 2005, as part of the final listing determinations for 16 ESUs of West Coast salmon, 

NMFS amended and streamlined the 4(d) protective regulations for threatened salmon and 

steelhead (70 FR 37160) as described in the Protective Regulations for Threatened Salmonid 

Species section of this document. Under this change, the section 4(d) protections apply to natural 

and hatchery fish with an intact adipose fin, but not to listed hatchery fish that have had their 

adipose fin removed prior to release into the wild.

4.15.4 Critical Habitat

Critical habitat will be discussed for each coho salmon ESU separately, below.

4.16 Coho Salmon (Central California Coast ESU)

The Central California Coast coho salmon ESU includes all naturally spawned populations of 

coho salmon from Punta Gorda in northern California south to and including the San Lorenzo 

River in central California, as well as populations in tributaries to San Francisco Bay, excluding 

the Sacramento-San Joaquin River system. The ESU also includes four artificial propagation 

programs. We used information available in status reviews (Weitkamp et al. 1995, Good et al. 

2005, NMFS 2011a, Spence and Williams 2011), “An analysis of historical population structure 

for evolutionarily significant units of Chinook salmon, coho salmon, and steelhead in the NorthCentral California Coast Recovery Domain” (Bjorkstedt et al. 2005), listing documents (60 FR 

38011; 61 FR 56138; 70 FR 37160), and previously issued biological opinions (NMFS 2012b) to 

summarize the status of the species.

4.16.1 Life History

Both run and spawn timing of coho salmon in this region are late (both peaking in January) 

relative to northern populations, with little time spent in fresh water between river entry and 

spawning. Spawning runs coincide with the brief peaks of river flow during the fall and winter.

Most juveniles of this ESU undergo smoltification and start their seaward migration one year 

after emergence from the redd. Juveniles spending two winters in fresh water have, however, 

been observed in at least one coastal stream within the range of the ESU. Smolt outmigration 

generally peaks in April and May (Shapovalov and Taft 1954). In general, coho salmon within 

California exhibit a three-year life cycle. However, two-year old males commonly occur in some 

streams.

4.16.2 Population Dynamics

The ESU consisted historically of 11 functionally independent populations and a larger number 

of dependent populations. One of the two historically independent populations in the Santa Cruz 

mountains (i.e., south of the Golden Gate Bridge) is extirpated. Coho salmon are considered 

effectively extirpated from the San Francisco Bay. The Russian River population, once the 

largest and most dominant source population in the ESU, is now at high risk of extinction 

because of low abundance and failed productivity. The Lost Coast to Navarro Point to the north 

contains the majority of coho salmon remaining in the ESU.
49

Limited information exists on abundance of coho salmon for this ESU. About 200,000 to 

500,000 coho salmon were produced statewide in the 1940s. This escapement declined to about 

99,000 by the 1960s with approximately 56,000 (56 percent) originating from streams within this 

ESU. The estimated number of coho salmon produced within the ESU in the late 1980s had 

further declined to 6,160 (46 percent of the estimated statewide production). Additionally, 

information on the abundance and productivity trends for the naturally spawning component of 

this ESU is extremely limited. There are no long-term time series of spawner abundance for 

individual river systems. Returns increased in 2001 in streams within the northern portion of the 

ESU; however, returns in 2006/07 and 2007/08 were extremely low (MacFarlane et al. 2008) and 

about 500 fish returned in 2010 across the entire range. Hatchery raised smolt have been released 

infrequently but occasionally in large numbers in rivers throughout the ESU. Releases have 

included transfer of stocks within California and between California and other Pacific states as 

well as smolt raised from eggs collected from native stocks.

4.16.3 Status

NMFS listed the central California coast coho salmon ESU as threatened on October 31, 1996 

(61 FR 56138) and later reclassified their status as endangered on June 28, 2005 (70 FR 37160).

The ESU was listed due to habitat loss and degradation from the combined effects of logging, 

agricultural, and mining activities; urbanization; stream channelization; damming; wetland loss; 

overharvest; artificial propagation; and prolonged drought and poor ocean conditions. ESU 

spatial structure has been substantially modified due to lack of viable source populations and loss 

of dependent populations. Limited information exists on abundance for central California coast 

coho salmon; therefore, the best data available are presence-absence surveys used as a proxy for 

abundance changes. At the time of the 1996 listing, coho salmon occurred in 47 percent of 

streams (62) and were considered extirpated from 53 percent (71) of streams that historically 

harbored coho salmon within the ESU (Brown et al. 1994). Later reviews have concluded that 

the number of occupied streams relative to historic has not changed and may actually have 

declined. Additionally, the low rates of return from 2006 to 2010 suggest that all three year 

classes are faring poorly across the species’ range. Though hatchery salmon have been released, 

genetic studies show little homogenization of populations (i.e., transfer of stocks between basins) 

has had little effect on the geographic genetic structure of the ESU (Hedgecock 2002). Salmon in 

this ESU likely have considerable diversity in local adaptations given that the ESU spans a large 

latitudinal diversity in geology and ecoregions, and include both coastal and inland river basins.

Based on these factors, this ESU would likely have a low resilience to additional perturbations.

4.16.4 Critical Habitat

NMFS designated critical habitat for central California coast coho salmon on May 5, 1999 (64 

FR 24049). Designated critical habitat includes accessible reaches of all rivers (including 

estuarine areas and tributaries) between Punta Gorda and the San Lorenzo River (inclusive) in 

California. Critical habitat for this species also includes two streams entering San Francisco Bay: 

Arroyo Corte Madera Del Presidio and Corte Madera Creek. Specific PCEs were not designated 

in the critical habitat final rule; instead five “essential habitat” categories were described: 1) 

juvenile summer and winter rearing areas; 2) juvenile migration corridors; 3) areas for growth 

and development to adulthood; 4) adult migration corridors; and 5) spawning areas. The 

“essential features” that characterize these sites include adequate 1) substrate; 2) water quality; 

3) water quantity; 4) water temperature; 5) water velocity; 6) cover/shelter; 7) food; 8) riparian 

vegetation; 9) space; and 10) safe passage conditions. NMFS (2008a) evaluated the condition of 
50

each habitat feature in terms of its current condition relative to its role and function in the 

conservation of the species. The assessment of habitat showed a distinct trend of increasing 

degradation in quality and quantity of all essential features as the habitat progresses south 

through the species range, with the area from the Lost Coast to the Navarro Point supporting the 

most favorable habitats and the Santa Cruz Mountains supporting the least. However, all 

populations are generally degraded regarding spawning and incubation substrate, and juvenile 

rearing habitat. Elevated water temperatures occur in many streams across the entire ESU.

4.17 Coho Salmon (Lower Columbia River ESU)

The lower Columbia River coho salmon ESU includes all naturally spawned populations of coho 

salmon in the Columbia River and its tributaries in Oregon and Washington, from the mouth of 

the Columbia up to and including the Big White Salmon and Hood Rivers, Washington; and the 

Willamette River to Willamette Falls, Oregon. This ESU includes 25 artificial propagation 

programs, however on June 26, 2013, NMFS proposed the number of artificial propagation 

programs included in the ESU be changed to 23 (78 FR 38270). We used information available 

in status reviews (Johnson et al. 1991, Good et al. 2005, Ford 2011, NMFS 2011d), recovery 

plans (Lower Columbia Fish Recovery Board 2010, Oregon Department of Fish and Wildlife 

2010, NMFS 2013c), “Viability status of Oregon salmon and steelhead populations in the 

Willamette and lower Columbia basins (McElhany et al. 2007), listing documents (70 FR 37160; 

78 FR 2725), and previously issued biological opinions (NMFS 2012b) to summarize the status 

of the species.

4.17.1 Life History

The majority of the Lower Columbia River coho salmon are of hatchery origin. Hatchery runs 

are currently managed for two distinct runs: early-returning and late-returning. Early-returning 

coho salmon return to the Columbia River in mid-August and to spawning tributaries in early 

September, with peak spawning from mid- October to early November. Late-returning coho 

salmon return from late September through December and enter spawning tributaries from 

October through January. Most late-returning spawning occurs from November through January.

Fry emerge from redds during a three-week period between early March and late July. Juveniles 

rear in fresh water for a year and smolt outmigration occurs from April through June with a peak 

in May. Juvenile coho are present in the Columbia River estuary from March to August. In 

general, salmon of this ESU return to freshwater as three-year-olds.

Analysis of run timing of coho salmon suggests that the Clackamas River population is 

composed of one late returning population and one early returning population. The late-returning 

population is believed to be descended from the native Clackamas River population and the 

early-returning population is believed to descend from hatchery fish introduced from Columbia 

River populations outside the Clackamas River basin. The naturally produced coho salmon 

return to spawn between December and March.

4.17.2 Population Dynamics

The ESU historically consisted of 24 independent populations. The vast majority (over 90 

percent) of these are either extirpated or nearly so. Of the 24 populations, only two have 

significant natural production: the Sandy and Clackamas Rivers. Wild coho salmon re-appeared 

in two additional basins (Scappoose and Clatskanie) after a 10-year period during the 1980s and 

1990s when they were largely absent. Prior to 1900, the Columbia River had an estimated annual 

run of more than 600,000 adults with about 400,000 spawning in the lower Columbia River. By 
51

the 1950s, the estimated number of coho salmon returning to the Columbia River had decreased 

to 25,000 adults (about five percent of historic levels). Massive hatchery releases since 1960 

have increased the Columbia River run size. Between 1980 and 1989, the run varied from 

138,000 adults to a historic high of 1,553,000 adults. However, only a small portion of these 

spawned naturally, and available information indicates that the naturally produced portion has 

continuously declined since the 1950s. The current number of naturally spawning fish during 

October and late November ranges from 3,000 to 5,500 fish. The majority of these are of 

hatchery origin. The 1996 to 1999 geometric mean for the late run in the Clackamas River, the 

only-run which is considered consisting mainly of native coho salmon, was 35 fish. Both longand short-term trends and median population growth rate for the natural origin (late-run) portion 

of the Clackamas River coho salmon are negative but with large confidence intervals. The shortterm trend for the Sandy River population is close to one, indicating a relatively stable 

population during the years 1990 to 2002. The long-term trend for this same population shows 

that the population has been decreasing (trend = 0.54) and there is a 43 percent probability that 

the median population growth rate was less than one.

4.17.3 Status

NMFS listed Lower Columbia River coho salmon as threatened on June 28, 2005 (70 FR 37160).

Lower Columbia River coho salmon have been—and continue to be—affected by habitat 

degradation, hydropower impacts, harvest, and hatchery production. Out of the 24 populations 

that make up this ESU, 21 are considered to have a very low probability of persisting for the next 

100 years, and none is considered viable. The very low persistence probability for most Lower 

Columbia River coho salmon populations is related to low abundance and productivity, loss of 

spatial structure, and reduced diversity. Though data quality has been poor because of inadequate 

spawning surveys and, until recently, the presence of unmarked hatchery-origin spawners, most 

populations are believed to have very low abundance of natural-origin spawners (50 fish or 

fewer). The spatial structure of some populations is constrained by migration barriers (such as 

tributary dams) and development in lowland areas. Low abundance, past stock transfers, other 

legacy hatchery effects, and ongoing hatchery straying may have reduced genetic diversity 

within and among coho salmon populations. It is likely that hatchery effects have also decreased 

population productivity. The generally poor baseline population status of coho salmon reflects 

long-term trends: natural-origin coho salmon in the Columbia Basin have been in decline for the 

last 50 years. Based on these factors, this ESU would likely have very low resilience to 

additional perturbations.

4.17.4 Critical Habitat

NMFS proposed critical habitat designation of approximately 2,288 miles of freshwater and 

estuarine habitat in Oregon and Washington on January 14, 2013 (78 FR 2725). A final 

designation has not been made.

4.18 Coho Salmon (Oregon Coast ESU)

The Oregon Coast coho salmon ESU includes all naturally spawned populations of coho salmon 

in Oregon coastal streams south of the Columbia River and north of Cape Blanco (63 FR 42587).

One hatchery population, the Cow Creek hatchery coho salmon, is considered part of the ESU. 

We used information available in the status review (Good et al. 2005), “Scientific conclusions of 

the status review for Oregon coast coho salmon (Oncorhynchus kisutch)” (Stout et al. 2012). 

“Identification of historical populations of coho salmon (Oncorhynchus kisutch) in the Oregon 
52

Coast Evolutionarily Significant Unit” (Lawson et al. 2007), listing documents (63 FR 42587; 73 

FR 7816), and previously issued biological opinions (NMFS 2012b) to summarize the status of 

the species.

4.18.1 Life History

In general, adults begin to migrate into rivers at the first fall freshet, usually in late October or 

early November, though there is some variation in run timing among watersheds. A delay in rain 

can delay river entry considerably. Some coho may spend up to two months in fresh water before 

spawning. Spawning usually occurs from November through January and may continue into 

February. Juveniles emerge from the gravel in spring and typically spend a summer and winter in 

fresh water before migrating to the ocean as smolts, usually in April or May of their second 

spring. Timing varies between years, among river systems, and based on small-scale habitat 

variability. Salmon in this ESU generally exhibit a three-year life cycle, though two- year-old 

males commonly occur in some streams and on average make up 20 percent of spawning males.

4.18.2 Population Dynamics

Lawson et al. (2007) considered the ESU to have historically consisted of 13 functionally 

independent populations and eight potentially dependent populations. Historical escapement in 

the 10 largest basins has been estimated to about 2.4 to 2.9 million spawners. The estimated 

median population of native spawners during the years 1990 to 1999 was 46,291 (min. 21,139, 

max. 82,661) spawners. After 1999, total ESU abundance increased. A median of 186,769 native 

spawners was estimated for the period 2000 through 2012 (min. 66,271, max. 356,243) (Oregon 

Department of Fish and Wildlife 2013). The encouraging increases in spawner abundance in 

2000 to 2002 were preceded by three consecutive brood years (the 1994 to 1996 brood years 

returning in 1997 to 1999, respectively) exhibiting recruitment failure.2 At the time of the 2005 

status report, these three years of recruitment failure were the only such instances observed in the 

abundance time series since 1950. The increases in natural spawner abundance from 2000 to 

2002 increases were primarily observed in populations in the northern portion of the ESU.

Despite the increase in spawner abundance in 2000 to 2002, the long-term trends in ESU 

productivity remained negative due to the low abundances observed during the 1990s. Recent 

data indicate that the total abundance of natural spawners in the OC coho salmon ESU again 

steadily decreased until 2007 with an estimated spawner abundance of 66,271 fish or 

approximately 25 percent of the 2002 peak abundance (258,418 spawners) (Oregon Department 

of Fish and Wildlife 2013). Thus, recruitment failed during the five years from 2002 through 

2007. Abundance increased each year from 179,686 native spawners in 2008 to the highest 

recorded abundance of native spawners in the time series: 356,243 native spawners in 2012; 

however, abundance in 2012 was estimated at 99,142 native spawners, indicating another 

recruitment failure.

4.18.3 Status 

NMFS listed the Oregon coast coho salmon as a threatened species on February 11, 2008 (73 FR 

7816). The ESU was listed because its biological status had not improved since NMFS’s January 

19, 2006 determination that the ESU’s listing was not warranted (71 FR 3033) and current efforts 

being made to protect the species did not provide sufficient certainty of implementation or 

 

2

Recruitment failure is when a given year class of natural spawners fails to replace itself when its offspring return 

to the spawning grounds three years later.
53

effectiveness to mitigate the assessed level of extinction risk. Current coho salmon coastal 

distribution has not changed markedly compared to historical distribution; however, river 

alterations and habitat destruction have significantly modified use and distribution within several 

river basins. Genetic diversity has been reduced by legacy effects of freshwater and tidal habitat 

loss, very low spawner returns within the past 20 years, and past high levels of hatchery releases; 

however, with recent reductions in hatchery releases, diversity should improve. Based on these 

factors, this ESU would likely have a moderate resilience to additional perturbations.

4.18.4 Critical Habitat

NMFS designated critical habitat for Oregon Coast coho salmon on February 11, 2008 (73 FR 

7816). The designation includes 72 of 80 watersheds within the range of the ESU, totals 

approximately 6,600 stream miles, and includes all or portions of the Nehalem, Nestucca/Trask, 

Yaquina, Alsea, Umpqua, and Coquille basins. PCEs include: spawning sites with water and 

substrate quantity to support spawning, incubation, and larval development; freshwater rearing 

sites with water quantity and floodplain connectivity to form and maintain physical habitat 

conditions and support juvenile growth, foraging, behavioral development (e.g., predator 

avoidance, competition), and mobility; freshwater migratory corridors free of obstruction with 

adequate water quantity and quality conditions; and estuarine, nearshore and offshore areas free 

of obstruction with adequate water quantity, quality and salinity conditions that support 

physiological transitions between fresh- and saltwater, predator avoidance, foraging and other 

life history behaviors.

PCEs vary widely throughout the critical habitat area designated the ESU; many watersheds have 

been heavily impacted and support low quality PCEs, while habitat in other watersheds have 

sufficient quality for supporting the conservation purpose of designated critical habitat. The 

spawning PCE has been impacted in many watersheds from the inclusion of fine sediment into 

spawning gravel from timber harvest and forestry related activities, agriculture, and grazing.

These activities have also diminished the channels’ rearing and overwintering capacity by 

reducing the amount of large woody debris in stream channels, removing riparian vegetation, 

disconnecting floodplains from stream channels, and changing the quantity and dynamics of 

stream flows. The rearing PCE has been degraded by elevated water temperatures in 29 of the 

watersheds within the Nehalem, North Umpqua, and the inland watersheds of the Umpqua 

subbasins. Water quality is impacted by contaminants from agriculture and urban areas in low 

lying areas in the Umpqua subbasin, and in coastal watersheds within the Siletz/Yaquina, 

Siltcoos, and Coos subbasins. Reductions in water quality have been observed in 12 watersheds 

due to contaminants and excessive nutrition. The migration PCE has been impacted throughout 

the ESU by culverts and road crossings that restrict passage.

4.19 Coho Salmon (Southern Oregon/Northern California Coast ESU)

The Southern Oregon/Northern California Coast coho salmon ESU consists of all naturally 

spawning populations of coho salmon that reside below long-term, naturally impassible barriers 

in streams between Punta Gorda, California and Cape Blanco, Oregon. This ESU also includes 

three artificial propagation programs. We used information available in status reviews (Good et 

al. 2005, NMFS 2011l, Williams et al. 2011), the draft recovery plan (NMFS 2012d), listing 

documents (62 FR 24588; 70 FR 37160), and previously issued biological opinions (NMFS 

2012b) to summarize the status of the species.
54

4.19.1 Life History

In this ESU, river entry occurs earlier in the north and later in the south. In Oregon, salmon of 

this ESU enter rivers in September or October; south of the Klamath River Basin to the Mattole 

River, California salmon entry occurs in November and December; and river entry occurs from 

mid-December to mid-February in rivers farther south. Because coho salmon enter rivers late and 

spawn late south of the Mattole River, they spend much less time in the river prior to spawning 

compared to populations farther north. Juveniles emerge from the gravel in spring, and typically 

spend a summer and winter in fresh water before migrating to the ocean as smolts in their second 

spring. Coho salmon adults spawn at age three, spending about a year and a half in the ocean.

4.19.2 Population Dynamics

Data on population abundance and trends are limited for this ESU. Historical point estimates of 

coho salmon abundance for the early 1960s and mid-1980s suggest that California statewide 

coho spawning escapement in the 1940s ranged between 200,000 and 500,000 fish. Numbers 

declined to about 100,000 fish by the mid-1960s with about 43 percent originating from this 

ESU. In 1994, Brown et al. estimated that about 7,000 wild and naturalized coho salmon were 

produced in the California portion of this ESU. Though long-term data on salmon abundance are 

scarce, the available monitoring data indicate that spawner abundance has generally declined for 

populations in this ESU. The Shasta River population has declined in abundance by almost 50 

percent from one generation to the next; two partial counts from Prairie Creek, a tributary of 

Redwood Creek, and Freshwater Creek, a tributary of Humboldt Bay show negative trends; and 

data from the Rogue River basin also show recent negative trends. Estimates from Huntley Park 

in the Rogue River basin show a strong return year of approximately 25,000 spawners in 2004, 

followed by a decline to 2,566 fish in 2009. The 12-year average estimated wild adult coho 

salmon in the Rogue River basin between 1998 and 2009 (excluding 2008)3is 8,050 fish. Based 

on extrapolations from cannery pack, the Rogue River had an estimated adult coho salmon 

abundance of 114,000 in the late 1800s (Meengs and Lackey 2005).

4.19.3 Status

NMFS listed the Southern Oregon/Northern California coast coho salmon as threatened on May 

7, 1997 (62 FR 24588), and reaffirmed their status on June 28, 2005 (70 FR 37160). The ESU 

was listed due to habitat loss and degradation from the combined effects of logging, agricultural, 

and mining activities; road building; urbanization; stream channelization; damming; wetland 

loss; beaver trapping, water withdrawals; overharvest; drought; flooding; poor ocean conditions 

and El Niño; and artificial propagation. Though distribution has been reduced and fragmented

within the ESU, extant populations can still be found in all major river basins within the ESU.

Presence-absence data indicate a disproportionate loss of southern populations compared to the 

northern portion of the ESU. Though long-term data on salmon abundance are scarce, the 

available monitoring data indicate that spawner abundance has generally declined for 

populations in this ESU. Many populations have been extirpated, are near extirpation, or are 

severely depressed. Based on available data, the draft recovery plan (NMFS 2012d) concluded 

that this ESU is at high risk of extinction and is not viable. Based on these factors, this ESU 

would likely have a very low resilience to additional perturbations.

 

3

2008 data were excluded from the average because the extremely low numbers were not consistent with that seen 

upstream at Gold Ray Dam, suggesting other reasons (sampling issues, data errors, etc.) for the dramatic drop in fish 

numbers from 2007 to 2008.
55

4.19.4 Critical Habitat

NMFS designated critical habitat for Southern Oregon/Northern California Coast coho salmon 

on May 5, 1999 (64 FR 24049). Designated critical habitat includes all accessible river reaches 

between Cape Blanco, Oregon, and Punta Gorda, California and consists of the water, substrate, 

and river reaches (including off-channel habitats) in specified areas. Accessible reaches are those 

within the historical range of the ESU that can still be occupied by any life stage of coho salmon.

Specific PCEs were not designated in the critical habitat final rule; instead five “essential 

habitat” categories were described: 1) juvenile summer and winter rearing areas; 2) juvenile 

migration corridors; 3) areas for growth and development to adulthood; 4) adult migration 

corridors; and 5) spawning areas. The “essential features” that characterize these sites include 

adequate: 1) substrate; 2) water quality; 3) water quantity; 4) water temperature; 5) water 

velocity; 6) cover/shelter; 7) food; 8) riparian vegetation; 9) space; and 10) safe passage 

conditions. Critical habitat designated for this ESU is generally of good quality in northern 

coastal streams. Spawning essential habitats have been degraded throughout the ESU by logging 

activities that have increased fine particles in spawning gravel. Rearing essential habitats have 

been considerably degraded in many inland watersheds from the loss of riparian vegetation 

resulting in unsuitably high water temperatures. Rearing and juvenile migration essential habitat 

quality has been reduced from the disconnection of floodplains and off-channel habitat in low 

gradient reaches of streams, consequently reducing winter rearing capacity.

4.20 Sockeye Salmon (General Overview)

We discuss the distribution, life history, population dynamics, status, and critical habitats of the 

two species (here we use the word “species” to apply to distinct population segments, DPSs, and 

evolutionary significant units, ESUs) separately; however, because listed sockeye salmon species 

are virtually indistinguishable in the wild and comprise the same biological species, we begin 

this section describing characteristics common across ESUs. We used information available in 

the status review (Good et al. 2005), various listing documents, and biological opinions (NMFS 

2012b) to summarize the status of the species.

Sockeye salmon occur in the North Pacific and Arctic oceans and associated freshwater systems.

In North America, the species ranges north from the Klamath River in California to Bathurst 

Inlet in the Canadian Arctic. In Asia sockeye salmon range from northern Hokkaido in Japan 

north to the Anadyr River in Siberia. The largest populations occur north of the Columbia River.

4.20.1 Life History

Most sockeye salmon exhibit a lake-type life history (i.e., they spawn and rear in or near lakes), 

though some salmon exhibit a river-type life history. Spawning generally occurs in late summer 

and fall, but timing can vary greatly among populations. In lakes, salmon commonly spawn 

along “beaches” where underground seepage provides fresh oxygenated water. Incubation is a 

function of water temperature, but generally lasts between 100 to 200 days (Burgner 1991).

Sockeye salmon fry primarily rear in lakes; river-emerged and stream-emerged fry migrate into 

lakes to rear. Juvenile sockeye salmon generally rear in lakes from one to three years after 

emergence, though some river-spawned salmon may migrate to sea in their first year. Juvenile 

sockeye salmon feeding behaviors change as they transition through life stages after emergence 

to the time of smoltification. In the early fry stage from spring to early summer, juveniles forage 

exclusively in the warmer littoral (i.e., shoreline) zone where they depend mostly on fly larvae 

and pupae, copepods, and water fleas. In summer, underyearling sockeye salmon move from the 
56

littoral habitat to a pelagic (i.e., open water) existence where they feed on larger zooplankton; 

however, flies may still make up a substantial portion of their diet. Older and larger fish may also 

prey on fish larvae. Distribution in lakes and prey preference is a dynamic process that changes 

daily and yearly depending on many factors, including: water temperature; prey abundance; 

presence of predators and competitors; and size of the juvenile. Peak emigration to the ocean 

occurs in mid-April to early May in southern sockeye populations (lower than 52oN latitude) and 

as late as early July in northern populations (62oN latitude) (Burgner 1991). Adult sockeye 

salmon return to their natal lakes to spawn after spending one to four years at sea. The diet of 

adult salmon consists of amphipods, copepods, squid, and other fish.

Certain populations of O. nerka become resident in the lake environment and are referred to as 

“kokanee”. Kokanee and sockeye often co-occur in many interior lakes, where access to the sea 

is possible but energetically costly; kokanee are rarely found in coastal lakes, where the 

migration to sea is relatively short and energetic costs are minimal. In some cases a single 

population will give rise to both the anadromous and freshwater life history form. Both sockeye 

and kokanee are semelparous.

4.20.2 Population Dynamics

The population dynamics of each sockeye salmon ESU will be discussed separately, below.

4.20.3 Status

On June 28, 2005, as part of the final listing determinations for 16 ESUs of West Coast salmon, 

NMFS amended and streamlined the 4(d) protective regulations for threatened salmon and 

steelhead (70 FR 37160) as described in the Protective Regulations for Threatened Salmonid 

Species section of this document. Under this change, the section 4(d) protections apply to natural

and hatchery fish with an intact adipose fin, but not to listed hatchery fish that have had their 

adipose fin removed prior to release into the wild.

4.20.4 Critical Habitat

Critical habitat for each sockeye salmon ESU is discussed separately, below.

4.21 Sockeye Salmon (Ozette Lake ESU)

The Ozette Lake sockeye salmon ESU includes all naturally spawned anadromous populations of 

sockeye salmon that migrate into and rear in in Ozette Lake, Ozette River, Coal Creek, and other 

tributaries flowing into Ozette Lake, near the northwest tip of the Olympic Peninsula in Olympic 

National Park, Washington. Composed of only one population, the Ozette Lake sockeye salmon 

ESU consists of five spawning aggregations or subpopulations, grouped according to their 

spawning locations: Umbrella and Crooked creeks, Big Rive, and Olsen’s and Allen’s beaches.

Two artificial populations are also considered part of this ESU. Sockeye salmon stock reared at 

the Makah Tribe’s Umbrella Creek Hatchery were included in the ESU, but were not considered 

essential for recovery of the ESU. However, once the hatchery fish return and spawn in the wild, 

their progeny are considered to be listed under the ESA. We used information available in status 

reviews (Good et al. 2005, NMFS 2011f), the recovery plan (NMFS 2009d), “Viability Criteria 

for the Lake Ozette Sockeye Salmon Evolutionarily Significant Unit” (Rawson et al. 2009), 

listing documents (63 FR 11750, 64 FR 14528), and previously issued biological opinions 

(NMFS 2012b) to summarize the status of the species. 
57

4.21.1 Life History

Salmon of this ESU enter Ozette Lake through the Ozette River from April to early August and 

spawning is delayed until late October to February. Spawning occurs primarily in lakeshore 

upwelling areas of the lake, though minor spawning may occur below the lake in the Ozette 

River or its tributary, Coal Creek. Native sockeye salmon do not presently spawn in tributary 

streams to Ozette Lake, though spawning may have occurred there historically. Hatchery salmon, 

however, do spawn in the Ozette Lake tributaries of Umbrella Creek and Big River. Fry in 

Ozette Lake and the tributaries emerge from late-February through May and disperse to open 

areas of the lake to rear. Juveniles rear for one year in the lake and emigrate seaward in their 

second spring. At the time of emigration, smolts are relatively large, averaging four and a half to 

five inches in length. Most adult salmon of this ESU return from the ocean to spawn as four-year 

old fish. Ozette Lake also supports a population of kokanee which is not listed under the ESA. 

4.21.2 Population Dynamics

The Ozette Lake sockeye salmon ESU is composed of one historical population with multiple 

spawning aggregations. Historically at least four beaches in the lake were used for spawning; 

today only two beach spawning locations, Allen’s and Olsen’s beaches, are used. The historical 

abundance of Ozette Lake sockeye salmon is poorly documented, but may have been as high as 

50,000 individuals (Blum 1988). Declines began to be reported in the 1920s. Escapement 

estimates (run size minus broodstock take) from 1996 to 2006 are variable and range from a low 

of 1,404 individuals in 1997 to a high of 6,461 individuals in 2004, with a median of 

approximately 3,800 sockeye per year (geometric mean: 3,353). No statistical estimation of 

trends for this ESU are reported. However, comparing four year averages (to include four brood 

years in the average because the species primarily spawn as four-year olds) shows an increase 

during the period 2000 to 2006. For return years 1996 to 1999 the run size averaged 2,460 

sockeye salmon; for years 2000 to 2003 the run size averaged just over 4,420 fish; and for years 

2004 to 2006, the average abundance estimate was 4,167 sockeye. The supplemental hatchery 

program began with out-of-basin stocks and make up an average of 10 percent of the run. The 

proportion of beach spawners originating from the hatchery is unknown, but it is likely that 

straying is low. Based on estimates of habitat carrying capacity, a viable sockeye salmon 

population in the Lake Ozette watershed would range between 35,500 to 121,000 spawners.

4.21.3 Status

NMFS listed the Ozette Lake sockeye salmon ESU as threatened on March 25, 1999 (64 FR 

14528), and reaffirmed their threatened status on June 28, 2005 (70 FR 37160). The ESU was 

listed due to habitat loss and degradation from the combined effects of logging; road building; 

predation; invasive plant species; and overharvest. Ozette Lake sockeye salmon have not been 

commercially harvested since 1982 and only minimally harvested by the Makah Tribe since 

1982 (0 to 84 fish per year); there are also no known marine area harvest impacts to fish of this 

ESU. Overall abundance is substantially below historical levels and it is not known if this 

decrease in abundance is a result of fewer spawning aggregations, lower abundances at each 

aggregation, or a combination of both factors. The proportion of beach spawners is assumed to 

be low; therefore, hatchery originated fish are not believed to have had a major effect on the 

genetics of the naturally spawned population. However, Ozette Lake sockeye have a relatively 

low genetic diversity compared to other O. nerka populations examined in Washington State 

(Crewson et al. 2001). Genetic differences do occur between age cohorts, but as different age 

groups do not spawn with each other, the population may be more vulnerable to significant 
58

reductions in population structure due to catastrophic events or unfavorable conditions affecting 

one year class. Based on these factors, this ESU would likely have a low resilience to additional 

perturbations.

4.21.4 Critical Habitat

NMFS designated critical habitat for Ozette Lake sockeye salmon on September 2, 2005 (70 FR 

52630). It encompasses areas within the Hoh/Quillayute subbasin, Ozette Lake, and the Ozette 

Lake watershed. The entire occupied habitat for this ESU is within the single watershed for 

Ozette Lake. PCEs identified for Lake Ozette sockeye salmon are areas for spawning, freshwater 

rearing and migration, estuarine areas free of obstruction, nearshore marine areas free of 

obstructions, and offshore marine areas with good water quality. The physical or biological 

features that characterize these sites include water quality and quantity, natural cover, forage, and 

adequate passage conditions. Spawning habitat has been affected by loss of tributary spawning 

areas and exposure of much of the available beach spawning habitat due to low water levels in 

summer. Further, native and non-native vegetation as well as sediment have reduced the quantity 

and suitability of beaches for spawning. The rearing PCE is degraded by excessive predation and 

competition with introduced non-native species, and by loss of tributary rearing habitat.

Migration habitat may be adversely affected by high water temperatures and low water flows in 

summer which causes a thermal block to migration (La Riviere 1991).

4.22 Sockeye Salmon (Snake River ESU)

The Snake River sockeye salmon ESU includes all anadromous and residual sockeye from the 

Snake River basin, Idaho, as well as artificially propagated sockeye salmon from the Redfish 

Lake Captive Broodstock Program. Redfish Lake is located in the Salmon River basin, a 

subbasin within the larger Snake River basin. We used information available in status reviews 

(Gustafson et al. 1997, Good et al. 2005, NMFS 2011i), listing documents (58 FR 68543, 70 FR 

37160), and previously issued biological opinions (NMFS 2008b, 2012b) to summarize the status 

of the species.

4.22.1 Life History

Snake River sockeye salmon are unique compared to other sockeye salmon populations. Sockeye 

salmon returning to Redfish Lake travel a greater distance from the sea (approximately 900 

miles) to a higher elevation (6,500 ft) than any other sockeye salmon population and are the 

southern-most population of sockeye salmon in the world (Bjornn et al. 1968). Salmon of this 

ESU are separated by 700 or more river miles from two other extant upper Columbia River 

populations in the Wenatchee River and Okanogan River drainages. These latter populations 

return to lakes at substantially lower elevations (Wenatchee at 1,870 ft, Okanagon at 912 ft) and 

occupy different ecoregions.

No natural origin anadromous adults have returned since 1998 and the species is currently 

entirely supported by adults produced through a captive propagation program. Historically, 

salmon of this ESU entered the Columbia River system in June and July, and arrived at Redfish 

Lake between August and September. Spawning occurred in lakeshore gravel and generally 

peaked in October. Fry emerged in the spring (generally April and May) then migrated to open 

waters of the lake to feed. Juvenile sockeye remained in the lake for one to three years before 

migrating through the Snake and Columbia Rivers to the ocean. While pre-dam reports indicate 

that sockeye salmon smolts migrate in May and June, PIT-tagged sockeye smolts from Redfish 

Lake pass Lower Granite Dam from mid-May to mid-July. Adult anadromous sockeye spent two 
59

or three years in the open ocean before returning to Redfish Lake to spawn. A resident form of 

Snake River sockeye salmon also occurs in Redfish Lake. The residuals are nonanadromous (i.e. 

they complete their entire life cycle in fresh water); however, studies have shown that some 

ocean migrating juveniles are progeny of resident females (Rieman et al. 1994). The resident 

salmon spawn at the same time and in the same location as anadromous sockeye salmon.

4.22.2 Population Dynamics

The only extant sockeye salmon population in the Snake River basin at the time of listing 

occurred in Redfish Lake. Other lakes in the Salmon River basin that historically supported 

sockeye salmon include Alturas Lake above Redfish Lake which was extirpated in the early 

1900s as a result of irrigation diversions, though residual sockeye may still exist in the lake.

From 1955 to 1965, the Idaho Department of Fish and Game eradicated sockeye salmon from 

Pettit, Stanley, and Yellowbelly lakes, and built permanent structures on each of the lake outlets 

that prevented re-entry of anadromous sockeye salmon (Chapman and Witty 1993). Other 

historic sockeye salmon populations within the Snake River basin now considered extinct 

include Wallowa Lake (Grande Ronde River drainage, Oregon), Payette Lake (Payette River 

drainage, Idaho), and Warm Lake (South Fork Salmon River drainage, Idaho).

Adult returns to Redfish Lake during the period 1954 through 1966 ranged from 11 to 4,361 fish 

(Bjornn et al. 1968). In 1985, 1986, and 1987, 11, 29, and 16 sockeye, respectively, were 

counted at the Redfish Lake weir. Only 18 natural origin sockeye salmon have returned to the 

Stanley Basin since 1987. The first adult returns from the captive brood stock program returned 

to the Stanley Basin in 1999. From 1999 through 2005, a total of 345 captive brood adults that 

had migrated to the ocean returned to the Stanley Basin. Recent years have seen an increase in 

returns to over 600 in 2008 and more than 700 returning adults in 2009.

4.22.3 Status

NMFS listed Snake River sockeye salmon as endangered on November 20, 1991 (56 FR 58619), 

and reaffirmed their status on June 28, 2005 (70 FR 37160). Subsequent to the 1991 listing, the 

residual form of sockeye residing in Redfish Lake was identified and in 1993, NMFS determined 

that residual sockeye salmon in Redfish Lake was part of the ESU. The ESU was listed due to 

habitat loss and degradation from the combined effects of damming and hydropower 

development; overexploitation; fisheries management practices; and poor ocean conditions.

Recent annual abundances of natural origin sockeye salmon in the Stanley Basin have been 

extremely low. This species is currently entirely supported by adults produced through the 

captive propagation program. No natural origin anadromous adults have returned since 1998 and 

the abundance of residual sockeye salmon in Redfish Lake is unknown. Current smolt-to-adult 

survival of sockeye originating from the Stanley Basin lakes is rarely greater than 0.3 percent 

(Hebdon et al. 2004). Based on these factors, this ESU would likely have a very low resilience to 

additional perturbations.

4.22.4 Critical Habitat

NMFS designated critical habitat for SR sockeye salmon on December 28, 1993 (58 FR 68543).

It encompass the waters, waterway bottoms, and adjacent riparian zones of specified lakes and 

river reaches in the Columbia River that are or were accessible to salmon of this ESU (except 

reaches above impassable natural falls, and Dworshak and Hells Canyon Dams). Specific PCEs 

were not designated in the critical habitat final rule; instead four “essential habitat” categories 

were described: 1) spawning and juvenile rearing areas, 2) juvenile migration corridors, 3) areas 
60

for growth and development to adulthood, and 4) adult migration corridors. The “essential 

features” that characterize these sites include substrate/spawning gravel; water quality, quantity, 

temperature, velocity; cover/shelter; food; riparian vegetation; space; and safe passage 

conditions. The quality and quantity of rearing and juvenile migration essential habitats have 

been reduced from activities such as tilling, water withdrawals, timber harvest, grazing, mining, 

and alteration of floodplains and riparian vegetation. These activities disrupt access to foraging 

areas, increase the amount of fines in the steam substrate that support production of aquatic 

insects, and reduce instream cover. Adult and juvenile migration essential habitat is affected by 

four dams in the Snake River basin that obstructs migration and increases mortality of 

downstream migrating juveniles. Water quality impairments in designated critical habitat include 

inputs from fertilizers, insecticides, fungicides, herbicides, surfactants, heavy metals, acids, 

petroleum products, animal and human sewage, dust suppressants (e.g., magnesium chloride), 

radionuclides, sediment in the form of turbidity, and other anthropogenic pollutants. Pollutants 

enter the surface waters and riverine sediments from the headwaters of the Salmon River to the 

Columbia River estuary as contaminated stormwater runoff, aerial drift and deposition, and via 

point source discharges.

4.23 Steelhead Trout (General Overview)

We discuss the distribution, life history, population dynamics, status, and critical habitats of the 

eleven species (here we use the word “species” to apply to distinct population segments, DPSs, 

and evolutionary significant units, ESUs) separately; however, because listed steelhead trout 

species are virtually indistinguishable in the wild and comprise the same biological species, we 

begin this section describing characteristics common across DPSs. We used information 

available in the 2005 West Coast salmon and steelhead status review (Good et al. 2005), various 

salmon ESU listing documents, and biological opinions (NMFS 2012b) to summarize the status 

of the species.

Steelhead is the common name of the anadromous form of O. mykiss. They are a Pacific 

salmonid with freshwater habitats that include streams extending from northwestern Mexico to 

Alaska in North America to the Kamchatka peninsula in Russia. Non-anadromous O. mykiss do 

not migrate to the ocean and remain in freshwater all their lives. These fish are commonly called 

rainbow trout.

4.23.1 Life History

Though steelhead have a longer run time than other Pacific salmonids and do not tend to travel in 

large schools, they can be divided into two basic run-types: the stream-maturing type (summer 

steelhead) and the ocean-maturing type (winter steelhead). Summer steelhead enter fresh water 

as sexually immature adults between May and October (Nickelson et al. 1992, Busby et al. 1996)

and hold in cool, deep pools during summer and fall before moving to spawning sites as mature 

adults in January and February (Barnhart 1986, Nickelson et al. 1992). Winter steelhead return to 

fresh water between November and April as sexually mature adults and spawn shortly after river 

entry (Nickelson et al. 1992, Busby et al. 1996). Steelhead typically spawn in small tributaries 

rather than large, mainstem rivers and spawning distribution often overlaps with coho salmon, 

though steelhead tend to prefer higher gradients (generally two to seven percent, but up to 12 

percent or more) and their distributions tend to extend further upstream than coho salmon.

Summer steelhead commonly spawn higher in a watershed than do winter steelhead, sometimes 

even using ephemeral streams from which juveniles are forced to emigrate as flows diminish.
61

Fry usually inhabit shallow water along banks and stream margins of streams (Nickelson et al. 

1992) and move to faster flowing water such as riffles as they grow. Some older juveniles move 

downstream to rear in larger tributaries and mainstem rivers (Nickelson et al. 1992). In Oregon 

and California, steelhead may enter estuaries where sand bars create low salinity lagoons.

Migration of juvenile steelhead to these lagoons occurs throughout the year, but is concentrated 

in the late spring/early summer and in the late fall/early winter periods (Shapovalov and Taft 

1954, Zedonis 1992). Juveniles rear in fresh water for one to four years, then smolt and migrate 

to the ocean in March and April (Barnhart 1986). Steelhead typically reside in marine waters for 

two or three years prior to returning to their natal streams to spawn as four or five-year olds.

Unlike Pacific salmon, steelhead are iteroparous, or capable of spawning more than once before 

death (Busby et al. 1996). Females spawn more than once more commonly than males, but rarely 

more than twice before dying (Nickelson et al. 1992). Iteroparity is also more common among 

southern steelhead populations than northern populations (Busby et al. 1996).

Steelhead feed on a variety of prey organisms depending upon life stage, season, and prey 

availability. In freshwater juveniles feed on common aquatic stream insects such as caddisflies, 

mayflies, and stoneflies but also other insects (especially chironomid pupae), zooplankton, and 

benthic organisms (Pert 1993, Merz 2002). Older juveniles sometimes prey on emerging fry, 

other fish larvae, crayfish, and even small mammals, though these are not a major food source 

(Merz 2002). The diet of adult oceanic steelhead is comprised primarily of fish and squid (Light 

1985, Burgner et al. 1992).

4.23.2 Status

On June 28, 2005, as part of the final listing determinations for 16 ESUs of West Coast salmon, 

NMFS amended and streamlined the 4(d) protective regulations for threatened salmon and 

steelhead (70 FR 37160) as described in the Protective Regulations for Threatened Salmonid 

Species section of this document. Under this change, the section 4(d) protections apply to natural 

and hatchery fish with an intact adipose fin, but not to listed hatchery fish that have had their 

adipose fin removed prior to release into the wild.

4.23.3 Population Dynamics

The population dynamics of each steelhead DPS will be discussed separately, below.

4.23.4 Critical Habitat

NMFS designated critical habitat for all but one of the listed steelhead DPSs on September 2, 

2005 (70 FR 52488). Proposed designation of critical habitat for the Puget Sound steelhead will 

be discussed separately in Section 6.6.5. Areas designated as critical habitat are important for the 

species’ overall conservation by protecting quality growth, reproduction, and feeding. At the 

time of designation, PCEs are identified and include sites necessary to support one or more 

steelhead life stage(s). PCEs in steelhead designated habitat include freshwater spawning and 

rearing sites, freshwater migration corridors, nearshore marine habitat, and estuarine areas. The 

physical or biological features that characterize these sites include water quality and quantity, 

natural cover, forage, adequate passage conditions, and floodplain connectivity. The critical 

habitat section for each listed DPS below identifies the areas included as part of the designation 

and discusses the current status of critical habitat.
62

4.24 Steelhead (California Central Valley DPS)

The California Central Valley steelhead DPS includes all naturally spawned steelhead 

populations below natural and manmade impassable barriers in the Sacramento and San Joaquin 

Rivers and their tributaries, excluding steelhead from San Francisco and San Pablo Bays and 

their tributaries. The DPS also includes two artificial propagation programs: the Coleman 

National Fish Hatchery and Feather River Hatchery. We used information available in status 

reviews (Good et al. 2005, NMFS 2011c), the draft recovery plan (NMFS 2009c), listing 

documents (69 FR 33102; 71 FR 834), and previously issued biological opinions (NMFS 2012b)

to summarize the status of the species.

4.24.1 Life History

Members of this DPS have the longest freshwater migration of any population of winter 

steelhead. Adults return to freshwater essentially continuously from July to May, with peaks in 

September and February. Spawning occurs from December to April, with peaks from January to 

March (McEwan and Jackson 1996). Spawning occurs in small streams and tributaries directly 

downstream of dams. Juvenile steelhead in the Sacramento River basin migrate downstream 

during most months of the year, but the peak period of emigration occurs in spring, with a much 

smaller peak in fall. Emigrating juveniles use the lower reaches of the Sacramento River and the 

Delta for rearing and as a migration corridor to the ocean; some may use tidal marsh areas, nontidal freshwater marshes, and other shallow water areas in the Delta as rearing areas for short 

periods prior to their final emigration to the sea (Hallock et al. 1961).

4.24.2 Population Dynamics

The California Central Valley steelhead DPS may have consisted of 81 historical and 

independent populations (Lindley et al. 2006). Existing wild steelhead stocks in the Central 

Valley are mostly confined to the upper Sacramento River and its tributaries. Until recently, 

steelhead were considered extirpated from the San Joaquin River system; in 2004, a total of 12 

steelhead smolts were collected in monitoring trawls at the Mossdale station in the lower San 

Joaquin River (California Department of Fish and Game, unpubl. data). Historically, annual 

steelhead run size for this ESU may have approached one to two million adults. By the early 

1960s, the run size had declined to about 40,000 adults (McEwan 2001). Steelhead were counted 

at the Red Bluff Diversion Dam until 1993; counts declined from an average of 11,187 from 

1967 to 1977 to an average of approximately 2,000 through the early 1990s. Estimated total 

annual run size for the entire Sacramento-San Joaquin system was no more than 10,000 adults 

during the early 1990s (McEwan and Jackson 1996, McEwan 2001). Based on catch ratios at

Chipps Island in the Delta and using generous survival assumptions, the average number of 

steelhead females spawning naturally in the entire Central Valley during the years 1980 to 2000 

was estimated at approximately 3,600.

4.24.3 Status

NMFS listed the California Central Valley steelhead DPS as threatened on March 19, 1998, and 

reaffirmed their status on January 5, 2006 (71 FR 834). Factors contributing to the listing of this 

DPS include the loss of most historical spawning and rearing habitat above impassable dams, 

restriction of natural production areas, the apparent continuing decline in abundance, and lack of 

monitoring efforts to assess the DPS’s abundance and trends. The DPS’s present distribution has 

been greatly reduced: about 80 percent of historic habitat has been lost behind dams and about 38 

percent of habitat patches that supported independent populations are no longer accessible to 
63

steelhead (Lindley et al. 2006). Though previously thought to be extirpated from these areas, 

populations may exist in Big Chico and Butte Creeks and steelhead have also been observed in 

Clear Creek and Stanislaus River (Demko and Cramer 2000). A few wild steelhead are produced 

in the American and Feather Rivers. Though annual monitoring data for calculating trends are 

lacking, available data indicate the DPS has had a significant long-term downward trend in 

abundance. The losses of populations and reductions in abundance have reduced genetic 

diversity in the DPS. Hatchery-origin fish have also compromised the genetic diversity of the 

majority of the spawning runs. Based on these factors, this DPS would likely have a low 

resilience to additional perturbations.

4.24.4 Critical Habitat

Designated critical habitat for the California Central Valley steelhead DPS encompasses about 

2,300 miles of stream habitat and about 250 square miles of estuarine habitat in the San 

Francisco-San Pablo-Suisan Bay estuarine complex and includes stream reaches such as those of 

the Sacramento, Feather, and Yuba Rivers, and Deer, Mill, Battle, and Antelope creeks in the 

Sacramento River basin; the lower San Joaquin River to the confluence with the Merced River, 

including its tributaries, and the waterways of the Delta. The critical habitat is degraded, and 

does not provide the conservation value necessary for species recovery. In addition, the 

Sacramento-San Joaquin River Delta provides very little function necessary for juvenile 

steelhead rearing and smoltification. The spawning PCE is subject to variations in flows and 

temperatures, particularly over the summer months. The rearing PCE is degraded by 

channelized, leveed, and riprapped river reaches, and sloughs common in the Sacramento-San 

Joaquin system. These areas typically have low habitat complexity, low abundance of food 

organisms, offer little protection from fish or avian predators, and commonly have elevated 

temperatures. The current conditions of migration corridors are substantially degraded. Both 

migration and rearing PCEs have reduced water quality from several contaminants introduced by 

dense urbanization and agriculture along the mainstems and in the Delta. In the Sacramento 

River, the migration corridor for both juveniles and adults is obstructed by the Red Bluff 

Diversion Dam gates from May 15 through September 15. The migration PCE is also obstructed 

by complex channel configuration making it difficult for fish to migrate successfully to the 

western Delta and the ocean. State and federal pumps and associated fish facilities alter flows in 

the Delta and impede and obstruct a functioning migration corridor. The estuarine PCE in the 

Delta is affected by contaminants from agricultural and urban runoff and release of wastewater 

treatment plants effluent. However, some complex, productive habitats with floodplains remain 

in the system and flood bypasses (i.e., Yolo and Sutter bypasses).

4.25 Steelhead (Central California Coast DPS)

The Central California Coast steelhead DPS includes all naturally spawned populations of 

steelhead in coastal streams from the Russian River to Aptos Creek; the drainages of San 

Francisco, San Pablo, and Suisun Bays eastward to Chipps Island at the confluence of the 

Sacramento and San Joaquin Rivers; and tributary streams to Suisun Marsh including Suisun 

Creek, Green Valley Creek, and an unnamed tributary to Cordelia Slough (commonly referred to 

as Red Top Creek). The DPS does not include the Sacramento-San Joaquin River Basin of the 

California Central Valley. Two artificial propagation programs are considered to be part of the 

DPS: the Don Clausen Fish Hatchery, and Kingfisher Flat Hatchery/Scott Creek (Monterey Bay 

Salmon and Trout Project). We used information available in status reviews (Good et al. 2005, 

NMFS 2011b), the recovery outline (NMFS 2007a), “An analysis of historical population 
64

structure for evolutionarily significant units of Chinook salmon, coho salmon, and steelhead in 

the North-Central California Coast Recovery Domain” (Bjorkstedt et al. 2005), listing 

documents (61 FR 41541, 62 FR 43937; 71 FR 834), and previously issued biological opinions 

(NMFS 2008a, 2012b) to summarize the status of the species.

4.25.1 Life History

The DPS, like those to the south, is entirely composed of winter-run fish. Adults return to the 

Russian River and migrate upstream from December to April. Most spawning occurs from 

January to April. Smolts emigrate between March and May (Shapovalov and Taft 1954, Hayes et 

al. 2004), typically at one to four years of age, though recent studies indicate that growth rates in 

Soquel Creek likely prevent juveniles from undergoing smoltification until age two (Sogard et al. 

2009). 

4.25.2 Population Dynamics

The Central California Coast steelhead DPS consisted of nine historic functionally independent 

populations and 23 potentially independent populations. Of the historic functionally independent 

populations, at least two are extirpated and most of the remaining populations are nearly 

extirpated. Historically, the entire CCC steelhead DPS may have consisted of an average runs 

size of 94,000 adults in the early 1960s. Information on current steelhead populations in the DPS 

consists of anecdotal, sporadic surveys that are limited to only smaller portions of watersheds.

Though it is not possible to calculate long-term trends for individual watersheds or the entire 

DPS, the limited data that do exist indicate that abundance has declined for all populations 

sampled compared to historical data. Current runs in the basins that originally contained the two 

largest steelhead populations for the DPS, the San Lorenzo and the Russian Rivers, both have 

been estimated at less than 15 percent of their abundances compared to 30 years earlier. The 

interior Russian River winter-run steelhead has the largest runs with an estimate of an average of 

over 1,000 spawners.

4.25.3 Status

NMFS listed the Central California Coast steelhead as threatened on August 18, 1997 (62 FR 

43937), and reaffirmed their status on January 5, 2006 (71 FR 834). Factors contributing to the 

listing of this DPS include the generalized listing factors for West Coast salmon (i.e., destruction 

and modification of habitat, overutilization for recreational purposes, and natural and humanmade factors), as well as the more specific issue of sedimentation and channel restructuring due 

to floods. Spatial structure has been reduced throughout the DPS. Impassible dams have cut off 

substantial portions of habitat in some basins and it is estimated that 22 percent of the DPS’s 

historical habitat has been lost behind (primarily man-made) barriers, including significant 

portions of the upper Russian River. Long-term population sustainability is extremely low for the 

southern populations in the Santa Cruz Mountains and in the San Francisco Bay, and declines in 

juvenile southern populations are consistent with the more general estimates of declining 

abundance in the region. The interior Russian River population may be able to be sustained over 

the long-term, but hatchery management has eroded the population’s genetic diversity. Though 

the information for individual populations is limited, available information strongly suggests that 

no population is viable. Based on these factors, this DPS would likely have a low resilience to 

additional perturbations.
65

4.25.4 Critical Habitat

Designated critical habitat for the Central California coast steelhead DPS includes the Russian 

River watershed, coastal watersheds in Marin County, streams within the San Francisco Bay, and 

coastal watersheds in the Santa Cruz Mountains, southeast to Aptos Creek. The spawning PCE 

have reduced quality throughout the critical habitat; sediment fines in spawning gravel have 

reduced the ability of the substrate attribute to provide well oxygenated and clean water to eggs 

and alevins. The forage PCE has been degraded in some areas where high proportions of fines in 

bottom substrate limit the production of aquatic stream insects adapted to high velocity water.

Elevated water temperatures and impaired water quality have further reduced the quality, 

quantity, and function of the rearing PCE within most streams. These impacts have diminished 

the ability of designated critical habitat to conserve the Central California Coast steelhead.

4.26 Steelhead (Lower Columbia River DPS)

The Lower Columbia River steelhead DPS includes all naturally spawned steelhead populations 

below natural and manmade impassable barriers in streams and tributaries to the Columbia River 

between the Cowlitz and Wind Rivers, Washington, and the Willamette and Hood Rivers, 

Oregon. The DPS also includes seven hatchery populations. We used information available in 

status reviews (Busby et al. 1996, Good et al. 2005, Ford 2011, NMFS 2011d), recovery plans 

(Lower Columbia Fish Recovery Board 2010, Oregon Department of Fish and Wildlife 2010, 

NMFS 2013c), listing documents (61 FR 41541, 63 FR 13347, 71 FR 834), and previously 

issued biological opinions (NMFS 2012b) to summarize the status of the species.

4.26.1 Life History

The Lower Columbia River steelhead DPS includes populations of summer- and winter-run 

steelhead. Summer-run steelhead return sexually immature to the Columbia River from May to 

October, and spend several months in fresh water prior to spawning between February and April.

Winter-run steelhead enter fresh water from December to May at sexual maturity. Peak spawning 

occurs from April to May. Where both races spawn in the same stream, summer-run steelhead 

tend to spawn at higher elevations than winter-run steelhead. Fry emerge from March to July, 

with peaks between April and May. Steelhead smolts generally migrate at ages ranging from one 

to four years, but most smolt after two years in freshwater. Emigration of both summer- and 

winter-run steelhead generally occurs from March to June, with peak migration in April to May.

Both winter- and summer-run adults normally return to freshwater after two years in the ocean.

4.26.2 Population Dynamics

The Lower Columbia River steelhead had 17 historically independent winter-run steelhead 

populations and six independent summer-run steelhead populations (McElhany et al. 2003, 

Myers et al. 2006). All historic populations are considered extant. All populations declined from 

1980 to 2000, with sharp declines beginning in 1995. Historical counts in some of the larger 

tributaries (Cowlitz, Kalama, and Sandy Rivers) suggest the population probably exceeded 

20,000 fish. During the 1990s, fish abundance dropped to 1,000 to 2,000 fish. Recent abundance 

estimates of natural-origin spawners range from extirpation of some populations above 

impassable barriers to over 700 fishes in the Kalama and Sandy winter-run populations. A 

number of the populations have a substantial fraction of hatchery-origin spawners in spawning 

areas. Many of the long-and short-term trends in abundance of individual populations are 

negative.
66

4.26.3 Status and trends

NMFS listed Lower Columbia River steelhead as threatened on March 19, 1998 (63 FR 13347), 

and reaffirmed their status on January 5, 2006 (71 FR 834). Factors contributing to the listing of 

this DPS include the generalized listing factors for West Coast salmon (i.e., destruction and 

modification of habitat, overutilization for recreational purposes, and natural and human-made 

factors), as well as the more specific issue of genetic introgression from hatchery stocks. Spatial 

structure remains relatively high for most populations (Lower Columbia Fish Recovery Board 

2010, Oregon Department of Fish and Wildlife 2010). Except in the North Fork Lewis subbasin, 

where dams have impeded access to historical spawning habitat, most summer-run steelhead 

populations continue to have access to historical production areas in forested, mid- to-highelevation subbasins that remain largely intact. Most populations of winter-run steelhead have 

maintained their spatial structure, though many of these habitats no longer support significant 

production (Lower Columbia Fish Recovery Board 2010, Oregon Department of Fish and 

Wildlife 2010). Out of the 23 populations in this DPS, 16 are considered to have a low or very 

low probability of persisting over the next 100 years, and six populations have a moderate 

probability of persistence (Lower Columbia Fish Recovery Board 2010, Oregon Department of 

Fish and Wildlife 2010). Only the summer-run Wind population is considered viable. The low to 

very low baseline persistence probabilities of most Lower Columbia River steelhead populations 

reflects low abundance and productivity. In addition, it is likely that genetic and life history 

diversity has been reduced as a result of pervasive hatchery effects and population bottlenecks.

Although current Lower Columbia River steelhead populations are depressed compared to 

historical levels and long-term trends show declines, many populations are substantially healthier 

than their salmon counterparts, typically because of better habitat conditions in core steelhead 

production areas (Lower Columbia Fish Recovery Board 2010). Based on these factors, this DPS 

would likely have a moderate resilience to additional perturbations.

4.26.4 Critical Habitat

Designated critical habitat for the Lower Columbia River steelhead DPS includes the following 

subbasins: Middle Columbia/Hood, Lower Columbia/Sandy, Lewis, Lower 

Columbia/Clatskanie, Upper Cowlitz, Cowlitz, Clackamas, and Lower Willamette. The Lower 

Columbia River corridor is also included in the designated critical habitat. Critical habitat is 

affected by reduced quality of rearing and juvenile migration PCEs within the lower portion and 

alluvial valleys of many watersheds. Contaminants from agriculture further affect both water 

quality and food production in these degraded reaches of tributaries and in the mainstem 

Columbia River. Several dams affect adult migration PCE by obstructing the migration corridor.

Watersheds which consist of a large proportion of Federal lands (e.g., the Sandy River 

watershed) have relatively healthy riparian corridors that support attributes of the rearing PCE 

such as cover, forage, and suitable water quality.

4.27 Steelhead (Middle Columbia River DPS)

The Middle Columbia River steelhead DPS includes all naturally spawned steelhead populations 

below natural and manmade impassable barriers in streams from above the Wind River, 

Washington, and the Hood Rivers, Oregon and upstream to, and including, the Yakima River, 

Washington, excluding O. mykiss from the Snake River Basin. The DPS also includes seven 

artificial propagation programs. Steelhead from the Snake River basin (described in Section 6.7) 

are not included in this DPS. We used information available in status reviews (Busby et al. 1996, 

Good et al. 2005, Ford 2011, NMFS 2011e), the recovery plan (NMFS 2009b), listing documents 
67

(63 FR 11798, 64 FR 14517, 71 FR 834), and previously issued biological opinions (NMFS 

2012b) to summarize the status of the species.

4.27.1 Life History

Middle Columbia River steelhead populations are mostly of the summer-run type, with the 

exception of inland winter-run steelhead that occur in the Klickitat River and Fifteenmile Creek. 

Adult summer-run steelhead enter fresh water from June through August and adults may spend 

up to a year in freshwater before spawning. The majority of juveniles smolt and emigrate to the 

ocean as two-year olds. About equal numbers of adults in the DPS return to freshwater after 

spending one or two years in the ocean; however, summer-run steelhead in Klickitat River have a 

life cycle more like Lower Columbia River steelhead where most of returning adults have spent 

two years in the ocean. 

4.27.2 Population Dynamics

The Interior Columbia Technical Review Team identified 16 extant populations in four major 

population groups (Cascades Eastern Slopes Tributaries, John Day River, Walla Walla and 

Umatilla Rivers, and Yakima River) and one extant unaffiliated population (Rock Creek) 

(Interior Columbia Technical Review Team 2003). There are three extirpated populations: two in 

the Cascades Eastern Slope major population group and one in the Walla Walla and Umatilla 

Rivers major population group. Historic run estimates for the Yakima River indicate that annual 

species abundance may have exceeded 300,000 returning adults. The 10-year geometric mean for 

each population ranges from a low of 85 fish (Upper Yakima River) to 1,800 fish (Lower 

Mainstem John Day). The 10-year average proportion of hatchery-origin spawners ranges from 

two percent (Walla Walla Mainstem) to 39 percent (Eastside Deschutes); the majority of 

populations have a hatchery proportion of spawners between six to eight percent. Fifteenmile 

Creek has no hatchery-origin spawners.

4.27.3 Status

NMFS listed Middle Columbia River steelhead as threatened on March 25, 1999 (64 FR 14517), 

and reaffirmed their threatened status on January 5, 2006 (71 FR 834). Factors contributing to 

the listing of this DPS include the generalized listing factors for West Coast salmon (i.e., 

destruction and modification of habitat, overutilization for recreational purposes, and natural and 

human-made factors), as well as impacts from artificial propagation. NMFS considers spatial 

structure and diversity of the DPS to be at moderate risk. Relative to the brood cycle just prior to 

listing (1992 to 1996 spawning year), current brood cycle (five-year geometric mean) natural 

abundance is substantially higher (more than twice) for seven of the populations, lower for three, 

and at similar levels for four populations. Three populations have insufficient data to calculate 

long-term trends. Short-term trends are positive for all but three populations. Viability ratings for 

the 17 populations are: four viable, seven maintained, one highly variable, and five high risk.

Impacts from Tribal fisheries targeting Chinook salmon continue to harvest approximately five 

percent of summer-run steelhead in the Middle Columbia, Upper Columbia, and Snake River 

Basins per year. Based on these factors, this DPS would likely have a moderate resilience to 

additional perturbations.

4.27.4 Critical Habitat

Designated critical habitat for the Middle Columbia River steelhead DPS includes the following 

subbasins: Upper Yakima, Naches, Lower Yakima, Middle Columbia/Lake Wallula, Walla 

Walla, Umatilla, Middle Columbia/Hood, Klickitat, Upper John Day, North Fork John Day, 
68

Middle Fork John Day, Lower John Day, Lower Deschutes, Trout, the Upper Columbia/Priest 

Rapids subbasins, and the Columbia River corridor. The current condition of Middle Columber 

River critical habitat is moderately degraded. Quality of juvenile rearing and migration PCEs has 

been reduced in several watersheds and in the mainstem Columbia River by contaminants from 

agriculture that affect both water quality and food production. Loss of riparian vegetation from 

grazing has resulted in high water temperatures in the John Day basin. Reduced quality of the 

rearing PCEs has diminished its contribution to the conservation value necessary for the recovery 

of the species. Several dams affect adult migration PCE by obstructing the migration corridor.

4.28 Steelhead (Northern California DPS)

The Northern California steelhead DPS includes all naturally spawned steelhead populations 

below natural and manmade impassable barriers in California coastal river basins from Redwood 

Creek southward to, but not including, the Russian River. The DPS also includes two artificial 

propagation programs: the Yeager Creek Hatchery and the North Fork Gualala River Hatchery 

(Gualala River Steelhead Project). We used information available in status reviews (Busby et al. 

1996, Good et al. 2005, NMFS 2011b), the recovery outline (NMFS 2007b), “An analysis of 

historical population structure for evolutionarily significant units of Chinook salmon, coho 

salmon, and steelhead in the North-Central California Coast Recovery Domain” (Bjorkstedt et al. 

2005), “A framework for assessing the viability of Threatened and Endangered Salmon and 

Steelhead in the North-central California Coast Recovery Domain” (Spence et al. 2008), listing 

documents (61 FR 41541, 62 FR 43937; 71 FR 834), and previously issued biological opinions 

(NMFS 2008a, 2012b) to summarize the status of the species.

4.28.1 Life History

This DPS includes both winter- and summer-run steelhead. In the Mad and Eel Rivers, immature 

steelhead may return to fresh water as “half-pounders” after spending only two to four months in 

the ocean. Generally, a half-pounder will overwinter in fresh water and return to the ocean in the 

following spring. Juvenile out-migration appears more closely associated with size than age; 

though juveniles generally, throughout their range in California, spend two years in fresh water.

Smoltification occurs when they are between 14 to 21 cm in length.

4.28.2 Population Dynamics

Historically, this DPS encompassed 42 independent populations of winter-run steelhead (19 

functionally independent and 23 potentially independent) and 10 independent populations of 

summer-run steelhead. All historic populations of winter-run salmon are extant. Of the 10 

summer-run steelhead populations, four are extant and six are assumed to be either extirpated or 

extremely depressed. Long-term data sets are limited for the Northern California steelhead. Prior 

to 1960, estimates of abundance specific to this DPS were available from dam counts. Cape Horn 

Dam in the upper Eel River reported annual average numbers of adults as 4,400 in the 1930s); 

Benbow Dam in the South Fork Eel River reported annual averages of 19,000 in the 1940s; and 

the Sweasey Dam in the Mad River reported annual averages of 3,800 in the 1940s. Estimates of 

steelhead spawning populations for many rivers in this DPS totaled 198,000 by the mid-1960s.

For winter-run populations that have had recent counts, returns have not exceeded more than a 

few hundred fish, with the exception of a portion of the Gualala River population (counts of 

adult steelhead have averaged 1,915 fish) and at the Mad River Hatchery (average of 2,300 

adults). The only summer-run steelhead population with a comprehensive time series of 

abundance is the Middle Fork Eel River, which has been monitored since the mid-1960s. Counts 
69

have averaged 780 fish over the period of record and 609 fish in the past 16 years. Both shortterm and long-term trends are negative, though not significantly.

4.28.3 Status

NMFS listed Northern California steelhead as threatened on June 7, 2000 (65 FR 36074), and 

reaffirmed their status on January 5, 2006 (71 FR 834). Factors contributing to the listing of this 

DPS include the generalized listing factors for West Coast salmon (i.e., destruction and 

modification of habitat, overutilization for recreational purposes, and natural and human-made 

factors), as well as the more specific issue of the introduction of a salmonid predator, the 

Sacramento pikeminnow (formerly known as Sacramento squawfish [Ptychocheilus grandis], 

and concern about the influence of hatchery stocks on native fish (i.e., genetic introgression and 

ecological interactions). Overall, spatial structure of the DPS is relatively intact and all diversity 

strata appear to be represented by extant populations. However, spatial structure and distribution 

within most watersheds has been adversely affected by barriers and high water temperatures. The 

scarcity of time series of abundance at the population level spanning more than a few years 

hinders assessment of the DPS’s status; population level estimates of abundance are available for 

four of the 42 winter-run populations and for one of the 10 summer-run populations. Trend 

information from the available datasets suggests a mixture of patterns, with slightly more 

populations showing declines than increases, though few of these trends are statistically 

significant. Where population level estimates of abundance are available, only the Middle Fork 

Eel River summer-run populations are considered to have a low-risk of extinction. The 

remaining populations for which adult abundance has been estimated appear to be at either 

moderate- or high-risk of extinction. Although surveys within the summer-run steelhead 

watersheds do not encompass all available summer habitats, the chronically low numbers 

observed during surveys suggest that those populations are likely at high risk of extinction. The 

high number of hatchery fish in the Mad River basin, coupled with uncertainty regarding relative 

abundances of hatchery and wild spawners is also of concern. Based on these factors, this DPS 

would likely have a low resilience to additional perturbations.

4.28.4 Critical Habitat

Designated critical habitat for the Northern California steelhead DPS includes the following 

CALWATER hydrological units: Redwood Creek, Trinidad, Mad River, Eureka Plain, Eel River, 

Cape Mendocino, and the Mendocino Coast. The total area of critical habitat includes about 

3,000 miles of stream habitat and about 25 square miles of estuarine habitat, mostly within 

Humboldt Bay. The current condition of designated critical habitat is moderately degraded.

Portions of the rearing PCE, especially the interior Eel River, are affected by elevated 

temperatures from riparian vegetation removal. Spawning PCE attributes (i.e., the quality of 

substrate that supports spawning, incubation, and larval development) have been generally 

degraded throughout designated critical habitat by silt and sediment fines. The adult migration 

PCE function has been reduced by bridges and culverts that restrict access to tributaries in many 

watersheds, especially in watersheds with forest road construction.

4.29 Steelhead (Puget Sound DPS)

This Puget Sound DPS includes all naturally-spawned anadromous winter-run and summer-run 

steelhead in the river basins of Strait of Juan de Fuca, Puget Sound, and Hood Canal, 

Washington. The DPS is bounded to the west by the Elwha River (inclusive) and to the north by 

the Nooksack River and Dakota Creek (inclusive). Hatchery production of steelhead is 
70

widespread throughout the DPS, but only two artificial propagation programs are included in the 

DPS. On June 26, 2013, NMFS proposed to change the number of artificial propagation 

programs included in the DPS to six (78 FR 38270). We used information available in status 

reviews (NMFS 2005b, 2007e, Ford 2011, NMFS 2011g), the recovery outline (NMFS 2013d), 

and previously issued biological opinions (NMFS 2012b) to summarize the status of the species.

4.29.1 Life History

The Puget Sound steelhead DPS contains both winter-run and summer-run steelhead, but is 

dominated by winter-run fish. Adult winter-run steelhead generally return to Puget Sound 

tributaries from December to April. Spawning occurs from January to mid-June and peaks from 

mid-April through May. Less information exists for summer-run steelhead as their smaller run 

size and higher altitude headwater holding areas have not been conducive for monitoring. Based 

on information from four streams, adult run time occurs from mid-April to October with a higher 

concentration from July to September. The majority of juveniles reside in the river system for 

two years with a minority migrating to the ocean as one or three-year olds. Smoltification and 

seaward migration occur from April to mid-May. Puget Sound steelhead spend one to three years 

in the ocean before returning to freshwater (Busby et al. 1996). Due to the protection of the 

fjord-like marine environment of Puget Sound, juveniles and adults may hold there during 

emigration and immigration.

4.29.2 Population Dynamics

Fifty-three populations of steelhead have been identified in this DPS, of which 37 are winter-run.

In the early 1980s, run size for this DPS was calculated at about 100,000 winter-run fish and 

20,000 summer-run fish. Available data for calculating abundance and trends are not 

comprehensive for the DPS, primarily represent winter-run steelhead populations, and date from 

1985. Since 1985 Puget Sound winter-run steelhead abundance has shown a widespread 

declining trend over much of the DPS. Four of the 16 winter-run populations evaluated exhibit 

estimates of long-term population positive growth rates, only one significantly. Thirteen winterrun steelhead populations have sufficient data to determine recent annual abundances (2005 to 

2009). Of the 13 populations, two have geometric mean abundances greater than 4,500 fish 

annually. The remaining populations have low geometric mean abundances; none exceeds 1,000 

fish annually and only two populations exceed 500 fish annually.

4.29.3 Status

NMFS listed Puget Sound steelhead as threatened on May 11, 2007 (72 FR 26722). Factors 

contributing to the listing of this DPS include habitat loss and degradation from damming, 

agricultural practices, and urbanization; historic overexploitation; predation; poor oceanic and 

climatic conditions; and impacts from artificial propagation. Spatial structure, complexity, and 

connectivity have been reduced throughout the DPS. Most populations of steelhead in Puget 

Sound have declining estimates of mean population growth rates (typically three to 10 percent 

annually) and extinction risk within 100 years for most populations is estimated to be moderate 

to high. Effects of hatchery fish on the natural populations remain unknown. Based on these 

factors, this DPS would likely have a low resilience to additional perturbations.

4.29.4 Critical Habitat

NMFS proposed designation of critical habitat for the Puget Sound steelhead on January 14, 

2013 (78 FR 2725). Designated critical habitat would include approximately 1,880 mi (3,026 

km) of freshwater and estuarine habitat in Puget Sound, Washington, and exclude a number of 
71

areas from designation. Notable is the proposed exclusion of nearshore areas. Though the 

physical or biological features of critical habitat proposed for Puget Sound steelhead are the 

same as those designated for Puget Sound Chinook and Hood Canal summer-run chum, 

watershed conservation values for steelhead may be different because of differences in 

population structure and habitat use.

4.30 Steelhead (Snake River DPS)

The Snake River basin steelhead DPS includes all naturally spawned steelhead populations 

below natural and man-made impassable barriers in streams in the Columbia River Basin 

upstream from the Yakima River, Washington, to the U.S./Canada border. Six artificial 

propagation programs are also included in the DPS. We used information available in status 

reviews reviews (Good et al. 2005, Ford 2011, NMFS 2011i), listing documents (62 FR 43937, 

71 FR 834), and previously issued biological opinions (NMFS 2012b) to summarize the status of 

the species.

4.30.1 Life History

Snake River basin steelhead are generally classified as summer-run fish. They return to the 

Columbia River from late June to October and spawn the following spring (March to May). Two 

life history patterns are recognized within the DPS, primarily based on ocean age and adult size 

upon return: A-run and B-run. A-run steelhead are typically smaller, have shorter freshwater and 

ocean residences (generally one year in the ocean), and begin their up-river migration earlier in 

the year. B-run steelhead are larger, spend more time in fresh water and the ocean (generally two 

years in ocean), and appear to start upstream migration later in the year. Snake River basin 

steelhead smoltification usually occurs at two to three years of age.

4.30.2 Population Dynamics

The Interior Columbia Technical Review Team identified six historical major population groups 

in the Snake River steelhead DPS: Clearwater River, Salmon River, Grande Ronde River, 

Imnaha River, Lower Snake River, and Hells Canyon Tributaries. The Hells Canyon population 

is now extirpated; construction of Hells Canyon Dam blocked passage of upstream of the dam.

The five extant major population groups support 24 extant independent populations (Interior 

Columbia Technical Review Team 2003). Population data are lacking for the Snake River 

steelhead DPS. Annual return estimates are limited to counts of the aggregate return (both A-run 

and B-run steelhead) over Lower Granite Dam, estimates for two populations in the Grande 

Ronde major population group, and index area or weir counts for portions of several other 

populations. The recent geometric five-year mean abundance (2003 to 2008) for Lower Granite 

Dam was 18,847 natural-origin returning adults. This natural origin return average represented 

10 percent of total returns (of both natural and artificial origin fish) over Lower Granite Dam.

The previous five-year geometric mean abundance (1997 to 2001) was 10,693 natural-origin 

returning adults and represented 13 percent of total returns. The five-year periods for the two 

Grande Ronde populations for which population-level abundance data series are available are the 

same as above. The recent five-year geometric mean abundance of natural origin steelhead for 

the Joseph Creek population was 1,925 fish compared to 2,134 fish for the previous five-year 

period. These returns are made up entirely of natural origin fish. The recent five-year geometric 

mean abundance of natural origin steelhead for the Upper Grande Ronde River was 1,425 fish 

compared to 1,332 fish for the previous five-year period. The returns represent 99 and 76 percent 

of total returns, respectively.
72

4.30.3 Status

NMFS listed Snake River Basin steelhead as threatened on August 18, 1997 (62 FR 43937), and 

reaffirmed their status on January 5, 2006 (71 FR 834). Factors contributing to the listing of this 

DPS include the generalized listing factors for West Coast salmon (i.e., destruction and 

modification of habitat, overutilization for recreational purposes, and natural and human-made 

factors), and, more specifically, widespread habitat blockage from hydrosystem management and 

potentially deleterious genetic effects from straying and introgression from hatchery fish. The 

level of natural production in the two populations with full data series and one of the index areas 

is encouraging, but the status of most populations in the DPS remains highly uncertain. The DPS 

is not currently considered to be viable due to high risk population ratings, uncertainty about the 

viability status of many populations, and overall lack of population data. A great deal of 

uncertainty remains regarding the relative proportion of hatchery fish in natural spawning areas 

near major hatchery release sites. Based on these factors, this DPS would likely have a low 

resilience to additional perturbations.

4.30.4 Critical Habitat

Designated critical habitat for the Snake River Basin steelhead DPS includes the following 

subbasins: Hells Canyon, Imnaha River, Lower Snake/Asotin, Upper Grand Ronde River, 

Wallowa River, Lower Grand Ronde, Lower Snake/Tucannon, Upper Salmon, Pahsimeroi, 

Middle Salmon-Panther, Lemhi, Upper Middle Fork Salmon, Lower Middle Fork Salmon, 

Middle Salmon, South Fork Salmon, Lower Salmon, Little Salmon, Upper and Lower Selway, 

Lochsa, Middle and South Fork Clearwater, and the Clearwater subbasins, and the Lower 

Snake/Columbia River corridor. The current condition of critical habitat designated for Snake 

River basin steelhead is moderately degraded. Critical habitat is affected by reduced quality of 

juvenile rearing and migration PCEs within many watersheds. Contaminants from agriculture 

affect both water quality and food production in several watersheds and in the mainstem 

Columbia River. Loss of riparian vegetation to grazing has resulted in high water temperatures in 

the John Day basin. These factors have substantially reduced the rearing PCEs’ contribution to 

the conservation value necessary for species recovery. Several dams affect adult migration PCE 

by obstructing the migration corridor.

4.31 Steelhead (South-central California Coast DPS)

The South-central California coast steelhead DPS includes all naturally spawned steelhead 

populations in streams from the Pajaro River watershed (inclusive) to, but not including, the 

Santa Maria River, (71 FR 5248) in northern Santa Barbara County, California. There are no 

artificially propagated steelhead stocks within the range of the DPS. We used information 

available in status reviews reviews (Busby et al. 1996, Good et al. 2005, NMFS 2011j, Williams 

et al. 2011), the recovery plan (NMFS 2013f), “Steelhead of the South-central/Southern 

California coast: population characterization for recovery planning” (Boughton et al. 2006), 

“Viability criteria for steelhead of the South-central and Southern California Coast” (Boughton et 

al. 2007), listing documents (61 FR 41541, 62 FR 43937; 71 FR 834), and previously issued 

biological opinions (NMFS 2012b, 2013a) to summarize the status of the species.

4.31.1 Life History

NMFS recognizes two life-history types of winter-run steelhead in the South-central California 

coast DPS: fluvial-anadromous and lagoon-anadromous. Freshwater resident steelhead (rainbow 

trout) are not included in the DPS. Fluvial-anadromous fish spend one or two summers 
73

(occasionally more) in freshwater streams as juveniles, then smolt and migrate to the ocean, 

using the estuary only for acclimation to saltwater and as a migration corridor (and occasionally 

for spring feeding). Lagoon-anadromous fish spend either their first or second summer as 

juveniles in a seasonal lagoon at the mouth of a stream. Adults of both winter-run types spend 

two to three years in the ocean before returning to freshwater.

4.31.2 Population Dynamics

The steelhead populations in this region have declined dramatically from estimated annual runs 

totaling 27,000 adults near the turn of the 19th century to approximately 4,740 adults in 1965, 

with a large degree of inter-annual variability. These run-size estimates are based on information 

from only five major watersheds in the northern portion of the DPS. Run-size estimates from 

coastal and inland watersheds south of the Big Sur have not been estimated or recorded. Only 

one population in the DPS has sufficient data to compute a trend for adult escapement, the 

Carmel River above San Clemente Dam. This population experienced a decline of 22 percent per 

year from 1963 to 1993 and an average five-year adult count of 16 adult spawners. The most 

recent counts (2012 to 2013) in the Carmel River indicate 452 adults at the San Clemente Dam 

and 204 adults at the Los Padres Dam.

4.31.3 Status

NMFS listed South-Central California Coast steelhead as threatened August 18, 1997 (62 FR 

43937), and reaffirmed their status on January 5, 2006 (71 FR 834). Factors contributing to the 

listing of this DPS include the generalized listing factors for West Coast salmon (i.e., destruction 

and modification of habitat, overutilization for recreational purposes, and natural and humanmade factors), as well as the more specific concerns about genetic effects from widespread 

stocking of rainbow trout. The DPS consists of 12 discrete sub-populations which represent 

localized groups of interbreeding individuals. None of these sub-populations are considered to be 

viable. Most of the sub-populations are characterized by low population abundance, variable or 

negative population growth rates, and reduced spatial structure and diversity. Though steelhead 

are present in most streams in the DPS, their populations are small, fragmented, and unstable, or 

more vulnerable to stochastic events. In addition, severe habitat degradation and the 

compromised genetic integrity of some populations pose a serious risk to the survival and 

recovery of the DPS. The DPS is in danger of extinction. Based on these factors, this DPS would 

likely have a low resilience to additional perturbations.

4.31.4 Critical Habitat

Designated critical habitat for the South-Central California coast steelhead DPS includes the 

following CALWATER hydrological units: Pajaro River, Carmel River, Santa Lucia, Salinas 

River and Estero Bay. Migration and rearing PCEs are degraded throughout designated critical 

habitat by elevated stream temperatures and contaminants from urban and agricultural areas. The 

estuarine PCE is impacted due to breaching of estuarine areas, removal of structures, and 

contaminants.

4.32 Steelhead (Southern California DPS)

The Southern California Steelhead DPS includes all naturally spawned populations of steelhead 

in streams from the Santa Maria River, San Luis Obispo County, California (inclusive) to the 

U.S.-Mexico Border (62 FR 43937; 67 FR 21586). No artificially propagated steelhead stocks 

are currently recognized within the range of the DPS; however, two artificial propagation 
74

programs, the Don Clausen Fish Hatchery and the Kingfisher Flat Hatchery (Monterey Bay 

Salmon and Trout Project) have been proposed for inclusion in the DPS, as they were 

inadvertently omitted from the original listing (78 FR 38270). We used information available in 

status reviews (Busby et al. 1996, Good et al. 2005, NMFS 2011k, Williams et al. 2011), the 

recovery plan (NMFS 2012f), “Contraction of the southern range limit for anadromous 

Oncorhynchus mykiss” (Boughton et al. 2005), listing documents (62 FR 43937; 71 FR 834), and 

previously issued biological opinions (NMFS 2012b, 2013b) to summarize the status of the 

species.

4.32.1 Life History

Life history of the Southern California Steelhead is similar to that of the South-Central California 

Coast steelhead; see Section 4.31.1 for additional information.

4.32.2 Population Dynamics

Limited information exists for Southern California steelhead runs. Run‐size estimates from 

coastal and inland watersheds south of the Los Angeles Watershed have generally not been 

estimated or recorded and no long term (greater than 20 years) time‐series data are available for 

any of the populations. Based on combined estimates for only four major watersheds in the 

northern portion of the DPS, steelhead runs declined from estimated historic levels of 32,000 to 

46,000 adults to less than 500 adults in 1996. More recent counts from various monitoring 

locations in the DPS have reported very small runs of less than 10 fish, with the exception of a 

monitoring location in Santa Ynez River that reported 16 adults in 2008.

4.32.3 Status

NMFS listed the Southern California steelhead as endangered on August 18, 1997 (62 FR 

43937), and reaffirmed their status on January 5, 2006 (71 FR 834). Factors contributing to the 

listing of this DPS include the generalized listing factors for West Coast salmon (i.e., destruction 

and modification of habitat, overutilization for recreational purposes, and natural and humanmade factors), as well as the more specific concern about the widespread, dramatic declines in 

abundance relative to historical levels. Construction of dams and a corresponding increase in 

water temperatures have excluded steelhead distribution in many watersheds throughout southern 

California. Streams in southern California containing steelhead have declined over the last 

decade, with a southward proportional increase in loss of populations. Consequently, the DPS 

has experienced a contraction of its southern range. This range contraction affects the DPS’s 

ability to maintain genetic and life history diversity for adaptation to environmental change. The 

2005 status review concluded the chief causes for the DPS’s decline include urbanization, water 

withdrawals, channelization of creeks, human-made barriers to migration, and the introduction of 

exotic fishes and riparian plants. The most recent status review indicates these threats are 

essentially unchanged and the species remains in danger of extinction. Based on these factors, 

this DPS would likely have a very low resilience to additional perturbations.

4.32.4 Critical Habitat

Designated critical habitat for the Southern California steelhead DPS includes the following 

CALWATER hydrological units: Santa Maria River, Santa Ynez, South Coast, Ventura River, 

Santa Clara Calleguas, Santa Monica Bay, Callequas and San Juan hydrological units. All PCEs 

have been affected by degraded water quality by pollutants from densely populated areas and 

agriculture within the DPS. Elevated water temperatures impact rearing and juvenile migration 

PCEs in all river basins and estuaries. Rearing and spawning PCEs have been affected 
75

throughout the DPS by water management or reduction in water quantity. The spawning PCE has 

been affected by the combination of erosive geology features and land management activities 

that have resulted in excessive fines in spawning gravel of most rivers.

4.33 Steelhead (Upper Columbia River DPS)

The Upper Columbia River steelhead DPS includes all naturally spawned steelhead populations 

below natural and man-made impassable barriers in streams in the Columbia River basin 

upstream from the Yakima River, Washington, to the U.S.-Canada border. The DPS also 

includes six artificial propagation programs. We used information available in status reviews 

reviews (Good et al. 2005, Ford 2011, NMFS 2011m), the recovery plan (Upper Columbia 

Salmon Recovery Board 2007), listing documents (62 FR 43937; 71 FR 834; 74 FR 42605), and 

previously issued biological opinions (NMFS 2012b) to summarize the status of the species.

4.33.1 Life History

All Upper Columbia River steelhead are summer-run fish. Adults return in the late summer and 

early fall. Most adults migrate quickly to their natal tributaries, though a portion of returning 

adults overwinter in mainstem reservoirs, beyond upper-mid-Columbia dams in April and May 

of the following year. Spawning occurs in the late spring of the year following river entry.

Juvenile steelhead spend one to seven years rearing in fresh water before migrating to sea. Smolt 

emigrate primarily at ages two and three, though some smolts in the DPS have been reported at 

ages up to seven. Most adult steelhead return to fresh water after one or two years in the ocean.

4.33.2 Population Dynamics

The Upper Columbia River steelhead consists of five historic independent populations, four of 

which are extant (Wenatchee, Entiat, Methow, and Okanogan) and one that is functionally 

extinct (Crab Creek). Two additional major population groups likely existed prior to the 

construction of Grand Coulee and Chief Joseph dams. No direct counts of adult steelhead in the 

DPS are available prior to dam construction. Estimates of spawning escapement for all four 

extant populations are available through the 2008/2009 cycle year, along with preliminary 

estimates of the aggregate counts over Priest Rapids Dam for the 2009/2010 cycle year. The 

most recent five-year geometric mean abundance (2005 to 2009) of natural origin fish ranges 

from 116 to 819 adults in the four populations and is 3,604 adults for the aggregate count. These 

abundances represent nine to 47 percent of total spawner abundances (natural origin and hatchey 

origin). The most recent five-year average of percent of natural origin fish for the aggregate 

count is 19 percent.

4.33.3 Status

NMFS originally listed Upper Columbia River steelhead as endangered on August 18, 1997 (62 

FR 43937). NMFS changed the listing to threatened on January 5, 2006 (71 FR 834). After 

litigation resulting in a change in the DPS’ status to endangered and then again to threatened. On 

August 24, 2009, NMFS reaffirmed the species’ status as threatened (74 FR 42605). Factors 

contributing to the listing of this DPS include the generalized listing factors for West Coast 

salmon (i.e., destruction and modification of habitat, overutilization for recreational purposes, 

and natural and human-made factors), as well as the more specific issues of extremely low 

estimates of adult replacement ratios, habitat degradation, juvenile and adult mortality in the 

hydrosystem, unfavorable marine and freshwater environmental conditions, overharvest, and 

genetic homogenization from composite broodstock collections. Though steelhead in the DPS 
76

must pass over several dams to access spawning areas, three of the four populations are rated as 

low risk for spatial structure. The proportions of hatchery-origin returns in natural spawning 

areas remain extremely high across the DPS and continue to be a major concern. Though there 

has been an increase in abundance and productivity for all populations, the improvements have 

been minor, and none of the populations meet recovery criteria. All populations remain at high 

risk of extinction and the DPS, as a whole, is not viable. Based on these factors, this DPS would 

likely have a low resilience to additional perturbations.

4.33.4 Critical Habitat

Designated critical habitat for the Upper Columbia River steelhead DPS includes the following 

subbasins: Chief Joseph, Okanogan, Similkameen, Methow, Upper Columbia/Entiat, Wenatchee, 

Lower Crab, and the Upper Columbia/Priest Rapids subbasins, and the Columbia River corridor.

Currently, designated critical habitat is moderately degraded. Habitat quality in tributary streams 

varies from excellent in wilderness and roadless areas, to poor in areas subject to heavy 

agricultural and urban development. The water quality and food production features of juvenile 

rearing and migration PCEs in several watersheds and the mainstem Columbia River have been 

degraded by contaminants from agriculture. Several dams affect the adult migration PCE by 

obstructing the migration corridor.

4.34 Steelhead (Upper Willamette River DPS)

The UWR steelhead DPS includes all naturally spawned winter-run steelhead populations below 

natural and manmade impassable barriers in the Willamette River, Oregon, and its tributaries 

upstream from Willamette Falls to the Calapooia River (inclusive). No artificially propagated 

populations are included in the DPS. Hatchery summer-run steelhead occur in the Willamette 

Basin, but they are an out-of-basin population and not included in the DPS. We used information 

available in status reviews reviews (Busby et al. 1996, Good et al. 2005, Ford 2011, NMFS 

2011n), the recovery plan (Oregon Department of Fish and Wildlife and NMFS 2011), listing 

documents (64 FR 14517; 71 FR 834), and previously issued biological opinions (NMFS 2012b)

to summarize the status of the species.

4.34.1 Life History

Native steelhead in the Upper Willamette are late-migrating winter-run fish. Steelhead enter 

fresh water in January and February (Howell et al. 1985), but do not ascend to spawning areas 

until late March or April, later than other winter-run steelhead. Spawning occurs from April to

June. The majority of juveniles smolt and emigrate after two years. Peak smolt emigration past 

Willamette Falls occurs from early April to early June, with a peak in early- to mid-May (Howell 

et al. 1985). Smolts generally migrate through the Columbia River via Multnomah Channel 

rather than the mouth of the Willamette River. Most adults return to fresh water after spending 

two years in the ocean

4.34.2 Population Dynamics

Four basins on the east side of the Willamette River historically supported independent steelhead 

populations, all of which remain extant. There is intermittent spawning and rearing in tributaries on 

the west side of the Willamette River, but these areas are not considered to be independent 

populations. Because native winter-run steelhead also return outside of the DPS boundaries, 

Willamette Falls counts represent the best estimate for the DPS abundance. The average number of 

steelhead passing Willamette Falls in the 1990s was less than 5,000 fish. The number increased 

to over 10,000 fish in 2001 and 2002. The geometric and arithmetic mean number of steelhead 
77

passing Willamette Falls for the period 1998 to 2001 were 5,819 and 6,795 fish, respectively.

More recent abundances have declined. The total abundance of steelhead at Willamette Falls in 

2008 was 4,915 adults. In 2009, the abundance was 2,110 fish.

4.34.3 Status

NMFS originally listed Upper Willamette steelhead as threatened on March 25, 1999 (64 FR 

14517), and reaffirmed their status on January 5, 2006 (71 FR 834). Factors contributing to the 

listing of this DPS include the generalized listing factors for West Coast salmon (i.e., destruction 

and modification of habitat, overutilization for recreational purposes, and natural and humanmade factors), as well as the more specific issues of damming, water diversions, poor ocean 

conditions and overharvest. Though access to historical spawning grounds has been lost behind 

dams, the DPS remains spatially well-distributed. Three populations are considered to be in the 

moderate to high risk category for spatial structure and one is in the low risk category. The DPS 

continues to demonstrate an overall low abundance pattern. The elimination of winter-run hatchery 

releases reduces threats from artificial propagation, but non-native summer steelhead hatchery 

releases are still a concern. Human population growth within the Willamette Basin continues to be a 

significant risk factor for the populations. This DPS remains at a moderate risk of extinction. Based 

on these factors, this DPS would likely have a moderate resilience to additional perturbations.

4.34.4 Critical Habitat

Designated critical habitat for the Upper Willamette River steelhead DPS includes all Columbia 

River estuarine areas and river reaches proceeding upstream to the confluence with the 

Willamette River and specific stream reaches in the subbasins: Upper Willamette, North 

Santiam, South Santiam, Middle Willamette, Molalla/Pudding, Yamhill, Tualatin, and Lower 

Willamette. Designated critical habitat is currently degraded. The water quality and food 

production features of juvenile rearing and migration PCEs in several watersheds and the 

mainstem Columbia River have been degraded by contaminants from agriculture. Several dams 

affect the adult migration PCE by obstructing the migration corridor.

5 Eulachon

Eulachon are small smelt native to eastern North Pacific waters from the Bering Sea to Monterey 

Bay, California, or from 61o N to 31o N (Hart and McHugh 1944, Eschmeyer et al. 1983, 

Minckley et al. 1986, Hay and McCarter 2000) . 

5.1 Eulachon (Southern DPS)

Eulachon that spawn in rivers south of the Nass River of British Columbia to the Mad River of 

California comprise the southern DPS of eulachon. This species is designated based upon timing 

of runs and genetic distinctions (Hart and McHugh 1944, McLean et al. 1999, Hay and McCarter 

2000, McLean and Taylor 2001, Beacham et al. 2005) . 

5.1.1 Life History

Adult eulachon are found in coastal and offshore marine habitats (Allen and Smith 1988, Hay 

and McCarter 2000, Willson et al. 2006) . Larval and post larval eulachon prey upon 

phytoplankton, copepods, copepod eggs, mysids, barnacle larvae, worm larvae, and other 

eulachon larvae until they reach adult size (WDFW and ODFW 2001). The primary prey of adult 

eulachon are copepods and euphausiids, malacostracans and cumaceans (Smith and Saalfeld 
78

1955, Barraclough 1964, Drake and Wilson 1991, Sturdevant et al. 1999, Hay and McCarter 

2000) .

Although primarily marine, eulachon return to freshwater to spawn. Adult eulachon have been 

observed in several rivers along the west coast (Odemar 1964, Moyle 1976, Minckley et al. 

1986, Emmett et al. 1991, Jennings 1996, Wright 1999, Larson and Belchik 2000, Musick et al. 

2000, WDFW and ODFW 2001). For the southern population of eulachon, most spawning is 

believed to occur in the Columbia River and its tributaries as well as in other Oregonian and 

Washingtonian rivers (Emmett et al. 1991, Musick et al. 2000, WDFW and ODFW 2001). 

Eulachon take less time to mature and generally spawn earlier in southern portions of their range 

than do eulachon from more northerly rivers (Clarke et al. 2007). 

Spawning is strongly influenced by water temperatures, so the timing of spawning depends upon 

the river system involved (Willson et al. 2006). In the Columbia River and further south, 

spawning occurs from late January to March, although river entry occurs as early as December 

(Hay and McCarter 2000) . Further north, the peak of eulachon runs in Washington State is from 

February through March while Alaskan runs occur in May and river entry may extend into June 

(Hay and McCarter 2000) . Females lay eggs over sand, course gravel or detritial substrate. Eggs 

attach to gravel or sand and incubate for 30 to 40 days after which larvae drift to estuaries and 

coastal marine waters (Wydoski and Whitney 1979) . 

Eulachon generally die following spawning (Scott and Crossman 1973). The maximum known 

lifespan is 9 years of age, but 20 to 30% of individuals live to 4 years and most individuals 

survive to 3 years of age, although spawning has been noted as early as 2 years of age (Wydoski 

and Whitney 1979, Barrett et al. 1984, Hugg 1996, Hay and McCarter 2000, WDFW and ODFW 

2001) . The age distribution of spawners varies between river and from year-to-year (Willson et 

al. 2006). 

5.1.2 Population Dynamics

Microsatellite genetic work, in addition to other biological data including the number of 

vertebrae size at maturity, fecundity, river-specific spawning times, and population dynamics 

(Gustafson et al. 2010) appears to confirm the existence of significant differentiation among 

populations in the southern DPS of eulachon. NOAA Fisheries’ eulachon Biological Review 

Team separated the DPS into four subpopulations (Gustafson et al. 2010). These are the Klamath 

River (including the Mad River and Redwood Creek), the Columbia River (including all of its 

tributaries upstream to RM 180), the Fraser River, and the British Columbia coastal rivers (north 

of the Fraser River up to, and including, the Skeena River). 

Abundance declines have occurred in the Fraser and other coastal British Columbia rivers (Hay 

and McCarter 2000, Moody 2008). Over a three-generation span of 10 years (1999 to 2009), the 

overall Fraser River eulachon population biomass has declined by nearly 97% (Gustafson et al. 

2010). In 1999, the biomass estimates were 418 metric tons, and by 2010 had dropped to just 4 

metric tons. Abundance information is lacking for many coastal British Columbia sub-area 

populations, but Gustafson et al. (2010) found that eulachon runs were universally larger in the 

past. 

The Columbia River (including all of its tributaries upstream to RM 180) supports the largest 

known eulachon run. Although direct estimates of adult spawning stock abundance are limited, 

commercial fishery landing records begin in 1888 and continue as a nearly uninterrupted data set 

to 2010 (Gustafson et al. 2010). From about 1915 to 1992, historical commercial catch levels 
79

were typically more than 500 metric tons (500 metric tons equals approximately 12,728,100 fish 

at 11.55 fish per pound), occasionally exceeding 1,000 metric tons. In 1993, eulachon catch 

levels began to decline and averaged less than 5 metric tons from 2005 to 2008 (Gustafson et al. 

2010). 

From 2003 through 2013, the Fraser River eulachon population in Canada is estimated at 

676,599 to 908,966 (median values) adults (COSEWIC 2011). Beginning in 2010, ODFW and 

WDFW began eulachon biomass surveys similar to those conducted on the Fraser River. Based 

on the three years of available data that have been collected and analyzed, WDFW calculated a 

median spawner estimate of 37 million eulachon in the Columbia River in 2011 (range 

18,000,000 to 70,000,000 spawners), 34 million in 2012 (range 19,000,000 to 60,000,000 

spawners), and 110,000,000 million spawners in 2013 (range 45,000,000 to 200,000,000). 

The egg and larvae production estimates for the 2010-2011 sample-years calculated a minimum 

estimate of 300,000,000,000 (range 1,100,000,000,000 to 300,000,000,000, with a median 

estimate of 590,000,000,000) egg and larvae for the Columbia River Basin population. The egg 

and larvae production estimates for the 2011-2012 sample-year provided by WDFW calculated a 

minimum estimate of 330,000,000,000 (range 1,000,000,000,000 to 330,000,000,000, with a 

median estimate of 580,000,000,000) egg and larvae for the Columbia River Basin population. 

The egg and larvae production estimates for the 2012-2013 sample-year provided by WDFW 

calculated a minimum estimate of 710,000,000,000 (range 3,200,000,000,000,000 to 

330,000,000,000, with a median estimate of 1,700,000,000,000) egg and larvae for the Columbia 

River Basin population.

There are no long-term eulachon monitoring programs in Northern California. Large eulachon 

spawning aggregations once occurred regularly in the Klamath River, but abundance has 

declined substantially (Fry Jr. 1979, Moyle et al. 1995, Larson and Belchik 1998, Hamilton et al. 

2005). Recent reports from Yurok tribal fisheries biologists report capturing adult eulachon in 

presence/absence surveys (seine/dip nets) in the Klamath River over a four-year period [2011 (7 

eulachon), 2012 (40 eulachon), 2013 (112 eulachon), and 2014 (±1000 eulachon)]. All 

egg/larvae capture via plankton net tows in the Klamath River during this same period were 

determined not to be eulachon.

5.1.3 Status

The southern DPS of eulachon was listed as threatened on March 18, 2010 (75 FR 13012). The 

primary factors responsible for the decline of eulachon are the destruction, modification, or 

curtailment of habitat and inadequacy of existing regulatory mechanisms. Under the Species at 

Risk Act, Canada designated the Fraser River population as endangered in May 2011 because of 

a 98% decline in spawning stock biomass over the previous 10 years (COSEWIC 2011). The 

eulachon Biological Review Team was concerned that four out of seven coastal British 

Columbia spawning groups may be at risk of extirpation as a result of phenomena associated 

with small populations and random genetic effects (Gustafson et al. 2010).

There are few direct estimates of eulachon abundance. Escapement counts and spawning stock 

biomass estimates are only available for a small number of systems, and catch statistics from 

commercial and tribal fisheries are available for others. However, inferring population status or 

even trends from yearly catch-statistic changes requires assumptions that are difficult to 

corroborate (e.g., assuming that harvest effort and efficiency are similar from year to year, 
80

assuming a consistent relationship among the harvested and total stock portion, and certain 

statistical assumptions, such as random sampling). However, the combination of catch records 

and anecdotal information indicates that there were large eulachon runs in the past, which have 

severely declined. As a result, eulachon numbers are at, or near, historically low levels 

throughout the range of the southern DPS.

Although landings can be biased by level of fishing effort, evidence of persistent low eulachon 

returns as well as landings in the Columbia River from 1993 to 2000 prompted the states of 

Oregon and Washington to adopt a Joint State Eulachon Management Plan (WDFW and ODFW 

2001). All recreational and commercial fisheries for eulachon were closed in Washington and 

Oregon in 2011. However, in 2014, WDFW and ODFW opened a limited-duration recreational 

and commercial fishery for eulachon.

The Biological Review Team was concerned about risks to eulachon diversity because of data 

suggesting that Columbia River and Fraser River spawning stocks may be limited to a single age 

class combined with the species’ semelparous life history (individuals spawn once and die). 

These characteristics likely increase the species’ vulnerability to environmental catastrophes and 

perturbations and provide less of a buffer against year-class failure than species such as herring 

that spawn repeatedly and have variable ages at maturity (Gustafson et al. 2010).

Threats include human activities or natural events (e.g., fish harvest, volcanoes) that alter key physical, biological 

and/or chemical features and reduce a species’ viability. Both natural and human-related threats are outlined and 

organized under the following five ESA listing factors: (1) destruction or modification of habitat; (2) overutilization for 

commercial, recreational, scientific, or educational purposes; (3) disease or predation; (4) inadequacy of existing 

regulatory mechanisms; or (5) other natural or human factors. 

5.1.4 Critical Habitat

Critical habitat has been designated for the southern DPS of eulachon (76 FR 65323). The 

designated areas are a combination of freshwater creeks and rivers and their associated estuaries, 

comprising approximately 539 km (335 mi) of habitat. The physical or biological features 

essential to the conservation of the DPS include:

(1) Freshwater spawning and incubation sites with water flow, quality and temperature 

conditions and substrate supporting spawning and incubation, and with migratory access for 

adults and juveniles. These features are essential to conservation because without them the 

species cannot successfully spawn and produce offspring.

(2) Freshwater and estuarine migration corridors associated with spawning and incubation sites 

that are free of obstruction and with water flow, quality and temperature conditions supporting 

larval and adult mobility, and with abundant prey items supporting larval feeding after the yolk 

sac is depleted. These features are essential to conservation because they allow adult fish to swim 

upstream to reach spawning areas and they allow larval fish to proceed downstream and reach 

the ocean.

(3) Nearshore and offshore marine foraging habitat with water quality and available prey, 

supporting juveniles and adult survival. Eulachon prey on a wide variety of species including 

crustaceans such as copepods and euphausiids (Hay and McCarter 2000, WDFW and ODFW 

2001), unidentified malacostracans (Sturdevant et al. 1999), cumaceans (Smith and Saalfeld 

1955), mysids, barnacle larvae, and worm larvae (WDFW and ODFW 2001). These features are 

essential to conservation because they allow juvenile fish to survive, grow, and reach maturity, 

and they allow adult fish to survive and return to freshwater systems to spawn.
81

6 Sturgeon

Members of the family Acipenseridae share several life history traits. Sturgeons, or 

Acipenseriformes, are anadromous, spawning in freshwater and spending part of their lives at sea 

or in saline waters with some species migrating within or between river systems, or even 

undergoing coastal migrations. Four species of sturgeon are listed as threatened or endangered 

under the ESA: shortnose sturgeon, Atlantic sturgeon, green sturgeon, and Gulf sturgeon. 

6.1 Shortnose Sturgeon

Shortnose sturgeon were listed as endangered throughout its range on March 11, 1967 (32 FR 

4001) pursuant to the Endangered Species Preservation Act of 1966. Shortnose sturgeon 

remained on the list as endangered with enactment of the ESA in 1973. 

Shortnose sturgeon occur along the Atlantic Coast of North America, from the Saint John River 

in Canada to the Saint Johns River in Florida. The Shortnose Sturgeon Recovery Plan (NMFS 

1998a) describes 19 shortnose sturgeon populations that are managed separately in the wild. Two 

additional geographically separated populations occur behind dams in the Connecticut River 

(above the Holyoke Dam) and in Lake Marion on the Santee-Cooper River system in South 

Carolina (above the Wilson and Pinopolis Dams) (NMFS 1998a). While shortnose sturgeon 

spawning has been documented in several rivers across its range (including but not limited to:

Kennebec River, ME, Connecticut River, Hudson River, Delaware River, Pee Dee River, SC, 

Savannah, Ogeechee, and Altamaha rivers, GA), status for many other rivers remain unknown

(Shortnose Sturgeon Status Review Team 2010).

6.1.1 Life History

Sturgeon are a long-lived species, taking years to reach sexual maturity. Male shortnose sturgeon 

tend to sexually mature earlier than females, and sturgeon residing in more northern latitudes 

reach maturity later than those at southerly latitudes (Shortnose Sturgeon Status Review Team 

2010). Sturgeon are broadcast spawners, with females laying adhesive eggs on hard bottom, 

rocky substrate at upstream, freshwater sites. When the males arrive at the spawning site, they 

broadcast sperm into the water column to fertilize the eggs. Despite their high fecundity, 

sturgeon have low recruitment. 

Spawning periodicity varies by species and sex, but there can be anywhere from 1 to 5 years 

between spawning, as individuals need to rebuild gonadal material. There is difficulty in 

definitively assessing where and how reliably spawning occurs. Presence of eggs, age-1 juveniles 

and capture of “ripe” adults moving upstream (i.e., likely on a spawning run) serve as strong 

indicators, but due to their life history and the impacts sturgeon populations have taken, there are 

additional hurdles to successful spawning. Because sturgeon are iteroparous, and populations in 

some areas so depleted, eggs deposited at the spawning grounds may not be fertilized if males do 

not arrive at the spawning grounds that year.

Hatching occurs approximately 94-140 hrs after egg deposition, and larvae assume a bottomdwelling existence (Smith et al. 1980). The yolksac larval stage is completed in about 8-12 days,

during which time larvae move downstream to rearing grounds over a 6 – 12 day period (Kynard 

and Horgan 2002). Size of larvae at hatching and at the juvenile stage varies by species. During 

the daytime, larvae use benthic structure (e.g., gravel matrix) as refugia (Kynard and Horgan 

2002). Juvenile sturgeon continue to move further downstream into brackish waters, and 

eventually become residents in estuarine waters for months or years.
82

Generally, sturgeon are benthic omnivores, feeding on benthic invertebrates that are abundant in 

the substrate in that area. Shortnose sturgeon forage over sandy bottom, and eat benthic 

invertebrates like amphipods (Shortnose Sturgeon Status Review Team 2010).

Juvenile shortnose generally move upstream during spring and summer and downstream for fall 

and winter; however, these movements usually occur above the salt- and freshwater interface 

(Shortnose Sturgeon Status Review Team 2010). During summer and winter, adult shortnose 

sturgeon inhabit freshwater reaches of rivers reaches influenced by tides. During summer, at the 

southern end of its range, shortnose sturgeon congregate in cool, deep, areas of rivers taking 

refuge from high temperatures (Kynard 1997). Because they rarely leave their natal rivers, 

Kieffer and Kynard (1993) considered shortnose sturgeon to be freshwater amphidromous (i.e. 

adults spawn in freshwater but regularly enter saltwater habitats during their life).

6.1.2 Population Dynamics

Currently, there is no range-wide population estimate for shortnose sturgeon, although many 

individual river systems have been studied and population estimates have been generated for 

several rivers (Shortnose Sturgeon Status Review Team 2010). Some rivers have been more 

intensely studied than others, allowing for multiple estimates. Rivers with the largest shortnose 

sturgeon population estimates are the Hudson (ranging up to 61,000), St. John (18,000), 

Kennebec (9,500), Delaware (12,000), and Altamaha (6,300) (Dadswell 1979, Bain et al. 2000a, 

Brundage and Herron 2003, Squiers 2003, DeVries 2006).

Shortnose sturgeon populations are at risk from incidental bycatch, dams, dredging and pollution 

(Shortnose Sturgeon Status Review Team 2010). Despite the life span of adult sturgeon, the 

viability of sturgeon populations is highly sensitive to juvenile mortality resulting in lower 

numbers of sub-adults recruiting into the adult breeding population (Secor et al. 2002). This 

relationship caused Secor et al. (2002) to conclude sturgeon populations can be grouped into two 

demographic categories: populations having reliable (albeit periodic) natural recruitment and 

those that do not. The shortnose sturgeon populations without reliable natural recruitment are at 

more risk. Secor et al. (2002) note that sturgeon species are particularly vulnerable to the loss of 

juveniles from their natal populations. Sturgeon populations cannot survive fishing related 

mortalities exceeding 5 to 13% of an adult spawning run and they are vulnerable to declines and 

local extinction if juveniles die from fishing related mortalities (Boreman 1997, Secor et al. 

2000).

6.1.3 Status

The shortnose sturgeon is endangered, and much remains unknown about the population status in 

many rivers throughout its range. The threats that face shortnose sturgeon are likely to continue 

into the future. However, either due to recovery or increased sampling efficiency, it appears 

shortnose sturgeon populations are increasing in some rivers or remaining stable in others. The 

Altamaha River population estimate in 1998 was 2,800 and is now 6,300, the population in the 

Delaware River is unchanged from 1987 to 2003, the Ogeechee population has grown from 

roughly 250 in the early 90s to 350 in the late 2000s, Dovel (1979) estimated the Hudson 

population at 30,300 and Bain et al. (2000b) estimates the population at 61,000, the Kennebec 

has grown from 7,200 in 1977-1981 to 9,500 in 2003, and the last shortnose in the Penobscot had 

been seen in 1979 until some were caught in 2005 and now the population is thought to number 

over 1,000. The larger threat to shortnose sturgeon survival is the habitat fragmentation caused 

by extirpations throughout Florida, southern Georgia, all of North Carolina except for the Cape 
83

Fear River, all of Virginia, and all of Maryland (Rogers and Weber 1995, Kynard 1997, Kahnle 

et al. 1998, NMFS 1998c, Collins et al. 2000, Skjeveland et al. 2000, Welsh et al. 2002, Oakley 

2003). While it appears some populations may be increasing, none of these extirpated 

populations have been recolonized for various reasons.

6.1.4 Critical Habitat

No critical habitat has been designated for shortnose sturgeon. 

6.2 Atlantic Sturgeon (General Overview)

We discuss the distribution, life history, population dynamics, status, and critical habitats of the 

five species (here we use the word “species” to apply to distinct population segments, DPSs) 

separately; however, because listed Atlantic sturgeon species are virtually indistinguishable in 

the wild and comprise the same biological species, we begin this section describing 

characteristics common across DPSs. We used information available in the 2007 Atlantic 

Sturgeon Status Review (ASSRT 2007), and the listing documents (77 FR 5880, 77 FR 5914) to 

summarize the status of the species. 

The range of Atlantic sturgeon includes the St. John River in Canada, to St. Johns River in 

Florida. Five DPSs of Atlantic sturgeon were designated and listed under the ESA on February 6, 

2012 (Gulf of Maine, New York Bight, Chesapeake Bay, Carolina, and South Atlantic) (77 FR 

5880, 77 FR 5914). 

6.2.1 Life History

Although the Atlantic sturgeon DPSs are genetically distinct, their life history characteristics are 

the same and are discussed together below.

As Acipensieriformes, Atlantic sturgeon are anadromous and iteroparus. Like shortnose 

sturgeon, male Atlantic sturgeon tend to sexually mature earlier than females, and sturgeon 

residing in more northern latitudes reach maturity later than those at southerly latitudes. 

Evidence of Atlantic sturgeon spawning has been found in many of the same rivers as shortnose 

sturgeon (see discussion above). Atlantic sturgeon eggs are between 2.5-3.0mm, and larvae are 

about 7mm long upon hatching. Generally, sturgeon are benthic omnivores, feeding on benthic 

invertebrates that are abundant in the substrate in that area. Atlantic sturgeon commonly eat 

polychaetes and isopods.

Generally, sturgeon are benthic omnivores, feeding on benthic invertebrates that are abundant in 

the substrate in that area. Atlantic sturgeon commonly eat polychaetes and isopods (ASSRT 

2007).

As juveniles, Atlantic sturgeon migrate downstream from the spawning grounds into brackish 

water. Unlike shortnose sturgeon, subadult Atlantic sturgeon (76-92cm) may move out of the 

estuaries and into coastal waters where they can undergo long range migrations. At this stage in 

the coastal waters, individual subadult and adult Atlantic sturgeon originating from different 

DPSs will mix, but adults return to their natal river to spawn. 

6.2.2 Population Dynamics

Subadult and adult Atlantic sturgeon spend time in oceanic waters during coastal migrations. 

Evaluating the status of the species depends on the status of the smaller extant populations 

because maintaining those populations maintains genetic heterogeneity and having a broad range 
84

prevents a single catastrophic event from causing their extinction. A description of each Atlantic 

sturgeon DPS, with details regarding the smaller, in-river populations is below.

6.2.3 Status

The status of each Atlantic sturgeon DPS will be discussed separately below.

6.2.4 Critical Habitat

No critical habitat has been designated for any Atlantic sturgeon DPS.

6.3 Atlantic Sturgeon (Gulf of Maine DPS)

The Gulf of Maine (GOM) DPS includes all Atlantic sturgeon that are spawned in the Gulf of 

Maine watersheds from the Maine/Canada border to Chatham, MA. The GOM DPS was listed as 

threatened (77 FR 5880). A 4(d) Rule to apply take prohibitions to the GOM DPS was proposed 

separately (76 FR 34023; June 10, 2011). The proposed rulemaking identified several activities 

that may take GOM DPS Atlantic sturgeon, including incidental bycatch in fisheries, habitat 

alteration, and “entrainment and impingement of all life stages of GOM DPS Atlantic sturgeon 

during the operation of water diversions, dredging projects, and power plants...” (76 FR 34023).

6.3.1 Life History

Although the Atlantic sturgeon DPSs are genetically distinct, their life history characteristics are 

the same; please see the description in Seciton 6.2.1, above.

6.3.2 Population Dynamics

In the early 1800s, there were estimated to be 10,240 adult Atlantic sturgeon in the Kennebec 

River (ASSRT 2007); currently, the existing spawning population is thought to be less than 300 

adults annually. Spawning is known to occur in the Kennebec River, and it is suspected that the 

Penobscot River also supports spawning. Recent directed sampling has found eggs in the 

Kennebec, and ripe adults and age-1 fish have been captured (NMFS 16526 Report). Whether 

other river systems in the GOM DPS support spawning populations remains unknown. There is 

no current population estimate for the GOM DPS.

6.3.3 Status

Threats to GOM DPS Atlantic sturgeon include dredging, which can displace sturgeon, alter 

habitat, and allow saltwater to intrude further upstream, reducing freshwater spawning habitat, 

water quality degradation from run-off, and bycatch in commercial and recreational fisheries. 

Dams are also a threat to the GOM DPS, but recent dam removals in the region have begun to 

restore access to spawning habitat. The Edwards Dam on the Kennebec River was removed in 

1999 (Natural Resources Council of Maine 2014). Construction has been underway to remove 

the Veazie and Great Works dams by the Penobscot River Restoration Trust since 2012 

(Penobscot River Restoration Trust 2014).

The removal of dams on the Kennebec and Penobscot rivers is seen as a positive step towards 

restoring habitat, for the GOM DPS and for other anadromous species in the area. Recent 

research has detected the presence of adults, age-1 fish, and eggs in rivers where sturgeon were 

unknown to occur or had not been observed for many years. These observations suggest that 

abundance of the Gulf of Maine DPS of Atlantic sturgeon is sufficient such that recolonization to 

rivers historically suitable for spawning may be occurring. However, despite some positive signs, 

there is not enough information to establish a trend for this DPS. Still, in order to recover, the 

GOM DPS of Atlantic sturgeon can only withstand low levels of anthropogenic mortality
85

because as a threatened species, they are at risk of becoming endangered in the foreseeable 

future.

6.3.4 Critical Habitat

No critical habitat has been designated for the Gulf of Maine DPS.

6.4 Atlantic Sturgeon (New York Bight DPS)

The New York Bight (NYB) DPS is comprised of all Atlantic sturgeon that are spawned in 

watersheds that drain into the coastal waters from Chatham, MA, to the Delaware-Maryland 

border on Fenwick Island. The NYB DPS is listed as endangered (77 FR 5880).

6.4.1 Life History

Although the Atlantic sturgeon DPSs are genetically distinct, their life history characteristics are 

the same; please see the description in Section 6.2.1, above.

6.4.2 Population Dynamics

The NYB DPS contains two known spawning population on the Delaware and Hudson rivers. 

The Hudson River is thought to support one of the more robust Atlantic sturgeon populations in 

its entire range (ASSRT 2007). In the late 1800s, an estimated 6,000-8,000 females contributed 

to the Hudson River stock; estimates from fisheries data between 1985 and 1995 estimate the 

population at 870 spawning adults in the Hudson River (600 males and 270 females) (Kahnle et 

al. 2007). Peterson et al. (2000) reported that there were approximately 4,300 age-1 and -2 

Atlantic sturgeon in the Hudson River between 1985 and 1995.

Before 1890, the Delaware River is estimated to have supported around 180,000 adult female 

Atlantic sturgeon (ASSRT 2007). There have been attempts to generate a population estimate for 

Atlantic sturgeon on the Delaware River; estimates of juveniles have ranged from 5,600 to less 

than 1,000. A directed survey by the Delaware Division of Fish and Wildlife from conducted 

1991-1998 captured more than 1,700 juveniles, with a high of 565 individuals in 1991, and 14 in 

1998 (ASSRT 2007). More recent directed research has found Atlantic sturgeon eggs, mature 

adults, and juvenile fish present in the river, and it is believed that a remnant population of 

Delaware River Atlantic sturgeon exists (ASSRT 2007); NMFS 16507, 16431 reports). 

There is evidence to support Atlantic sturgeon presence in other New England rivers through 

either historical records or the existence of past Atlantic sturgeon fisheries (e.g., the Merrimack 

River (NH/MA), Taunton River (MA/RI), Thames and Housatonic rivers (CT)). Sub-adult 

individuals have been captured in the estuaries of these rivers, and the habitat is thought to be 

important for feeding, but there is no evidence that spawning populations occur (ASSRT 2007).

Although Atlantic sturgeon are captured in the estuary of the Connecticut River and in the 

Connecticut waters of Long Island Sound, it is believed that the native population has been 

extirpated (ASSRT 2007).

6.4.3 Status

Threats to the NYB DPS include habitat loss and water quality degradation through dredging and 

run-off, and incidental capture in fisheries. In addition, vessel strikes are of particular concern for 

Atlantic sturgeon in the Delaware River, as there have been numerous reports of recovered 

Atlantic sturgeon carcasses with injuries consistent with being struck with a boat propeller (i.e., 

the carcass was severed) (ASSRT 2007).
86

Although the Hudson River is believed to support one of the more robust populations, the status 

of Atlantic sturgeon in other rivers of the NYB DPS is either unknown or severely depleted from 

historic levels. The threats facing the NYB DPS are expected to continue into the future. A loss 

of any one of the riverine populations within this DPS would represent a loss in the number of 

reproducing individuals, a gap in the range of the DPS, and fragmentation of the species’ habitat.

6.4.4 Critical Habitat

No critical habitat has been designated for the New York Bight DPS.

6.5 Atlantic Sturgeon (Chesapeake Bay DPS)

The Chesapeake Bay (CB) DPS includes Atlantic sturgeon that are spawned in the watersheds 

that drain into the Chesapeake Bay from Fenwick Island to Cape Henry, VA. Major rivers that 

are a part of the CB DPS include the York, James, Potomac, Susquehanna, and Rappahannock 

rivers.

6.5.1 Life History

Although the Atlantic sturgeon DPSs are genetically distinct, their life history characteristics are 

the same; please see the description in Section 6.2.1, above.

6.5.2 Population Dynamics

Pre-harvest (i.e., before 1890) levels of Atlantic sturgeon in the Chesapeake Bay and its 

tributaries are estimated to be ~20,000 adult females. The current spawning population in the 

James River is thought to be less than 300 individuals per year (ASSRT 2007). Recently, 

evidence of a spawning population on the York River was found when researchers captured 

mature, ripe adults (Hager et al. In Review). Status of spawning on other major tributaries in the 

CB DPS is unknown, although spawning once occurred on the Potomac, Susquehanna, and 

Rappahannock rivers.

6.5.3 Status

The CB DPS is listed as endangered (77 FR 5880). The CB DPS has been reduced to a fraction 

of its historical levels by overfishing. Although there is no longer a commercial fishery, the 

species still faces the threats described above throughout its range. Threats to the CB DPS are the 

same as those facing the NYB DPS (see section 6.4.3, above); Atlantic sturgeon mortality from 

vessel strikes has been documented on the James River (ASSRT 2007). Many of these threats are 

expected to continue into the future (e.g., ship strikes, dredging, dams, fisheries bycatch). Low 

population numbers of every river population in the CB DPS put them in danger of extinction; 

none of the populations are large or stable enough to provide with any level of certainty for 

continued existence of Atlantic sturgeon in this part of its range. The loss of any one riverine 

spawning population within the DPS will result in a decrease in genetic diversity, reduction in 

the number of reproducing individuals, a gap in the range of the DPS that is unlikely to be 

recolonized, and lower recruitment. NMFS concludes that the resiliency of the CB DPS to 

further perturbations is low.

6.5.4 Critical Habitat

No critical habitat has been designated for the Chesapeake Bay DPS.
87

6.6 Atlantic Sturgeon (Carolina DPS)

The Carolina DPS includes Atlantic sturgeon that originated from the Roanoke, Tar/Pamlico, 

Cape Fear, Winyah Bay, and Santee-Cooper rivers in North and South Carolina. 

6.6.1 Life History

Although the Atlantic sturgeon DPSs are genetically distinct, their life history characteristics are 

the same; please see the description in Section 6.2.1, above.

6.6.2 Population Dynamics

Before commercial harvest began in 1890, it is estimated that there were 7,000-10,500 adult 

females in North Carolina, and 8,000 in South Carolina. Riverine spawning populations are 

thought to be at less than 3% of their historic levels (ASSRT 2007).

The spawning population in the Sampit River, part of the Winyah Bay system, is believed to 

have been eliminated; the status of other spawning populations in the Carolina DPS remain 

uncertain (ASSRT 2007). The Roanoke River has been confirmed to support a spawning 

population, as have the Tar-Pamlico, Cape Fear, Waccamaw, Great Pee Dee, Combahee, and 

Edisto rivers, with possible spawning occurring in the Neuse, Santee and Cooper Rivers (77 FR 

5914).

6.6.3 Status

The Carolina DPS is listed as endangered (77 FR 5914). The Carolina DPS has been reduced to a 

fraction of its historical levels by past commercial harvest. Although there is no longer a 

commercial fishery, the species still faces threats throughout its range. Threats to the Carolina 

DPS include habitat loss due to dams, dredging, degraded water quality, and incidental capture in 

fisheries. Climate change is also expected to exacerbate water quantity and quality problems like 

elevated water temperatures and lower levels of dissolved oxygen (77 FR 5914). Many of these 

threats are expected to continue into the future (e.g., dredging, dams, fisheries bycatch), or even 

grow worse (e.g., climate change). Low population numbers of every river population in the 

Carolina DPS put them in danger of extinction; none of the populations are large or stable

enough to provide with any level of certainty for continued existence of Atlantic sturgeon in this 

part of its range. The loss of any one riverine spawning population within the DPS will result in a 

decrease in genetic diversity, reduction in the number of reproducing individuals, a gap in the 

range of the DPS that is unlikely to be recolonized, and lower recruitment. NMFS concludes that 

the resiliency of the Carolina DPS to further perturbations is low. 

6.6.4 Critical Habitat

No critical habitat has been designated for the Carolina DPS.

6.7 Atlantic Sturgeon (South Atlantic DPS)

The South Atlantic (SA) DPS includes Atlantic sturgeon originating from the ACE Basin 

(Ashepoo, Combahee, and Edisto rivers) in South Carolina, the Savannah, Ogeechee, Altamaha, 

and Satilla rivers in Georgia, and the St. Mary’s and St. Johns rivers in Florida. 

6.7.1 Life History

Although the Atlantic sturgeon DPSs are genetically distinct, their life history characteristics are 

the same; please see the Section 6.2.1, above.
88

6.7.2 Population Dynamics

Prior to 1890, there were thought to be ~11,000 adult females in Georgia, and ~8,000 in South 

Carolina. The Altamaha River is thought to be the largest spawning population in the Southeast; 

Peterson et al. (2008) reported that approximately 324 (in 2004) and 386 (in 2005) adults per 

year returned. Other water systems suspected of still supporting a spawning population are the 

ACE Basin, the Savannah, Ogeechee, and Satilla rivers, and each is believed to have fewer than 

300 adults annually (ASSRT 2007). The Ogeechee River subpopulation is considered to be 

particularly stressed as research has found that juvenile abundance is rare with high inter-annual 

variability, indicating spawning or recruitment failure. Spawning populations in the St. Mary’s 

and St. Johns rivers are believed to be eliminated (Florida Fish and Wildlife Conservation 

Commission 2001).

6.7.3 Status

The SA DPS is listed as endangered (77 FR 5914). Threats to the SA DPS are similar to those 

faced by the Carolina DPS; see Section 6.6.3, above. These threats will likely continue into the 

future. Like the other Atlantic sturgeon DPSs, the SA DPS was severely depleted by overfishing, 

and what little is known about the current population in several rivers indicates that the 

populations are at low levels or have been extirpated. The loss of any one riverine spawning 

population within the DPS will result in a decrease in genetic diversity, reduction in the number 

of reproducing individuals, a gap in the range of the DPS that is unlikely to be recolonized, and 

lower recruitment. NMFS concludes that the resiliency of the SA DPS to further perturbations is 

low.

6.7.4 Critical Habitat

No critical habitat has been designated for the South Atlantic DPS.

6.8 Green Sturgeon (Southern DPS)

Green sturgeon occur in coastal Pacific waters from San Francisco Bay to Canada. The Southern 

DPS of green sturgeon includes populations south of (and exclusive of) the Eel River (75 FR 

30714). 

6.8.1 Life History

As members of the family Acipenseridae, green sturgeon share similar reproductive strategies 

and life history patterns with other sturgeon species; see Section 6.1.1, above.

The Sacramento River is the location of the single, known spawning population for the green 

sturgeon Southern DPS (Adams et al. 2007). Size of larvae at hatching and at the juvenile stage 

varies by species (see discussion above). Generally, sturgeon are benthic omnivores, feeding on 

benthic invertebrates that are abundant in the substrate in that area. Little is known specifically 

about green sturgeon foraging habits; generally, adults feed upon invertebrates like shrimp, 

mollusks, amphipods and even small fish, while juveniles eat opossum shrimp and amphipods 

(Adams et al. 2002). Juvenile green sturgeon spend 1-3 years in freshwater, disperse widely in 

the ocean, and return to freshwater as adults to spawn (about age 15 for males, age 17 for 

females) (NMFS 2010a).

6.8.2 Population Dynamics

Trend data for green sturgeon is severely limited. Available information comes from two 

predominant sources, fisheries and tagging. Only three data sets were considered useful for the 
89

population time series analyses by NMFS’s biological review team: the Klamath Yurok Tribal 

fishery catch, a San Pablo sport fishery tag returns, and Columbia River commercial landings 

(NMFS 2005a). Using San Pablo sport fishery tag recovery data, the California Department of 

Fish and Game produced a population time series estimate for the southern DPS. San Pablo data 

suggest that green sturgeon abundance may be increasing, but the data showed no significant 

trend. The data set is not particularly convincing, however, as it suffers from inconsistent effort 

and since it is unclear whether summer concentrations of green sturgeon provide a strong 

indicator of population performance (NMFS 2005a). Although there is not sufficient information 

available to estimate the current population size of southern green sturgeon, catch of juveniles 

during state and federal salvage operations in the Sacramento delta are low in comparison to 

catch levels before the mid-1980s.

6.8.3 Status 

The Southern DPS is listed as threatened (71 FR 17757; April 7, 2006). On June 2, 2010, NMFS 

issued a 4(d) Rule for the Southern DPS, applying certain take prohibitions (75 FR 30714). The 5 

Year Status Review for the Southern DPS was initiated in 2012 (77 FR 64959). Current threats 

to the Southern DPS include reduction in spawning habitat (mostly from impoundments), 

entrainment by water projects, temperature regulations through water releases from upstream 

dams, contaminants, incidental bycatch and poaching (NMFS 2010a). Given the small 

population size, the species’ life history traits (e.g., slow to reach sexual maturity), and that the 

threats to the population are likely to continue into the future, we conclude that the Southern 

DPS is not resilient to further perturbations.

6.8.4 Critical Habitat

Green sturgeon critical habitat for the Southern DPS was designated on October 9, 2009 (74 FR 

52300), including coastal U.S. marine waters within 60 fathoms deep from Monterey Bay, CA to 

Cape Flattery, WA, including the Strait of Juan de Fuca, and numerous coastal rivers and 

estuaries: see the Final Rule for a complete description (74 FR 52300). Food resources were 

identified as a primary constituent element.

6.9 Gulf Sturgeon

Gulf sturgeon historically occurred in coastal river systems from the Mississippi River to the 

Suwannee River, Florida, and in the Gulf of Mexico to the Florida Bay (USFWS and Gulf States 

Marine Fisheries Commission 1995). Currently, Gulf sturgeon are distributed from the 

Suwannee River to Lake Pontchartrain and the Pearl River system, Louisiana. 

6.9.1 Life History

As members of the family Acipenseridae, Gulf sturgeon share similar reproductive strategies and 

life history patterns with other sturgeon species; see Section 6.1.1, above.. 

Evidence of Gulf sturgeon spawning has been found in the Suwannee, Pearl, Pascagoula, 

Escambia, Yellow, Choctawhatchee, or Apalachicola Rivers (Fox et al. 2000, Heise et al. 2004, 

USFWS and NMFS 2009). Size of larvae at hatching and at the juvenile stage varies by species 

(see discussion above). Generally, sturgeon are benthic omnivores, feeding on benthic 

invertebrates that are abundant in the substrate in that area. Gulf sturgeon eat isopods, 

amphipods, polychaete and oligochaete annelids, as well as crustaceans (Mason Jr. and Clugston 

1993). Gulf sturgeon less than two years old reside in riverine and estuarine habitats throughout 

the year, but evidence shows that most sub-adult and adult Gulf sturgeon feed for 3-4 months 
90

while in the marine environment, and then do not feed for the next 8-9 months after they enter 

freshwater (Randall and Sulak 2012).

6.9.2 Population Dynamics

There are no range-wide population estimates for Gulf sturgeon, although particular river 

systems have been studied, including the Suwannee and Apalachicola rivers. The Suwannee 

River is considered to have the most robust population of Gulf sturgeon, with a population size 

estimated at 2,250-3,300 (87-211cm, 18kg fish) (USFWS and NMFS 2009). Zehfuss et al. 

(1999) estimated about 100 Gulf sturgeon (>45cm) at the Jim Woodruff Lock and Dam on the 

Apalachicola (which is likely an underestimate, based on high rates of tag loss); 293 Gulf 

sturgeon were captured from 1982-1991.

6.9.3 Status 

Gulf sturgeon were listed as threatened on September 30, 1991 (56 FR 49653) and are managed 

jointly by USFWS and NMFS. Like other sturgeon species, Gulf sturgeon were historically 

overfished, which played a large role in the decline in its population. Although no directed 

fisheries are in operation today, Gulf sturgeon are still at risk from incidental bycatch in other 

state and federal fisheries. Habitat reduction from dams blocking access to spawning areas, 

dredging, groundwater extraction, poor water quality and contaminants all remain current threats, 

which will likely continue into the future. 

According to the Gulf sturgeon 5 year review, NMFS considers the population stable, with seven 

riverine systems showing evidence of spawning, although variability in population size has been 

noted. This variability is attributed to Hurricanes Ivan (2004) and Katrina (2005) (USFWS and 

NMFS 2009). The 5-Year Review concluded that the threatened status for Gulf sturgeon was still 

appropriate. We conclude that Gulf sturgeon population is stable and somewhat resilient to 

further perturbation.

6.9.4 Critical Habitat

Critical habitat has been designated for Gulf sturgeon (68 FR 13370; March 19, 2003) in coastal 

rivers and estuarine areas of the Gulf of Mexico from Florida to Louisiana. Abundant food items 

were identified as a primary constituent element in Gulf sturgeon critical habitat.

7 Sawfish

Sawfish, like sharks, skates, and rays, belong to a group of fish called elasmobranchs, whose 

skeletons are made of cartilage. The proposed project may affect the ESA-listed smalltooth 

sawfish, described below.

7.1 Smalltooth Sawfish (U.S. DPS)

The smalltooth sawfish is a tropical marine and estuarine elasmobranch (e.g., sharks and rays) 

that uses its tooth-lined rostrum to forage on fish and benthic invertebrates. The United States 

DPS of smalltooth sawfish was listed as endangered on April 1, 2003 (68 FR 15674). Smalltooth 

sawfish can be found in Florida waters, primarily in the southern tip of the state, centered around 

Charlotte Harbor, Everglades National Park, and Florida Bay. On June 4, 2013, NMFS proposed 

a rule to list five species of sawfish (Pristis spp.) found outside U.S. waters (78 FR 33300), 

including the non-listed DPSs of smalltooth sawfish. We used information available in the 2009 
91

Recovery Plan (NMFS 2009e), the 5-year Review (NMFS 2010c), and the proposed listing of 

other sawfish (78 FR 33300) to summarize the status of the species, as follows. 

7.1.1 Life History

At birth, smalltooth sawfish are approximately 31 inches (80cm). For the first three years of life 

(until they reach about 2.5 m in length), juveniles reside in shallow, red mangrove estuaries with 

salinities between 18 and 24 ppt. Adults, which can grow to be 18 ft long, remain in warm 

coastal waters at shallow depths. Estimates of age at maturity range from 10 to 33 years. 

Gestation is approximately 5 months and females likely produce litters every second year. Litter 

sizes may be similar to that of the largetooth sawfish, which produces brood sizes of 1-13 

individuals (mean: 7.3). Overall, much uncertainty still remains in estimating life history 

parameters for smalltooth sawfish since very little information exists on size classes other than 

juveniles.

7.1.2 Population Dynamics

Since actual abundance data are limited, researchers compiled capture and sightings data 

(collectively referred to as encounter data) in the National Sawfish Encounter Database. From 

1998 to 2011, over 3,000 smalltooth sawfish encounters were reported and compiled in the 

database (Florida Museum of Natural History 2014). Although this data cannot be used to assess 

the population because of the opportunistic nature in which they are collected (i.e., encounter 

data are a series of random occurrences rather than an evenly distributed search over a defined 

period of time), researchers can use this database to assess the spatial and temporal distribution 

of smalltooth sawfish. We expect that as the population grows, the geographic range of 

encounters will also increase. Seitz and Poulakis (2002) and Poulakis and Seitz (2004) document 

recent (1990 to 2002) occurrences of sawfish along the southwest coast of Florida, and in Florida 

Bay and the Florida Keys, respectively. This information is confirmed by Wiley and 

Simpfendorfer (2010) who show the core range has expanded.

The majority of smalltooth sawfish encounters today are from the southwest coast of Florida 

between the Caloosahatchee River and Florida Bay. Outside of this core area, the smalltooth 

sawfish appears more common on the west coast of Florida and in the Florida Keys than on the 

east coast, and occurrences decrease the greater the distance from the core area (Simpfendorfer 

and Wiley 2004). The capture of a smalltooth sawfish off Georgia in 2002 is the first record 

north of Florida since 1963. New reports during 2004 extend the current range of the species to 

Panama City, offshore Louisiana (south of Timbalier Island in 100 ft of water), southern Texas, 

and the northern coast of Cuba. The Texas sighting was not confirmed to be a smalltooth sawfish 

and may have been a largetooth sawfish.

Despite the lack of scientific data on abundance, recent encounters with young-of-the-year, older 

juveniles, and sexually mature smalltooth sawfish indicate that the U.S. population is currently 

reproducing (Seitz and Poulakis 2002, Simpfendorfer 2003). The abundance of juveniles 

encountered, including very small individuals, suggests that the population remains viable 

(Simpfendorfer and Wiley 2004) and data analyzed from Everglades National Park as part of an 

established fisheries-dependent monitoring program (angler interviews) indicate an increase of 

between 2 and 5% per year in abundance within the park over the past decade (Carlson et al. 

2007, Carlson and Osborne 2012). Also, the declining numbers of individuals with increasing 

size is consistent with the historic size composition data (Simpfendorfer and Wiley 2004).
92

The effective population size, the number of animals in the population that produce offspring 

was recently estimated to be between 250 and 350 individuals (Chapman et al. 2011). Given the 

small effective population size and the increasing number of neonates produced, inbreeding 

depression was suspected to be a concern for smalltooth sawfish. Given the degree of decline and 

range contraction that smalltooth sawfish have experienced over the last few generations, it was 

originally hypothesized that the remnant smalltooth sawfish population has experienced a genetic 

bottleneck. However, an analysis of tissue samples (fin clips) collected under the previous permit 

(number 13330) indicates inbreeding is rare (Chapman et al. 2011). Results of this study also 

suggest that the remnant smalltooth sawfish population will probably retain 90% of its current 

genetic diversity and there is no evidence of a genetic bottleneck accompanying last century’s 

demographic bottleneck.

The status and trends and recent encounters in new areas beyond the core abundance area 

suggest that the population may be increasing. However, smalltooth sawfish encounters are still 

rare along much of their historical range and they are thought to be extirpated from areas of 

historical abundance such as the Indian River Lagoon and John’s Pass (Snelson and Williams 

1981, Simpfendorfer and Wiley 2004).

7.1.3 Status

It is believed that sawfish are at less than 5% of its population size than at the time of European 

settlement. Historically common in coastal waters from Texas to North Carolina, the range of 

the DPS has been contracted to southwestern Florida. Like other elasmobranchs, smalltooth 

sawfish are a k-selected species, characterized by a low rate of intrinsic population growth and 

able to maintain relatively small population sizes in stable environments, but vulnerable to 

excessive mortalities. The decline in sawfish abundance is attributed to bycatch in fisheries, 

entanglement in marine debris, and loss of juvenile habitat through destruction of mangroves and 

dredging and filling projects. These factors continue to be significant threats to smalltooth 

sawfish survival and recovery. Therefore, the species has little resilience to additional 

perturbations.

7.1.4 Critical Habitat

Two units of critical habitat were designated for smalltooth sawfish in 2009 (74 FR 45353): the 

Charlotte Harbor Estuary and the Ten Thousand Islands/Everglades. Primary constituent 

elements were not identified, although the final rule identified the red mangroves and shallow 

euryhaline habitats as essential to the conservation of smalltooth sawfish because both serve 

nursery area functions. Activities that may affect smalltooth sawfish critical habitat include 

dredging, filling, in-water construction, installation of water control structures, and hard clam 

aquaculture activities.

8 Rockfish

Rockfish are classified in the taxonomic family Sebastidae. Worldwide, there are about 130 

species in the family. The proposed project may affect three ESA-listed species, discussed 

below.

8.1 Bocaccio (Puget Sound/Georgia Basin DPS)

Bocaccio is a rockfish species that occurs from the central Baja peninsula of Mexico north along 

the continental shelf and slope as far as Stepovac Bay, Alaska (Love et al. 2002). Genetic 
93

analyses suggest is composed of two distinct populations (Wishard et al. 1980, Matala et al. 

2004). A southern population exists along the Pacific coasts of Mexican and California and is 

separated from a northern population by a region of apparent scarcity from northern California to 

southern Oregon (MacCall and He 2002b). It has been proposed that oceanographic features, 

such as current patterns restricting larval movement, are responsible for population discreteness 

(Matala et al. 2004, NMFS 2008d). Bocaccio of the Puget Sound/Georgia Basin were determined

to be a DPS and listed as endangered in 2010. However, the presence of a third population has 

also been suggested (Queen Charlotte Island, Vancouver Island to Point Conception, California, 

and south of Point Conception) (Matala et al. 2004). For stock management purposes, the NMFS 

and Pacific Fisheries Management Council recognize these populations as separate stocks.

8.1.1 Life History

Preferred bocaccio habitat is largely dependent upon the life stage of an individual. Larvae and 

young juveniles tend to be found in deeper offshore regions (1-148 km offshore), but associated 

with the surface and occasionally with floating kelp mats (Hartmann 1987, Love et al. 2002, 

Emery et al. 2006). As individuals mature into older juveniles and adults, they transition into 

shallow waters and settle to the bottom, preferring algae-covered rocky, eelgrass, or sand habitats 

and aggregating into schools (Eschmeyer et al. 1983, Love et al. 1991). After a few weeks, fish 

move into slightly deeper waters of 18-30 m and occupy rocky reefs (Feder et al. 1974, Carr 

1983, Eschmeyer et al. 1983, Johnson 2006, Love and Yoklavich 2008). As adults, bocaccio may 

be found in depths of 12-478 m, but tend to remain in shallow waters on the continental shelf 

(20-250 m), still associating mostly with reefs or other hard substrate, but may move over mud 

flats (Feder et al. 1974, Kramer and O'Connell 1995, Love et al. 2002, Love et al. 2005, Love 

and York 2005, Love et al. 2006). Artificial habitats, such as platform structures, also appear to 

be suitable habitat for bocaccio (Love and York 2006). Adults may occupy territories of 200-400 

hectares, but can venture outside of this territory (Hartmann 1987). Adults tend to occupy deeper 

waters in the southern population compared to the northern population (Love et al. 2002). Adults 

are not as benthic as juveniles and may occur as much as 30 m above the bottom and move 100 

m vertically during the course of a day as they move between different areas (Love et al. 2002, 

Starr et al. 2002). Prior to severe population reductions, bocaccio appeared to frequent the 

Tacoma Narrows in Washington State (DeLacy et al. 1964, Haw and Buckley 1971, Miller and 

Borton 1980).

Bocaccio are live-bearers with internal fertilization. Once females become mature (at 54-61 cm 

total length), they produce 20,000-2.3 million eggs annually, with the number increasing as 

females age and grow larger (Hart 1973, Echeverria 1987, Love et al. 2002). However, either sex 

has been known to attain sexual maturity as small as 35 cm or 3 years of age and, in recent years 

as populations have declined, average age at sexual maturity may have declined as well (Hart 

1973, Echeverria 1987, Love et al. 2002, MacCall 2002b). Mating occurs between August and 

November, with larvae born between January and April (Lyubimova 1965, Moser 1967, 

Westrheim 1975, Wyllie Echeverria 1987, Love et al. 2002, MacCall and He 2002b).

Upon birth, bocaccio larvae measure 4-5 mm in length. These larvae move into pelagic waters as 

juveniles when they are 1.5-3 cm and remain in oceanic waters from 3.5-5.5 months after birth 

(usually until early June), where they grow at ~0.5-1 mm per day (Moser 1967, Matarese et al. 

1989, Woodbury and Ralston 1991, Love et al. 2002, MacCall and He 2002b, MacCall 2003). 

However, growth can vary from year-to-year (Woodbury and Ralston 1991). Once individuals 

are 3-4 cm in length, they return to nearshore waters, where they settle into bottom habitats. 
94

Females tend to grow faster than males, but fish may take 5 years to reach sexual maturity 

(MacCall 2003). Individuals continue to grow until they reach maximum sizes of 91 cm, or 9.6 

kg, at an estimated maximum age of 50 years (Eschmeyer et al. 1983, Halstead et al. 1990, 

Ralston and Ianelli 1998, Love et al. 2002, Andrews et al. 2005, Piner et al. 2006). However, 

individuals tend to grow larger in more northerly regions (Dark et al. 1983).

Prey of bocaccio vary with fish age, with bocaccio larvae starting with larval krill, diatoms, and 

dinoflagellates (Love et al. 2002). Pelagic juveniles consume fish larvae, copepods, and krill, 

while older, nearshore juveniles and adults prey upon rockfishes, hake, sablefish, anchovies, 

lanternfish, and squid (Reilly et al. 1992, Love et al. 2002).

8.1.2 Population Dynamics

Although population estimates are not available for the northern population, the southern 

population has been estimated to number 1.6 million fish of 1 year of age or older in 2002 

(MacCall 2002a). Of these, 1.0 million were estimated to occur south of Pt. Conception, where 

recruitment has been stronger. However, individuals north of Pt. Conception tend to be larger 

and, hence, more fecund. In 2002, the southern population was estimated to produce 720 billion 

eggs annually (243 billion south of Pt. Conception). North of Pt. Conception, bocaccio are most 

abundant in the Monterey Bay area, where prime habitat seems to be over the continental slope 

and, secondarily, over the shelf (Dark et al. 1983).

The rate of decline for rockfish in Puget Sound has been estimated at ~3% annually for the 

period 1965-2007. Various rebuilding estimates for bocaccio populations have predicted 

recovery, but require long periods (98-170 years) and assume no mortality from fishing 

(intentional harvests are closed, but bycatch still occurs) (MacCall and He 2002a, MacCall 2008, 

NMFS 2008d).

8.1.3 Status

The Puget Sound/Georgia Basin DPS of bocaccio was listed as endangered on April 28, 2010 (75 

FR 22276). Bocaccio as a species has undergone severe decline in the past several decades, with 

the species currently estimated to be 3.6% of its abundance in 1970 (MacCall and He 2002b). In 

Puget Sound prior to World War II, commercial landings of rockfish species generally remained 

under 20,000 lbs, but sky-rocketed during the war to 375,000 lbs annually and fluctuated 

between 50,000 and 220,000 lbs until 1970, when landings increased linearly with fishing effort 

to a peak of 900,000 lbs by 1980 (Palsson et al. 2009). Levels fluctuated after this between 

48,000 and 300,000 lbs for the next decade and clearly crashed in the 1990’s, with landings 

below 30,000 lbs annually. At the cessation of commercial fishing in 2003, 2,600 lbs of rockfish 

were harvested. Similar trends are seen in recreational landings from Puget Sound (WDF 1975-

1986).

Among rockfish of the Puget Sound, bocaccio appear to have undergone a particular decline 

(MacCall and He 2002b). This has likely because of the removal of the largest, most fecund 

individuals of the population due to overfishing and the frequent failure of recruitment classes, 

possibly because of unfavorable climactic/oceanographic conditions (MacCall and He 2002b).

Bocaccio resistance to depletion and recovery is also hindered by demographic features (Love et 

al. 1998a). Bocaccio are long-lived fishes, taking several years to reach sexual maturity and 

becoming more fecund with age (Dorn 2002). As harvesting targeted the largest individuals 

available, bocaccio have become less capable of recovering population numbers (Love et al. 
95

1998b). Bocaccio reproduction appears to be characterized by frequent recruitment failures, 

punctuated by occasional high success years (Love et al. 1998b, MacCall and He 2002b). 

Recruitment success appears to be linked to oceanographic/climactic patterns and may be related 

to cyclic warm/cool ocean periods, with cool periods having greater success (Sakuma and 

Ralston 1995, MacCall 1996, Love et al. 1998b, Moser et al. 2000). Harvey et al. (2006)

suggested that bocaccio may have recently diverted resources from reproduction, potentially 

resulting in additional impairment to recovery. Overall, bocaccio have the highest variability of 

recruitment of any rockfish studied to date, with recruitment exhibiting a random walk and high 

temporal variability (MacCall and He 2002b, Tolimieri and Levin 2005).

8.1.4 Critical Habitat

NMFS proposed critical habitat designation of approximately 1,185 mi2of marine habitat for 

bocaccio in Puget Sound, Washington, on August 6, 2013 (78 FR 47635). A final designation 

has not been made.

8.2 Yelloweye Rockfish (Puget Sound/Georgia Basin DPS)

Yelloweye rockfish occur from Baja California to the Aleutian Islands, but are most common 

from central California to Alaska (Love et al. 2002). This species likely composed of at least two 

populations and possibly more. Yamanaka et al. (2006) found that those individuals found within 

the Georgia Basin and Queen Charlotte Strait were genetically distinct from other samples from 

Oregon to Alaska. 

8.2.1 Life History

As with other rockfishes, yelloweye habitat varies based upon life stage. Larvae maintain a 

pelagic existence but as juveniles, move into shallow high relief rocky or sponge garden habitats 

(Eschmeyer et al. 1983, Richards et al. 1985, Love et al. 1991). Juveniles may also associate with 

floating debris or pilings (Lamb and Edgell 1986). As adults, yelloweye rockfish move in to 

deeper habitats. Individuals have been found in waters as deep as 549 m, but are generally found 

in waters of less than 180 m (Eschmeyer et al. 1983, Love et al. 2002). However, adults continue 

to associate with rocky, high relief habitats, particularly with caves and crevices, pinnacles, and 

boulder fields (Carlson and Straty 1981, Richards 1986, Love et al. 1991, O'Connell and Carlisle 

1993, Yoklavich et al. 2000). Yelloweye generally occur as individuals, with loose, residential 

aggregations infrequently found (Coombs 1979, DeMott 1983, Love et al. 2002). In the Puget 

Sound region, sport catch records from the 1970’s indicate that Sucia Island and other islands of 

the San Juans as well as Bellingham Bay had the highest concentrations of catches (Delacy et al. 

1972, Miller and Borton 1980).

Yelloweye rockfish are live bearers with internal fertilization. Copulation occurs between 

September and April, with fertilization taking place later as latitude increases (Hitz 1962, 

DeLacy et al. 1964, Westrheim 1975, O'Connell 1987, Wyllie Echeverria 1987, Lea et al. 1999). 

Puget Sound yelloweye mate between winter and summer, giving birth from spring to late 

summer (Washington et al. 1978). Gestation lasts roughly 30 days (Eldridge et al. 2002).

Although yelloweye rockfish were once believed to reproduce annually, evidence exists that 

indicate the potential for multiple births per year (MacGregor 1970, Washington et al. 1978). 

Females produce more eggs as they grow older and larger, with each individual producing 

roughly 300 eggs per year per gram of body weight (1.2-2.7 million eggs per year) (MacGregor 

1970, Hart 1973). In addition, older females of several rockfish species may be capable of 
96

provisioning their offspring better than their younger counterparts, meaning that they may be 

more a more influential component in a given year’s recruitment success (Sogard et al. 2008).

Larvae are born at 4-5 mm in length and maintain a pelagic existence for the first 2 months of 

life, before moving to nearshore habitats and settling into rocky reef habitat at about 25 mm in 

length (DeLacy et al. 1964, Matarese et al. 1989, Moser 1996a, Love et al. 2002). Yelloweye 

growth is thought to vary by latitudinal gradient, with individuals in more northerly regions 

growing faster and larger. Year class strength appears to be most strongly linked to survival of 

the larval stage (Laidig et al. 2007). In general, sexual maturity appears to be reached by 50% of 

individuals by 15-20 years of age and 40-50 cm in length (Yamanaka and Kronlund 1997). As 

with other rockfish, yelloweye can be long-lived (reported oldest age is 118 years) (Munk 2001). 

Maximum size has been reported as 910 cm, but assymptotic size in Alaskan waters for both 

males and females was estimated to be 690 cm and 659-676 mm along British Columbia 

(Clemens and Wilby 1961, Westrheim and Harling 1975, Rosenthal et al. 1982, Love et al. 2005, 

Yamanaka et al. 2006). 

Individuals shift to deeper habitats as they age. Juveniles tend to begin life in shallow rocky reefs 

and graduate to deeper rocky habitats as adults. Once adult habitat is established, individuals 

tend to remain at a particular site (Love 1978, Coombs 1979, DeMott 1983).

As with other rockfish species, yelloweye rockfish prey upon different species and size classes 

throughout their development. Larval and juvenile rockfish prey upon phyto- and zooplankton 

(Lee and Sampson 2009). Adult yelloweyes eat other rockfish (including members of their own 

species), sand lance, gadids, flatfishes, shrimp, crabs, and gastropods (Love et al. 2002, 

Yamanaka et al. 2006).

8.2.2 Population Dynamics

Over the period of 1965-2007, it is estimated that rockfish species has declined by 3% per year. 

Yelloweye rockfish within the Puget Sound/Georgia Basin (in U.S. waters) are very likely most 

abundant within the San Juan Basin. Though there is no reliable population census (ROV or 

otherwise) within the basins of Puget Sound proper, the San Juan Basin has the most suitable 

rocky benthic habitat (Palsson et al. 2009) and historically was the area of greatest numbers of 

angler catches (Moulton and Miller 1987, Olander 1991). Productivity for yelloweye rockfish is 

influenced by long generation times that reflect intrinsically low annual reproductive success. 

Natural mortality rates have been estimated from 2 to 4.6 percent (Yamanaka and Kronlund 

1997, Wallace 2007). Productivity may also be particularly impacted by Allee effects, which 

occur as adults are removed by fishing and the density and proximity of mature fish decreases. 

Adult yelloweye rockfish typically occupy relatively small ranges (Love et al. 2002) and it is 

unknown the extent they may move to find suitable mates.

8.2.3 Status

The Puget Sound/Georgia Basin DPS of yelloweye rockfish was listed as endangered on April 

28, 2010 (75 FR 22276). It has been estimated that yelloweye rockfish have fallen 30% in 

abundance within 1/3 of a generation in the past few decades, an astonishing rate of decline. 

Yelloweye rockfish abundance has been variable in the Puget Sound region over the past 60 

years, ranging from less than 1% to greater than 3% of samples, although Wallace (2001)

documented large historical population in the Strait of Georgia. The latest samples have been 

historic lows in abundance. Perhaps more importantly, age classes appear to have been truncated
97

to younger, smaller fish, severely hampering the ability of the species to recover from its primary 

cause of decline: overfishing (Berkeley et al. 2004).

In Puget Sound, prior to World War II, commercial landings of rockfish species generally 

remained under 20,000 lbs, but sky-rocketed during the war to 375,000 lbs annually and 

fluctuated between 50,000 and 220,000 lbs until 1970, when landings increased linearly with 

fishing effort to a peak of 900,000 lbs by 1980 (Palsson et al. 2009). Levels fluctuated after this 

between 48,000 and 300,000 lbs for the next decade and clearly crashed in the 1990’s, with 

landings below 30,000 lbs annually. At the cessation of commercial fishing in 2003, 2,600 lbs of 

rockfish were harvested. Over the period of 1965-2007, it is estimated that rockfish species has 

declined by 3% per year.

8.2.4 Critical Habitat

NMFS proposed critical habitat designation of approximately 575 mi2of marine habitat for 

yelloweye rockrish in Puget Sound, Washington, on August 6, 2013 (78 FR 47635). A final 

designation has not been made.

8.3 Canary Rockfish (Puget Sound/Georgia Basin DPS)

Canary rockfish are found from the northern Baja peninsula north to the western Gulf of Alaska, 

and with the greatest abundance along British Columbia to central California (Miller and Lea 

1972, Hart 1973, Cailliet et al. 2000, Love et al. 2002). It is unclear how many populations 

compose canary rockfish as a species. Genetic analyses have found that individuals south of 

Cape Blanco in southern Oregon lack an allele that individuals north of this point have (Wishard 

et al. 1980). The Puget Sound/Georgia Basin DPS includes all canary rockfish in the waters of 

Puget Sound, the Strait of Georgia, and the Strait of Juan de Fuca east of Victoria Sill. In 

addition, canary rockfish are managed as two stocks in Canadian waters (COSEWIC in press). 

8.3.1 Life History

Canary rockfish occupy a variety of habitats based upon their life stage. Larvae and younger 

juveniles tend to occupy shallow waters at the beginning of their lives, but generally remain in 

the upper 100 m of the water column (Love et al. 2002).. Juveniles initially settle into tide pools 

and rocky reefs (Miller and Geibel 1973, Love et al. 1991, Cailliet et al. 2000, Love et al. 2002). 

Juveniles have also been observed in diurnal movements, occurring near sand-rock interfaces in 

groups by day and moving over sandy areas at night (Love et al. 2002). After as much as 3 years, 

juveniles move into deeper rocky reefs, forming loose schools, rarely on but generally near the 

bottom (Phillips 1960, Boehlert 1980, Lamb and Edgell 1986, Rosenthal et al. 1998, Starr 1998, 

Cailliet et al. 2000, Johnson et al. 2003, Methot and Stewart 2005, Tissot et al. 2007). Adults 

may be found in waters of up to 400 m, but tend to be most common in the 80-200 m range, or 

even shallower (Moser 1996b, Methot and Stewart 2005, Tissot et al. 2007). Mid shelf locations 

seem to have the highest concentrations of canary rockfish off Washington and Oregon 

(Weinberg 1994). Adults tend to occur in shallow areas in higher latitudes than their southern 

counterparts, although adults do appear to move into progressively deeper waters as they age 

(Vetter and Lynn 1997, Methot and Stewart 2005). It is believed that, within Puget Sound, 

canary rockfish were most common in the 1960’s and 1970’s in Tacoma Narrows, Hood Canal, 

San Juan Islands, Bellingham, and Appletree Cove (Delacy et al. 1972, Miller and Borton 1980). 
98

A latitudinal gradient may be present by age class, with older and larger individuals preferably 

occupying more northerly habitat (Dark et al. 1983).

Individual canary rockfish can range widely (up to 700 km over several years), although patterns 

of residency have been observed (Gascon and Miller 1981, DeMott 1983, Casillas et al. 1998, 

Lea et al. 1999, Love et al. 2002). In addition, seasonal movements have been found, with 

individuals moving from 160-210 m depths in late winter to 100-170 m in late summer 

(COSEWIC in press).

Canary rockfish develop their young internally before giving birth to live young as larvae. 

During each annual spawning event, a female can produce 260,000 to 1.9 million eggs, 

depending upon her size and age (Guillemot et al. 1985, NMFS 2008d). Unlike some other 

rockfish, there does not appear to be a latitudinal or geographic gradient associated with number 

of eggs produced (Gunderson et al. 1980, Love et al. 2002). Birth takes place in Oregonian and 

Washingtonian waters between September through March, with a peak in December and 

January. The peak in British Columbian waters is slightly later (February) (Hart 1973, 

Westrheim and Harling 1975, Wyllie Echeverria 1987, Barss 1989).

When born, larvae are 3.6-4.0 mm in length and take from 1-4 months to develop into juveniles 

(Waldron 1968, Richardson and Laroche 1979, Stahl-Johnson 1985, Moser 1996a, Krigsman 

2000, Love et al. 2002). As with other rockfish, females seem grow more quickly than do males, 

with females reaching sexual maturity at 7-9 years of age (35-45 cm in length) versus males at 7-

12 years (~41 cm in length) off Oregon (Westrheim and Harling 1975, Boehlert and Kappenman 

1980, Lenarz and Echeverria 1991, STAT 1999). Mean length at sexual maturity off Vancouver 

Island is 41 cm for females and 48 cm for males (Westrheim and Harling 1975). Canary rockfish 

are known to frequently reach 60-75 years of age and have been found to be as old as 84 years 

(Cailliet et al. 2000, Cailliet et al. 2001, Andrews et al. 2007). Maximum reported sizes are 76 

cm and 4.5 kg (Boehlert 1980, IGFA 1991, Williams et al. 1999, Love et al. 2002, Methot and 

Stewart 2005).

Canary rockfish prey upon different species as they age. Larvae are planktivores, consuming 

invertebrate eggs, copepods, and nauplii (Moser and Boehlert 1991, Love et al. 2002). Juveniles 

feed upon zooplankton, including crustaceans, juvenile polychaetes barnacle cyprids, and 

euphasiid eggs and larvae (Gaines and Roughgarden 1987, Love et al. 1991). However, adults 

move into a carnivorous lifestyle as well as eating euphasiids and other crustaceans. Adults 

consume other fishes such as shortbelly rockfish, mytophids and stomiatiods (Cailliet et al. 2000, 

Love et al. 2002). However, oceanographic and climactic shifts can alter foraging such that 

canary rockfish feed on other available species (Lee and Sampson 2009).

8.3.2 Population Dynamics

The rate of decline for rockfish in Puget Sound has been estimated at ~3% annually for the 

period 1965-2007.

8.3.3 Status

The Puget Sound/Georgia Basin DPS of canary rockfish was listed as threatened on April 28, 

2010 (75 FR 22276). Canary rockfish were once considered common in Puget Sound, but has 

declined at a faster rate than any other rockfish species in the region (Holmberg et al. 1967, 

NMFS 2008d). In Puget Sound, prior to World War II, commercial landings of rockfish species 

generally remained under 20,000 lbs, but sky-rocketed during the war to 375,000 lbs annually 
99

and fluctuated between 50,000 and 220,000 lbs until 1970, when landings increased linearly with 

fishing effort to a peak of 900,000 lbs by 1980(Palsson et al. 2009). Levels fluctuated after this 

between 48,000 and 300,000 lbs for the next decade and clearly crashed in the 1990’s, with 

landings below 30,000 lbs annually. At the cessation of commercial fishing in 2003, 2,600 lbs of 

rockfish were harvested. Canary rockfish have been noted for being much less frequently caught 

in the Puget Sound and Georgia Basin region since 1965 (NMFS 2008d). The rate of decline for 

rockfish in Puget Sound has been estimated at ~3% annually for the period 1965-2007.

Declines have been noted in both numbers as well as frequencies. This likely due to the targeted 

removal of larger, older, and more fecund individuals by commercial fisheries, reducing the 

ability of canary rockfish to rebound from excessive mortality (NMFS 2008d). For example, 

recreational fishing data have not reported any individuals caught greater than 55 cm since 2000, 

whereas a variety of large size classes had formerly been caught. There are concerns that even 

now some populations have been lost entirely, primarily due to over harvesting, but also due to 

low dissolved oxygen levels in some areas of Puget Sound (NMFS 2008d).

8.3.4 Critical Habitat

NMFS proposed critical habitat designation of approximately 1,185 mi2of marine habitat for 

canary rockfish in Puget Sound, Washington, on August 6, 2013 (78 FR 47635). A final 

designation has not been made.

9 Abalone

Abalone are molluscs classified in the taxonomic family Haliotidae. Two ESA-listed species 

may be affected by the proposed action and are described below.

9.1 White Abalone

The white abalone is a large marine gastropod mollusk found in deep (20 – 60 m), rocky habitats 

interspersed with sand channels, from Point Conception, California to Punta Abreojos, Baja 

California, Mexico. The species was listed as endangered under the ESA on May 29, 2001 (66 

FR 29046). We used information available in the status review report (Hobday and Tegner 2000)

and the recovery plan (NMFS 2008c) to summarize the status of the species, as follows.

9.1.1 Life History

White abalone are “broadcast” spawners, releasing gametes in synchrony during the winter. 

Fertilization is reliant upon dense adult aggregations and high gamete density. Fertilized eggs 

sink and hatch into free-swimming larvae. After one or two weeks, larvae settle and becoming 

increasingly sedentary with age. They mature at 4 – 6 years of age and can live 35 – 40 years. 

Females release hundreds of thousands to millions of eggs each year. White abalone are 

herbivorous, feeding on attached or drifting algae.

9.1.2 Population Dynamics

Surveys conducted in 2002 and 2003 resulted in population estimates of 12,818 (± 3,582) and 

7,365 (± 5,340) individuals on two banks in southern California. These estimates are larger than 

the estimate of total abundance (600 – 1,600 individuals) in the late 1990s. Though current 

abundance remains unknown, it is likely less than one percent of pre-exploitation population size 
100

9.1.3 Status

Surveys conducted between 1972 and 1997 indicate that the density of white abalone declined by 

four orders of magnitude (99 percent). Furthermore, juvenile shells are rarely observed, 

indicating a lack of recruitment. The species is endangered as a result of overharvest by 

commercial and recreational fisheries. The Californian commercial fishery began in 1968 and 

peaked at 144,000 lbs (86,000 individuals) in 1972. By 1978, white abalone catch had declined 

dramatically, such that individuals were rarely landed (< 1000 lbs annually). The Californian 

recreational fishery peaked in 1975, at ~35,000 individuals. The commercial and recreational 

fisheries were closed in 1996. White abalone were also harvested in Baja California, Mexico, 

although catch numbers are not available. Its continued existence is threatened by illegal 

poaching and low recruitment (the current density of white abalone limits the success rate of 

fertilization and recruitment). Therefore, species’ resilience to future perturbations is low. 

9.1.4 Critical Habitat

Critical habitat has not been designated because it was determined to be “not prudent,” due to 

concern that disclosure of white abalone whereabouts would increase the threat of poaching (66 

FR 29048).

9.2 Black Abalone

Black abalone is a large marine gastropod mollusk found in shallow (< 6 m) rocky intertidal and 

subtidal habitats, from Point Arena, California to Bahia Tortugas and Isla Guadalupe, Baja 

California, Mexico. The species was listed as endangered under the ESA on January 14, 2009 

(74 FR 1937). We used information available in the status review report (Butler et al. 2009) to 

summarize the status of the species, as follows.

9.2.1 Life History

Black abalone are “broadcast” spawners, releasing gametes in synchrony during the spring and 

summer. Fertilization is reliant upon dense adult aggregations, high gamete density. Within days, 

fertilized eggs sink and hatch into free-swimming larvae. After 4 – 10 days, larvae settle and 

becoming increasingly sedentary with age. They mature at ~3 years of age and can live for 30 

years. Small females release a hundred thousand eggs each year, but larger individuals release 

millions of eggs annually. Black abalone are herbivorous, feeding on attached or drifting algal 

material.

9.2.2 Population Dynamics

Fisheries data indicate that black abalone populations have declined > 95% in recent decades, 

such that the species now exhibits a patchy distribution along the coasts of California and 

northern Baja California. The populations appear to be reproductively isolated by distance, 

emphasizing the importance of local spawning and recruitment. 

9.2.3 Status

Long-term monitoring sites from most of the geographical range of black abalone in the United 

States indicate that black abalone have become locally extinct at 11 of the 32 study locations 

(34%), have declined between 90–99% in abundance at an additional 10 (31%) study locations, 

and have declined between 80–89% at 2 sites (Neuman et al. 2010). At 8 northern sites (25%), 

there have been no instances of declines, and average abundance has increased by 56% (Neuman 

et al. 2010). Thus, significant declines (>80%) have occurred at the majority (72%) of study 

sites, including all sites in southern California (Neuman et al. 2010). There is evidence of recent 
101

recruitment in northern Baja California. Black abalone are endangered as a result of overharvest 

and disease. The Californian commercial fishery peaked at 1,860 metric tons in 1879, reached 

868 metric tons in 1973, and fell to <20 metric tons in 1993, when the commercial and 

recreational fisheries were closed. Between 1972 and 1981, over 3.5 million individuals were 

harvested. The Mexican commercial fishery peaked in 1990 with 28 metric tons and declined to 

< 0.5 metric tons by 2003. The severe declines were caused primarily by withering syndrome. 

Withering syndrome is a disease caused by bacteria that prevents assimilation of nutrients in the 

digestive system. The first appearance along mainland California occurred in 1988, when 

approximately 85% of the resident black abalone in Diablo Cove died as a result of the disease 

and warm-water effluent from a nuclear power facility. Previous overharvest, continued 

poaching, and withering syndrome have resulted in extremely low population densities, which 

further reduce the potential for fertilization and recruitment and limit the recovery potential of 

the species. Its resilience to future perturbations is extremely low. 

9.2.4 Critical Habitat

On October 27, 2011, the NMFS designated critical habitat for black abalone as follows: rocky 

areas from mean high water to six meters water depth in the Farallon, Channel, and Año Nuevo 

islands; the California coastline from Del Mar Ecological Reserve south to Government Point 

(excluding some stretches, such as in Monterey Bay and between Cayucos and Montaña de Oros 

State Park); and between the Palos Verdes and Torrance border south to Los Angeles Harbor. 

These areas include primary constituent elements required by black abalone, such as: rocky 

substrates, food resources, juvenile settlement habitat, suitable water quality, and suitable 

nearshore circulation patterns. 

10 Corals

Corals include a diverse range of animals that are taxonomically complex. Most corals are 

classified in the taxonomic Class Anthozoa. Most reef-building corals are further classified in the 

Order Scleractinia Thousands of species of reef-building corals occur worldwide. The proposed 

project may affect two ESA-listed coral species and 66 species proposed for ESA-listing, 

discussed below.

10.1 Elkhorn Coral

Elkhorn coral is a branching coral found in reef crest and fore reef environments (1 – 5 m) in 

Florida, Bahamas, and the Caribbean. It was listed as threatened under the ESA on May 9, 2006 

(71 FR 26852); it was proposed as endangered on December 7, 2012 (77 FR 73219). We used 

information available in the status review report (Acropora Biological Review Team 2005) and 

the proposed listing (77 FR 73219) to summarize the status of the species, as follows.

10.1.1 Life History

Elkhorn corals reproduce sexually and asexually (i.e., fragmentation). Sexual reproduction is 

accomplished by releasing sperm and egg during spawning events, which last only a few nights 

during July, August, and/or September. After fertilization, planktonic planulae larvae form. In 

response to physical and biological settlement cues, larvae settle on exposed, hard surfaces. 

Larger colonies have higher fertility and fecundity rates. Colony maintenance is achieved mainly 

by asexual reproduction, whereas sexual reproduction and recruitment is required for colony 

growth. Nutrients are provided by symbiotic, photosynthesizing zooxanthellae, which require 
102

sunlight and relatively clear, well-circulated water. The species’ optimal water temperatures 

range from 25 to 29°C; elevated temperature may result in bleaching (i.e., loss of zooxanthellae).

10.1.2 Population Dynamics

Once abundant throughout its range, elkhorn coral has experienced precipitous declines since the 

1980s. In areas where quantitative data are available, the species has declined in abundance 

(coverage and colony numbers) by greater than 97 percent. Since 2006, some populations have 

declined by an additional 50 percent and experienced recruitment failure; however no 

populations have been extirpated, and the species retains its historical range. 

10.1.3 Status

Elkhorn coral was once one of the most abundant and important Caribbean coral species, in 

terms of accretion of reef structure. Disease, temperature-induced bleaching, and physical 

damage from hurricanes led to severe declines in the 1980s. Current major threats include 

climate change (ocean warming and acidification), disease, sedimentation, and nutrient overenrichment. Current levels of abundance and recruitment are extremely low, and the species 

continues to decline without any signs of recovery; however, there is no evidence of extirpation. 

Therefore, the species’ resilience to future perturbations is limited.

10.1.4 Critical Habitat

On November 26, 2008, NMFS designated critical habitat for elkhorn coral. They designated 

marine habitat in four specific areas: Florida (1,329 square miles), Puerto Rico (1,383 square 

miles), St. John/St. Thomas (121 square miles), and St. Croix (126 square miles). These areas 

support the following physical or biological features that are essential to the conservation of the 

species: substrate of suitable quality and availability to support successful larval settlement and 

recruitment and reattachment and recruitment of fragments. 

10.2 Staghorn Coral

Staghorn coral is a branching coral found in reef terraces and outer reef environments (5 – 15 m) 

in Florida, Bahamas, and the Caribbean. It was listed as threatened under the ESA on May 9, 

2006 (71 FR 26852); it was proposed as endangered on December 7, 2012 (77 FR 73219). We 

used information available in the status review report (Acropora Biological Review Team 2005)

and the proposed listing (77 FR 73219) to summarize the status of the species, as follows.

10.2.1 Life History

Staghorn corals reproduce sexually and asexually (i.e., fragmentation). Sexual reproduction is 

accomplished by releasing sperm and egg during spawning events, which last only a few nights 

during July, August, and/or September. After fertilization, planktonic planulae larvae form. In 

response to physical and biological settlement cues, larvae settle on exposed, hard surfaces. 

Larger colonies have higher fertility and fecundity rates. Colony maintenance is achieved mainly 

by asexual reproduction, whereas sexual reproduction and recruitment is required for colony 

growth. Nutrients for the coral are provided by symbiotic, photosynthesizing zooxanthellae, 

which require sunlight and relatively clear, well-circulated water. The species’ optimal water 

temperatures range from 26 to 29°C; elevated temperature may result in bleaching (i.e., loss of 

zooxanthellae), and lower temperatures reduce growth rates.
103

10.2.2 Population Dynamics

Once abundant throughout its range, staghorn coral has experienced precipitous declines since 

the 1980s. In areas where quantitative data are available, the species has declined in abundance 

(coverage and colony numbers) by greater than 97 percent. Since 2006, some populations have 

declined by an additional 50 percent and experienced recruitment failure; however no 

populations have been extirpated, and the species retains its historical range. 

10.2.3 Status

Staghorn coral was once one of the most abundant and important Caribbean coral species, in 

terms of accretion of reef structure. Disease, temperature-induced bleaching, and physical 

damage from hurricanes led to severe declines in the 1980s. Current major threats include 

climate change (ocean warming and acidification), disease, sedimentation, and nutrient overenrichment. Current levels of abundance and recruitment are extremely low, and the species 

continues to decline without any signs of recovery; however, there is no evidence of extirpation. 

Therefore, the species’ resilience to future perturbations is limited.

10.2.4 Critical Habitat

On November 26, 2008, NMFS designated critical habitat for staghorn coral. They designated 

marine habitat in four specific areas: Florida (1,329 square miles), Puerto Rico (1,383 square 

miles), St. John/St. Thomas (121 square miles), and St. Croix (126 square miles). These areas 

support the following physical or biological features that are essential to the conservation of the 

species: substrate of suitable quality and availability to support successful larval settlement and 

recruitment and reattachment and recruitment of fragments. 

11 Johnson’s Seagrass

Johnson’s seagrass is a rare species with an extremely limited distribution. It is found on the east 

coast of Florida from Sebastian Inlet to central Biscayne Bay. On September 14, 1998, NMFS 

issued a final rule to list the species as threatened pursuant to the ESA (69 FR 49035). We used 

information available in the final rule and the 5-year review (NMFS 2007c) to summarize the 

status of the species, as follows.

11.1.1 Life History

The life history and maintenance of populations is exclusively dependent on asexual 

reproduction and clonal growth dynamics. No male flowers have ever been reported, and there is 

no evidence of sexual reproduction. Female flowers, however, are common; they are 

morphologically and physiologically capable of being fertilized if male pollen was available. 

Growth and the occupation of space, as well as the dispersal of the species, depend on the 

division of apical meristems. Populations disappear and reappear on both short- (months) and 

long-term (years) time scales (NMFS 2007c). Johnson’s seagrass is able to colonize and thrive in 

environments where other seagrasses cannot, as a result of its potential for vegetative expansion, 

a perennial and intertidal growth habit, and a relatively high tolerance for fluctuating salinity and 

temperature (Kenworthy and Virnstein 1997).

11.1.2 Population Dynamics

The species distribution is characterized as patchy, disjunct, and temporally fluctuating. Surveys 

indicate, however, that the present geographic ranges of the southern and northern limits of the 

species have been stable for at least 10 years. It appears that the populations in the northern range 
104

of the species (Sebastian Inlet to Jupiter Inlet) are stable and capable of sustaining themselves 

despite stochastic events related to severe storms and fluctuating climatology. Although it is 

disjunctly distributed and patchy, there is some continuity in the southern distribution, at least 

during periods of relatively good environmental conditions, and no significant large-scale 

disturbances.

11.1.3 Status

Johnson’s seagrass was listed as a threatened species in 1998 because of its limited reproductive 

potential and energy storage capacity restrict its ability to repopulate an area after anthropogenic 

or natural disturbances (69 FR 49035). At the time of listing, five threats were identified:

dredging, prop scoring, storm surge, altered water quality, and siltation. Given its limited 

distribution and inability to quickly repopulate, the species’ is expected to have little resilience to 

these perturbations. Despite the continuation, or increase, of these threats, however, abundance 

and distribution have remained constant over the past decade.

11.1.4 Critical Habitat

Critical habitat for Johnson’s seagrass was designated on April 5, 2000 (65 FR 17786). Ten areas 

were designated: a portion of the Indian River Lagoon, north of the Sebastian Inlet Channel; a 

portion of the Indian River Lagoon, south of the Sebastian Inlet Channel; a portion of the Indian 

River Lagoon near the Fort Pierce Inlet; a portion of the Indian River Lagoon, north of the St. 

Lucie Inlet; a portion of Hobe Sound; a site on the south side of Jupiter Inlet; a site in central 

Lake Worth Lagoon; a site in Lake Worth Lagoon, Boynton Beach; a site in Lake Wyman, Boca 

Raton; and a portion of Biscayne Bay. These areas are characterized by one or more of the 

following criteria: (1) locations with populations that have persisted for 10 years; (2) locations 

with persistent flowering populations; (3) locations at the northern and southern range limits of 

the species; (4) locations with unique genetic diversity; and (5) locations with a documented high 

abundance of Johnson’s seagrass compared to other areas in the species’ range. Important 

physical and biological features of the critical habitat areas include adequate water quality, 

salinity levels, water transparency, and stable, unconsolidated sediments that are free from 

physical disturbance.

Acropora Biological Review Team. 2005. Atlantic Acropora status review. Report to Southeast 

Regional Office, NMFS, NOAA, U.S. Department of Commerce.

Adams, P. B., C. Grimes, J. E. Hightower, S. T. Lindley, M. L. Moser, and M. J. Parsley. 2007. 

Population status of North American green sturgeon, Acipenser medirostris. 

Environmental Biology of Fishes 79:339-356.

Adams, P. B., C. B. Grimes, J. E. Hightower, S. T. Lindley, and M. L. Moser. 2002. Status 

review for North American green sturgeon, Acipenser medirostris. National Oceanic and 

Atmospheric Administration, National Marine Fisheries Service.

Allen, B. M., and R. P. Angliss. 2011. Alaska marine mammal stock assessments, 2010. National 

Oceanic and Atmospheric Administration, National Marine Fisheries Service, Alaska 

Fisheries Science Center.

Allen, B. M., and R. P. Angliss. 2012. Alaska marine mammal stock assessments, 2011.

Allen, B. M., and R. P. Angliss. 2013. Alaska marine mammal stock assessments, 2012. NOAA, 

National Marine Fisheries Service, Alaska Fisheries Science Center.
105

Allen, M. J., and G. B. Smith. 1988. Atlas and zoogeography of common fishes in the Bering 

Sea and Northeastern Pacific.

Andrews, A. H., E. J. Burton, L. A. Kerr, G. M. Cailliet, K. H. Coale, C. C. Lundstrom, and T. 

A. Brown. 2005. Bomb radiocarbon and lead-radium disequilibria in otoliths of bocacio 

rockfish (Sebstes paucispinis): a determination of age and longevity for a difficult-to-age 

fish. Marine and Freshwater Research 56:517-528.

Andrews, A. H., L. A. Kerr, G. M. Cailliet, T. A. Brown, C. C. Lundstrom, and R. D. Stanley. 

2007. Age validation of canary rockfish (Sebastes pinniger) using two independent 

otolith techniques: lead-radium and bomb radiocarbon dating. Marine and Freshwater 

Research 58:531-541.

ASSRT. 2007. Status review of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus). National 

Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast 

Regional Office, Atlantic Sturgeon Status Review Team.

Avens, L., J. C. Taylor, L. R. Goshe, T. T. Jones, and M. Hastings. 2009. Use of 

skeletochronological analysis to estimate the age of leatherback sea turtles (Dermochelys 

coriacea) in the western North Atlantic. Endangered Species Research 8:165-177.

Bain, M., N. Haley, D. Peterson, J. R. Waldman, and K. Arend. 2000a. Harvest and habitats of 

Atlantic sturgeon Acipenser oxyrinchus Mitchill, 1815 in the Hudson River estuary: 

Lessons for sturgeon conservation. Boletín. Instituto Español de Oceanografía 16:43-53.

Bain, M. B., N. Haley, D. Peterson, K. K. Arend, K. E. Mills, and P. J. Sullivan. 2000b. 

Shortnose sturgeon of the Hudson River: An endangered species recovery success. Page 

14 Twentieth Annual Meeting of the American Fisheries Society, St. Louis, Missouri.

Baird, R. W. 2009. A review of false killer whales in Hawaiian waters: Biology, status, and risk 

factors., U.S. Marine Mammal Commission.

Baird, R. W., M. B. Hanson, G. S. Schorr, D. L. Webster, D. J. McSweeney, A. M. Gorgone, S. 

D. Mahaffy, D. M. Holzer, E. M. Oleson, and R. D. Andrews. 2012. Range and primary 

habitats of Hawaiian insular false killer whales: informing determination of critical 

habitat. Endangered Species Research 18:47-61.

Baker, J. D., A. L. Harting, T. A. Wurth, and T. C. Johanos. 2011. Dramatic shifts in Hawaiian 

monk seal distribution predicted from divergent regional trends. Marine Mammal Science 

27:78-93.

Bakkala, R. G. 1970. Synopsis of biological data on the chum salmon, Oncorhynchus keta 

(Walbaum) 1792. FAO Species Synopsis No. 41, USFWS, U.S. Department of the 

Interior.

Barnhart, R. A. 1986. Species profiles: life histories and environmental requirements of coastal 

fishes and invertebrates (Pacific Southwest) - steelhead. USFWS Biological Report 

82(11.60), U.S. Army Corps of Engineers TR EL-82-4.

Barraclough, W. E. 1964. Contribution to the marine life history of the eulachon Thaleichthys 

pacificus. Journal of the Fisheries Research Board of Canada 21:1333-1337.

Barrett, B. M., F. M. Thompson, and S. N. Wick. 1984. Adult anadromous investigations: MayOctober 1983. Alaska Department of Fish and Game.

Barss, W. H. 1989. Maturity and reproductive cycle for 35 species from the family Scorpaenidae 

found off Oregon. Oregon Department of Fish and Game, Portland, Oregon.

Beacham, T. D., D. E. Hay, and K. D. Le. 2005. Population structure and stock identification of 

eulachon (Thaleichthys pacificus), an anadromous smelt, in the Pacific Northwest. 

Marine Biotechnology 7:363-372.
106

Bennett, W. A. 2005. Critical assessment of the delta smelt population in the San Francisco 

Estuary, California. San Francisco Estuary and Watershed Science 3:73.

Berkeley, S. A., M. A. Hixon, R. J. Larson, and M. S. Love. 2004. Fisheries Sustainability via 

protection of age structure and spatial distribution of fish populations. Fisheries 29:23-32.

Bigler, B. 1985. Kotzebue Sound chum salmon (Oncorhynchus keta) escapement and return data, 

1962-1984. ADF&G Technical Data Report No. 149, Alaska Department of Fish and 

Game, Division of Commercial Fisheries, Kotzebue, Alaska.

Bjorkstedt, E., B. C. Spence, J. C. Garza, D. G. Hankin, D. Fuller, W. E. Jones, J. J. Smith, and 

R. Macedo. 2005. An analysis of historical population structure for evolutionarily 

signficant units of Chinook salmon, coho salmon, and steelhead in the north-Central 

California Coast Recovery Domain. NMFS, NOAA, U.S. Department of Commerce.

Bjornn, T., D. Craddock, and D. Corley. 1968. Migration and survival of Redfish Lake, Idaho, 

Sockeye salmon, Oncorhynchus nerka. Transactions of the American Fisheries Society 

97:360-373.

Bjornn, T. C., and N. Horner. 1980. Biological criteria for classification of Pacific salmon and 

steelhead as threatened or endangered under the Endangered Species Act. Idaho 

Cooperative Fisheries Research Unit and National Marine Fisheries Service, Moscow, 

Idaho.

Blum, J. P. 1988. Assessment of factors affecting sockeye salmon (Oncorhynchus nerka) 

production in Ozette Lake, WA. Master Thesis. University of Washington, Seattle, 

Washington.

Boehlert, G. W. 1980. Size composition, age composition, and growth of canary rockfish, 

Sebastes pinniger, and splitnose rockfish, S. diploproa, from the 1977 rockfish survey. 

Marine Fisheries Review 42:57-63.

Boehlert, G. W., and R. F. Kappenman. 1980. Variation of growth with latitude in two species of 

rockfish (Sebastes pinniger and S. diploproa) from the northeast Pacific Ocean. Marine 

Ecology Progress Series 3:1-10.

Boreman, J. 1997. Sensitivity of North American sturgeons and paddlefish to fishing mortality. 

Environmental Biology of Fishes 48:399-405.

Boughton, D. A., P. B. Adams, E. Anderson, C. Fusaro, E. Keller, E. Kelley, L. Lentsch, J. 

Nielsen, K. Perry, H. Regan, J. Smith, C. Swift, L. Thompson, and F. Watson. 2006. 

Steelhead of the South-central/Southern California Coast: population characterization for 

recovery planning. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-394, 

NMFS, NOAA, U.S. Department of Commerce.

Boughton, D. A., P. B. Adams, E. Anderson, C. Fusaro, E. Keller, E. Kelley, L. Lentsch, J. 

Nielsen, K. Perry, H. Regan, J. Smith, C. Swift, L. Thompson, and F. Watson. 2007. 

Viability criteria for steelhead of the South-central and Southern California Coast. 

Technical Memorandum NOAA-TM-NMFS-SWFSC-407, NMFS, NOAA, U. S. 

Department of Commerce.

Boughton, D. A., H. Fish, K. Pipal, J. Goin, F. Watson, J. Casagrande, J. Casagrande, and M. 

Stoecker. 2005. Contraction of the southern range limit for anadromous Oncorhynchus 

mykiss. Technical Memorandum NOAA-TM-NMFS-SWFSC-380, NMFS, NOAA, U.S. 

Department of Commerce.

Bradford, A. L., K. A. Forney, E. M. Oleson, and J. Barlow. 2012. Line-transect abundance 

estimates of false killer whales (Pseudorca crassidens) in the Pelagic Region of the 
107

Hawaiian Exclusive Economic Zone and in the insular waters of the northwestern 

Hawaiian Islands.

Brown, L. R., P. B. Moyle, and R. M. Yoshiyama. 1994. Historical decline and current status of 

coho salmon in California. North American Journal of Fisheries Management 14:237-

261.

Brundage, H. M., and J. C. O. Herron. 2003. Population estimate for shortnose sturgeon in the 

Delaware River. 2003 Shortnose Sturgeon Conference.

Burgner, R. L. 1991. Life history of sockeye salmon. Pages 3-117 in C. Groot and L. Margolis, 

editors. Pacific salmon life histories. University of British Columbia Press, Vancouver, 

British Columbia, Canada.

Burgner, R. L., S. T. Light, L. Margolis, T. Okazaki, A. Tautz, and S. Ito. 1992. Distribution and 

origins of steelhead trout (Oncorhynchus mykiss) in offshore waters of the North Pacific 

Ocean. International North Pacific Fisheries Commission, Vancouver, Canada.

Busby, P. J., T. C. Wainwright, G. J. Bryant, L. J. Lierheimer, R. S. Waples, F. W. Waknitz, and 

I. V. Lagomarsine. 1996. Status review of steelhead from Washington, Oregon, and 

California. NMFS-NWFSC-27, National Oceanic and Atmospheric Administration, 

National Marine Fisheries Service, Northwest Fisheries Science Center, Seattle, 

Washington.

Butler, J., A. DeVogelaere, R. G. Gustafson, C. Mobley, M. Neumann, D. Richards, S. Rumsey, 

B. L. Taylor, and G. VanBlaricom. 2009. Status review report for black abalone (Haliotis 

cracherodiiI Leach, 1814). National Oceanic and Atmospheric Administration, National 

Marine Fisheries Service, Southwest Region.

Cailliet, G. M., A. H. Andrews, E. J. Burton, D. L. Watters, D. E. Kline, and L. A. FerryGraham. 2001. Age determination and validation studies of marine fishes: do deepdwellers live longer? Pages 739-764.

Cailliet, G. M., E. J. Burton, J. M. Cope, and L. A. Kerr. 2000. Biological characteristics of 

nearshore fishes of California: A review of existing knowledge. Pacific States Marine 

Fisheries Commission and California Department of Fish and Game 

Calambokidis, J. 2010. Final report and recommendations.in Symposium on the Results of the 

SPLASH Humpback Whale Study, Quebec City, Canada.

California Department of Fish and Game. 1998. Report to the Fish and Game Commission: a 

status review of the spring-run chinook salmon (Oncorhynchus tshawytscha) in the 

Sacramento River drainage. 98-01.

California Department of Fish and Game. 2009. GrandTab: California Central Valley, 

Sacramento and San Joaquin River systems, Chinook salmon escapement, hatcheries and 

natural areas. Anadromous Resources Assessment, Fisheries Branch, California 

Department of Fish and Game.

Carlson, H. R., and R. R. Straty. 1981. Habitat and nursery grounds of Pacific rockfish, Sebastes

spp., in rocky coastal areas of southeastern Alaska. Marine Fisheries Review 43:13-19.

Carlson, J. K., and J. Osborne. 2012. Relative abundance of smalltooth sawfish (Pristis 

pectinata) based on the Everglades National Park creel survey. NOAA Technical 

Memorandum NMFS-SEFSC-626, Southeast Fisheries Science Center, NMFS, NOAA, 

U.S. Department of Commerce.

Carlson, J. K., J. Osborne, and T. W. Schmidt. 2007. Monitoring the recovery of smalltooth 

sawfish, Pristis pectinata, using standardized relative indices of abundance. Biological 

Conservation 136:195-202.
108

Carr, M. H. 1983. Spatial and temporal patterns of recruitment of young-of-the-year rockfishes 

(Genus Sebastes) into a central California kelp forest. San Francisco State University.

Carretta, J. V., K. A. Forney, E. Oleson, K. Martien, M. M. Muto, M. S. Lowry, J. Barlow, J. 

Baker, B. Hanson, D. Lynch, L. Carswell, R. L. Brownell Jr., J. Robbins, D. K. Mattila, 

K. Ralls, and M. C. Hill. 2011. U.S. Pacific marine mammal stock assessments: 2010.

Carretta, J. V., K. A. Forney, E. Oleson, K. Martien, M. M. Muto, M. S. Lowry, J. Barlow, J. 

Baker, B. Hanson, D. Lynch, L. Carswell, R. L. Brownell Jr., J. Robbins, D. K. Mattila, 

K. Ralls, and M. C. Hill. 2012. U.S. Pacific marine mammal stock assessments: 2011.

Carretta, J. V., E. Oleson, D. W. Weller, A. R. Lang, K. A. Forney, J. Baker, B. Hanson, K. 

Martien, M. M. Muto, M. S. Lowry, J. Barlow, D. Lynch, L. Carswell, R. L. Brownell Jr., 

D. K. Mattila, and M. C. Hill. 2013. U.S. Pacific marine mammal stock assessments: 

2012. National Oceanic and Atmospheric Administration, National Marine Fisheries 

Service, Southwest Fisheries Science Center.

Casey, J., J. Garner, S. Garner, and A. S. Williard. 2010. Diel foraging behavior of gravid 

leatherback sea turtles in deep waters of the Caribbean Sea. Journal of Experimental 

Biology 213:3961-3971.

Casillas, E., L. Crockett, Y. deReynier, J. Glock, M. Helvey, B. Meyer, C. Schmitt, M. 

Yoklavich, A. Bailey, B. Chao, B. Johnson, and T. Pepperell. 1998. Essential fish habitat 

west coast National Marine Fisheries Service, Seattle, Washington.

Chapman, D. D., C. A. Simpfendorfer, T. R. Wiley, G. R. Poulakis, C. Curtis, M. Tringali, J. K. 

Carlson, and K. A. Feldheim. 2011. Genetic diversity despite population collapse in a 

critically endangered marine fish: The smalltooth sawfish (Pristis pectinata). Journal of 

Heredity 102:643-652.

Chapman, D. W., and K. L. Witty. 1993. Habitat of weak salmon stocks in the Snake River basin 

and feasible recovery measures: recovery issues for threatened and endangered Snake 

River salmon. Division of Fish and Wildlife, Bonneville Power Administration, U.S. 

Department of Energy.

Clarke, A. D., A. Lewis, K. H. Telmer, and J. M. Shrimpton. 2007. Life history and age at 

maturity of an anadromous smelt, the eulachon Thaleichthys pacificus (Richardson). 

Journal of Fish Biology 71:1479-1493.

Clemens, W. A., and G. V. Wilby. 1961. Fishes of the Pacific Coast of Canada. Second edition. 

Fisheries Research Board of Canada.

Collins, M. R., S. G. Rogers, T. I. J. Smith, and M. L. Moser. 2000. Primary factors affecting 

sturgeon populations in the southeastern United States: Fishing mortality and degradation 

of essential habitats. Bulletin of Marine Science 66:917-928.

Conant, T. A., P. H. Dutton, T. Eguchi, S. P. Epperly, C. Fahy, M. Godfrey, S. MacPherson, E. 

Possardt, B. Schroeder, J. Seminoff, M. Snover, C. Upite, and B. Witherington. 2009. 

Loggerhead sea turtle (Caretta caretta) 2009 status review under the U.S. Endangered 

Species Act. Report of the Loggerhead Biological Review Team to the National Marine 

Fisheries Service August 2009:222 pages.

Connor, W. P., J. G. Sneva, K. F. Tiffan, R. K. Steinhorst, and D. Ross. 2005. Two alternative 

juvenile life history types for fall Chinook salmon in the Snake River Basin. Transactions 

of the American Fisheries Society 134:291-304.

Cook, D. 2008. Chinook salmon spawning study Russian River fall 2002-2007. Sonoma County 

Water Agency, Santa Rosa, California.
109

Coombs, C. I. 1979. Reef fishes near Depoe Bay, Oregon: Movement and the recreational 

fishery. Oregon State University.

COSEWIC. 2002. COSEWIC assessment and update status report on the blue whale 

Balaenoptera musculus (Atlantic population, Pacific population) in Canada.vi + 32.

COSEWIC. 2011. COSEWIC assessment and status report on the eulachon (Thaleichthys 

pacificus), Nass/Skeena Rivers population, Central Pacific Coast population, and the 

Fraser River population in Canada. Committee on the Status of Endangered Wildlife in 

Canada, Ottawa, Ontario, Canada.

COSEWIC. in press. COSEWIC assessment and status report on the canary rockfish Sebastes 

pinniger in Canada. Committee on the Status of Endangered Wildlife in Canada, Ottawa, 

Canada.

Crewson, M. J., M. J. Haggerty , A. C. Ritchie, S. F. Young, J. B. Shaklee, K. P. Currens, and W. 

Eldridge. 2001. Genetic Characterization of Lake Ozette sockeye salmon for 

enhancement recovery strategies Report for IAC Grant #01-038 prepared by Makah 

Fisheries Management, Neah Bay, Washington; Washington Department of Fish and 

Wildlife, Olympia, Washington; and Northwest Indian Fisheries Commission, Olympia, 

Washington.

Dadswell, M. J. 1979. Biology and population characteristics of the shortnose sturgeon, 

Acipenser brevirostrum LeSueur 1818 (Osteichthyes: Acipenseridae), in the Saint John 

River Estuary, New Brunswick, Canada. Canadian Journal of Zoology 57:2186-2210.

Dai, L., D. Vorselen, K. S. Korolev, and J. Gore. 2012. Generic indicators for loss of resilience 

before a tipping point leading to population collapse. Science 336:1175-1177.

Daly, E. A., R. D. Brodeur, J. P. Fisher, L. A. Weitkamp, D. J. Teel, and B. R. Beckman. 2012. 

Spatial and trophic overlap of marked and unmarked Columbia River Basin spring 

Chinook salmon during early marine residence with implications for competition between 

hatchery and naturally produced fish. Environmental Biology of Fishes 94:117-134.

Dark, T. A., M. E. Wilkins, and K. Edwards. 1983. Bottom trawl survey of canary rockfish 

(Sebastes pinninger), yellowtail rockfish (S. flavidus), bocaccio (S. paucispinis), and 

chilipepper (S. goodei) off Washington-California, 1980. NMFS, NWFSC and Alaska 

Fisheries Center, Seattle, Washington.

DeLacy, A. C., C. R. Hitz, and R. L. Dryfoos. 1964. Maturation, gestation, and birth of rockfish 

(Sebastodes) from Washington and adjacent waters. Washington Department of 

Fisheries.

Delacy, A. C., B. S. Miller, and S. F. Borton. 1972. Checklist of Puget Sound fishes. University 

of Washington, Seattle, Washington.

Demko, D. B., and S. P. Cramer. 2000. Effects of pulse flows on juvenile chinook migration in 

the Stanislaus River. S.P. Cramer and Associates, Inc., Oakdale, California.

DeMott, G. E. 1983. Movement of tagged lingcod and rockfishes off Depoe Bay, Oregon. 

Oregon State University.

DeVries, R. J. 2006. Population dynamics, movements, and spawning habitat of the shortnose 

sturgeon, Acipenser brevirostrum, in the Altamaha River. Thesis. University of Georgia.

Dodd, C. K. 1988. Synopsis of the biological data on the loggerhead sea turtle: Caretta caretta 

(Linnaeus, 1758). Fish and Wildlife Service, U.S. Dept. of the Interior, Washington, D.C.

Dorn, M. W. 2002. Advice on west coast rockfish harvest rates from Bayesian meta-analysis of 

stock-recruit relationships. North American Journal of Fisheries Management 22:280-

300.
110

Dovel, W. L. 1979. The biology and management of shortnose and Atlantic sturgeon of the 

Hudson River. Project Number: AFS9-R, New York State Department of Environmental 

Conservation.

Drake, A., and L. Wilson. 1991. Eulachon, a fish to cure humanity. Museum Note 32, UBC 

Museum of Anthropology.

Echeverria, T. W. 1987. Thirty-four species of California rockfishes: maturity and seasonality of 

reproduction. Fisheries Bulletin 85:229-250.

Eckert, K., B. Wallace, J. Frazier, S. Eckert, and P. Pritchard. 2012. Synopsis of the biological 

data on the leatherback sea turtle (Dermochelys coriacea). .172.

Eldridge, M. B., E. C. Norton, B. M. Jarvis, and R. B. MacFarlane. 2002. Energetics of early 

development in the viviparous yellowtail rockfish. Journal of Fish Biology 61:1122-1134.

Emery, B. M., L. Washburn, M. S. Love, M. M. Hishimoto, and J. C. Ohlmann. 2006. Do oil and 

gas platforms off California reduce recruitment of bocaccio (Sebastes paucispinis) to 

natural habitat? An analysis based on trajectories derived from high-frequency radar. 

Fishery Bulletin 104:391-400.

Emmett, R. L., G. K. Krutzikowsky, and P. Bentley. 2006. Abundance and distribution of pelagic 

piscivorous fishes in the Columbia River plume during spring/early summer 1998–2003: 

relationship to oceanographic conditions, forage fishes, and juvenile salmonids. Progress 

in Oceanography 68:1-26.

Emmett, R. L., S. L. Stone, S. A. Hinton, and M. E. Monaco. 1991. Distribution and abundance 

of fishes and invertebrates in West Coast estuaries. National Oceanic and Atmospheric 

Administration, National Ocean Service, Strategic Environmental Assessments Division, 

Rockville, Maryland.

Eschmeyer, W. N., E. S. Herald, and H. Hammann. 1983. A Field Guide to Pacific Coast Fishes 

of North America. Houghton Mifflin Company, Boston, Massachusetts.

Fay, C., M. Bartron, S. Craig, A. Hecht, J. Pruden, R. Saunders, T. Sheehan, and J. Trial. 2006. 

Status review for anadromous Atlantic salmon (Salmo salar) in the United States. 

Biological Review Team report submitted to NMFS, NOAA, U.S. Department of 

Commerce and USFWS, U.S. Department of the Interior.

Feder, H. M., C. H. Turner, and C. Limbaugh. 1974. Observations on fishes associated with kelp 

beds in southern California. Fisheries Bulletin 160:144.

Fisher, F. W. 1994. Past and present status of Central Valley Chinook salmon. Conservation 

Biology 8:870-873.

Fisher, T., and R. Hinrichsen. 2006. Abundance-based trend results for Columbia Basin salmon 

and steelhead ESUs. Bonneville Power Administration, Portland, Oregon.

Florida Fish and Wildlife Conservation Commission. 2001. Atlantic sturgeon biological status 

review report. Tallahassee, Florida.

Florida Museum of Natural History. 2014. National Sawfish Encounter Database. Type of 

sawfish encounters reported in the U.S. Interview data from January 1998 to May 2011, 

http://www.flmnh.ufl.edu/fish/sharks/sawfish/dataone.html.

Ford, M. J., editor. 2011. Status review update for Pacific salmon and steelhead listed under the 

Endangered Species Act: Pacific Northwest. NOAA Technical Memorandum NOAANWFSC-113, NMFS, NOAA, U.S. Department of Commerce.

Foster, N. W., and C. G. Atkins. 1869. Second report of the Commissioners of Fisheries of the 

state of Maine 1868. Augusta, Maine.
111

Fox, D. A., J. E. Hightower, and F. M. Parauka. 2000. Gulf sturgeon spawning migration and 

habitat in the Choctawhatchee River system, Alabama-Florida. Transactions of the 

American Fisheries Society 129:811-826.

Fry Jr., D. H. 1979. Anadromous fishes of California, revised. California Department of Fish and 

Game, Sacramento, California.

Fulton, L. A. 1968. Spawning areas and abundance of Chinook salmon (Oncorhynchus 

tschawytscha) in the Columbia River basin - past and present. Special Scientific ReportFisheries No. 571, U. S. Fish and Wildlife Service, U. S. Department of the Interior.

Gaines, S. D., and J. Roughgarden. 1987. Fish in offshore kelp forests affect recruitment to 

intertidal barnacle populations. Science 235:479-481.

Gascon, D., and R. A. Miller. 1981. Colonization by nearshore fish on small artificial reefs in 

Barkley Sound, British Columbia. Canadian Journal of Zoology 59:1635-1646.

Geist, D. R., C. J. Murray, T. P. Hanrahan, and Y. Xie. 2009. A model of the effects of flow 

fluctuations on fall Chinook salmon spawning habitat availability in the Columbia River. 

North American Journal of Fisheries Management 28:1911-1927.

Good, T. P., R. S. Waples, and P. Adams. 2005. Updated status of federally listed ESUs of West 

Coast salmon and steelhead. NOAA Technical Memorandum NMFS-NWFSC-66, 

NMFS, NOAA, U. S. Department of Commerce.

Guillemot, P. J., R. J. Larson, and W. H. Lenarz. 1985. Seasonal cycles of fat and gonad volume 

in five species of northern California rockfish (Scorpaenidae: Sebastes). Fishery Bulletin 

1983.

Gunderson, D. R., P. Callahan, and B. Goiney. 1980. Maturation and fecundity of four species of 

Sebastes. Marine Fisheries Review 42:74-79.

Gustafson, R. G., M. J. Ford, D. Teel, and J. S. Drake. 2010. Status review of eulachon 

(Thaleichthys pacificus) in Washington, Oregon,and California. National Oceanic and 

Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries 

Science Center.

Gustafson, R. G., T. C. Wainwright, G. A. Winans, F. W. Waknitz, L. T. Parker, and R. S. 

Waples. 1997. Status review of sockeye salmon from Washington and Oregon. NOAA 

Technical Memorandum NMFS-NWFSC-33, NMFS, NOAA, U.S. Department of 

Commerce.

Hallock, R. J., W. F. Van Woert, and L. Shapovalov. 1961. An evaluation of stocking hatcheryreared steelhead rainbow trout (Salmo gairdnerii gairdnerii) in the Sacramento River 

system. Fish Bulletin 114:1-74.

Halstead, B. W., P. S. Auerbach, and D. R. Campbell. 1990. A colour atlas of dangerous marine 

animals. Wolfe Medical Publications Ltd, W.S. Cowell Ltd, Ipswich, England.

Hamilton, J. B., G. L. Curtis, S. M. Snedaker, and D. K. White. 2005. Fisheries history -

distribution of anadromous fishes in the Upper Klamath River Watershed prior to 

hydropower dams -- A synthesis of the historical evidence Fisheries 30:11.

Hanson, M. B., R. W. Baird, J. K. B. Ford, J. Hempelmann-Halos, D. M. Van Doornik, J. R. 

Candy, C. K. Emmons, G. S. Schorr, B. Gisborne, K. L. Ayres, S. K. Wasser, K. C. 

Balcomb, K. Balcomb-Bartok, J. G. Sneva, and M. J. Ford. 2010. Species and stock 

identification of prey consumed by endangered southern resident killer whales in their 

summer range. Endangered Species Research 11:69-82.

Hart, J. L. 1973. Pacific fishes of Canada. Bulletin of the Fisheries Research Board of Canada 

180.
112

Hart, J. L., and J. L. McHugh. 1944. The smelts (Osmeridae) of British Columbia. Bulletin of the 

Fisheries Research Board of Canada 64.

Hartmann, A. R. 1987. Movement of scorpionfishes (Scorpaenidae: Sebastes and Scorpaena) in 

the Southern California Bight. Bulletin of the California Department of Fish and Game

73:68-79.

Harvey, C. J., N. Tolimieri, and P. S. Levin. 2006. Changes in body size, abundance, and energy 

allocation in rockfish assemblages of the Northeast Pacific. Ecological Applications 

16:1502-1515.

Hatten, J. R., and K. F. Tiffan. 2009. A spatial model to assess the effects of hydropower 

operations on Columbia River fall Chinook salmon spawning habitat. North American 

Journal of Fisheries Management 29:1379-1405.

Haw, F., and R. Buckley. 1971. Saltwater Fishing in Washington. Stanley N. Jones, Seattle, 

Washington.

Hay, D., and P. B. McCarter. 2000. Status of the eulachon Thaleichthys pacificus in Canada. 

1480-4883, Department of Fisheries and Oceans Canada, Canadian Stock Assessment 

Secretariat, Ottawa, Canada.

Hayes, S. A., M. H. Bond, C. V. Hanson, and R. B. MacFarlane. 2004. Interactions between 

endangered wild and hatchery salmonids: can the pitfalls of artificial propagation be 

avoided in small coastal streams? Journal of Fish Biology 65:101-121.

Hayman, R. A., E. M. Beamer, and R. E. McClure. 1996. FY 1995 Skagit River Chinook 

restoration research: Skagit System Cooperative Chinook restoration research progress 

report no. 1. NWIFC Contract #3311.

Hays, G. C. 2000. The implications of variable remigration intervals for the assessment of 

population size in marine turtles. J Theor Biol 206:221-227.

Healey, M. C. 1991. Life history of Chinook salmon (Oncorhynchus tshawytscha). Pages 313-

393 in C. Groot and L. Margolis, editors. Pacific salmon life histories. University of 

British Columbia Press, Vancouver, British Columbia, Canada.

Hebdon, J. L., P. Kline, D. Taki, and T. A. Flagg. 2004. Evaluating reintroduction strategies for 

Redfish Lake sockeye salmon captive broodstock progeny. American Fisheries Society 

Symposium 44:401-413.

Hedgecock, D. 2002. Documenting biodiversity of coastal salmon (Oncorhynchus spp.) in 

northern California. Sonoma County Water Agency Contract # TW 99/00-110, Bodega 

Marine Laboratory, University of California at Davis, Bodega Bay, California.

Heise, R. J., W. T. Slack, S. T. Ross, and M. A. Dugo. 2004. Spawning and associated 

movement patterns of Gulf Sturgeon in the Pascagoula River drainage, Mississippi. 

Transactions of the American Fisheries Society 133:221-230.

Hiruki, L. M., and T. J. Ragen. 1992. A compilation of historical monk seal, Monachus 

schauinslandi, counts.in D. o. Commerce, editor. NOAA Technical Memorandum 

NMFS.

Hitz, C. R. 1962. Seasons of birth of rockfish (Sebastodes) in Oregon coastal waters. 

Transactions of the American Fisheries Society 91:231-233.

Hobbs, R. C., and K. E. W. Shelden. 2008. Supplemental status review and extinction 

assessment of Cook Inlet belugas (Delphinapterus leucas). National Oceanic and 

Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries 

Science Center.
113

Hobbs, R. C., K. E. W. Shelden, D. J. Rugh, and S. A. Norman. 2008. 2008 status review and 

extinction risk assessment of Cook Inlet belugas (Delphinapterus leucas). National 

Oceanic and Atmospheric Administration, National Marine Fisheries Service, Alaska 

Fisheries Science Center.

Hobday, A. J., and M. J. Tegner. 2000. Status review of white abalone (Haliotis sorenseni) 

throughout its range In California and Mexico. National Oceanic and Atmospheric 

Administration, National Marine Fisheries Service, Southwest Regional Office.

Holmberg, E. K., D. Day, N. Pasquale, and B. Pattie. 1967. Research report on the Washington 

trawl fishery 1962-64. Washington Department of Fisheries, Research Division.

Howell, P., K. Jones, D. Scarnecchia, L. LaVoy, W. Rendra, and D. Ortmann. 1985. Stock 

assessment of Columbia River anadromous salmonids. Volume II: steelhead stock 

summaries stock transfer guidelines - information needs. Contract Number DE-AI79-

84BP12737, Project Number 83-335, final report to Division of Fish and Wildlife, 

Bonneville Power Administration, U.S. Department of Energy.

Hugg, D. O. 1996. MAPFISH georeferenced mapping database. Life Science Software, 

Edgewater, Maryland.

IGFA. 1991. World record game fishes. International Game Fish Association.

Interior Columbia Technical Review Team. 2003. Independent populations of Chinook, 

steelhead, and sockeye for listed evolutionarily significant units within the interior 

Columbia River domain, working draft. NMFS, NOAA, U.S. Department of Commerce.

Interior Columbia Technical Review Team. 2008a. Entiat spring Chinook population, ICTRT 

working draft. NMFS, NOAA, U.S. Department of Commerce.

Interior Columbia Technical Review Team. 2008b. Methow spring Chinook population, ICTRT 

working draft. NMFS, NOAA, U.S. Department of Commerce.

Interior Columbia Technical Review Team. 2008c. Wenatchee River Sprintg Chinook 

population, ICTRT working draft. NMFS, NOAA, U.S. Department of Commerce.

James, M. C., C. Andrea Ottensmeyer, and R. A. Myers. 2005. Identification of high-use habitat 

and threats to leatherback sea turtles in northern waters: new directions for conservation. 

Ecology Letters 8:195-201.

Jennings, M. R. 1996. Past occurrence of eulachon, Thaleichthys pacificus, in streams tributary 

to Humboldt Bay, California. California Fish and Game 82:147-148.

Johanos, T. C., B. L. Becker, and T. J. Ragen. 1994. Annual reproduction cycle of the female 

Hawaiian monk seal (Monachus schauinslandi). Marine Mammal Science 10:13-30.

Johnson, D. W. 2006. Predation, habitat complexity, and variation in density-dependent 

mortality of temperate reef fishes. Ecology 87:1179-1188.

Johnson, O. W., T. A. Flagg, D. J. Maynard, G. B. Milner, and F. W. Waknitz. 1991. Status 

review for Lower Columbia River coho salmon. NOAA Technical Memorandum NMFS 

F/NWC-202, NMFS, NOAA, U.S. Department of Commerce.

Johnson, O. W., W. S. Grant, R. G. Kope, K. Neely, F. W. Waknitz, and R. S. Waples. 1997. 

Status review of chum salmon from Washington, Oregon, and California. NOAA 

Technical Memorandum NMFS-NWFSC-32, NMFS, NOAA, U.S. Department of 

Commerce.

Johnson, S. W., M. L. Murphy, and D. J. Csepp. 2003. Distribution, habitat, and behavior of 

rockfishes, Sebastes spp., in nearshore waters of southeastern Alaska: Observations from 

a remotely operated vehicle. Environmental Biology of Fishes 66:259-270.
114

Kahnle, A. W., K. A. Hattala, and K. A. McKown. 2007. Status of Atlantic sturgeon of the 

Hudson River Estuary, New York, USA. American Fisheries Society Symposium 

56:347-363.

Kahnle, A. W., K. A. Hattala, K. A. McKown, C. A. Shirey, M. R. Collins, J. T. S. Squiers, and 

T. Savoy. 1998. Stock status of Atlantic sturgeon of Atlantic coast estuaries. Draft III. 

Atlantic States Marine Fisheries Commission.

Kanda, N., M. Goto, and L. A. Pastene. 2006. Genetic characteristics of western North Pacific 

sei whales, Balaenoptera borealis, as revealed by microsatellites. Marine Biotechnology 

8:86-93.

Kehaulani Watson, T., J. N. Kittinger, J. S. Walters, and T. D. Schofield. 2011. Culture, 

conservation, and conflict: Assessing the human dimensions of Hawaiian monk seal 

recovery. Aquatic Mammals 37:386-396.

Kenworthy, W. J., and R. W. Virnstein. 1997. An Updated Biological Status Review and 

Summary of the Proceedings of Workshop to Review the Biological Status of the 

Seagrass, Halophila Johnsonii Eiseman. Beaufort Laboratory, NMFS, NOAA.

Kieffer, M. C., and B. Kynard. 1993. Annual movements of shortnose and Atlantic sturgeons in 

the Merrimack River, Massachusetts. Transactions of the American Fisheries Society 

122:1088-1103.

Kramer, D. E., and V. M. O'Connell. 1995. Guide to Northeast Pacific rockfishes. Genera 

Sebastes and Sebastolobus. Alaska Sea Grant.

Krigsman, L. M. 2000. A review of larval duration for Pacific coast temperate reek fishes; 

including kelp rockfish, Sebastes atrovirens. University of California at Santa Cruz Santa 

Cruz, California.

Kynard, B. 1997. Life history, latitudinal patterns, and status of the shortnose sturgeon, 

Acipenser brevirostrum. Environmental Biology of Fishes 48:319-334.

Kynard, B., and M. Horgan. 2002. Ontogenetic behavior and migration of Atlantic sturgeon, 

Acipenser oxyrinchus oxyrinchus, and shortnose sturgeon, A. brevirostrum, with notes on 

social behavior. Environmental Biology of Fishes 63:137-150.

La Riviere, M. G. 1991. The Ozette Lake sockeye salmon enhancement program, unpublished 

report. Makah Fisheries Management Department.

Laidig, T. E., J. R. Chess, and D. F. Howard. 2007. Relationship between abundance of juvenile 

rockfishes (Sebastes spp.) and environmental variables documented off northern 

California and potential mechanisms for the covariation. Fishery Bulletin 105:39-48.

Lamb, A., and P. Edgell. 1986. Coastal fishes of the Pacific northwest. Harbour Publishing Co. 

Ltd.

Larson, Z. S., and M. R. Belchik. 1998. A preliminary status review of eulachon and Pacific 

lamprey in the Klamath River Basin. Yurok Tribal Fisheries Program, Klamath, 

California.

Larson, Z. S., and M. R. Belchik. 2000. A preliminary status review of eulachon and Pacific 

lamprey in the Klamath River Basin. Yurok Tribal Fisheries Program, Klamath, 

California.

Lawson, P. W., E. P. Bjorkstedt, M. W. Chilcote, C. W. Huntington, J. S. Mills, K. M. S. Moore, 

T. E. Nickelson, G. H. Reeves, H. A. Stout, T. C. Wainwright, and L. A. Weitkamp. 

2007. Identification of historical populations of coho salmon (Oncorhynchus kisutch) in 

the Oregon Coast evolutionarily significant unit. NOAA Technical Memorandum NMFSNWFSC-79, NMFS, NOAA, U.S. Department of Commerce.
115

Lea, R. N., R. D. McAllister, and D. A. VenTresca. 1999. Biological aspects of nearshore 

rockfishes of the genus Sebastes from central California. Fishery Bulletin 177:1-109.

Lee, Y. W., and D. B. Sampson. 2009. Dietary variations in three co-occurring rockfish species 

off the Pacific Northwest during anomalous oceanographic events in 1998 and 1999. 

Fishery Bulletin 107:510-522.

Lenarz, W. H., and T. W. Echeverria. 1991. Sexual dimorphism in Sebastes. Environmental 

Biology of Fishes 30:71-80.

Lichatowich, J. A. 1999. Salmon Without Rivers: A History of the Pacific Salmon Crisis. Island 

Press, Washington, D. C.

Light, J. T. 1985. Food and feeding of steelhead trout in the epipelagic waters of the North 

Pacific Ocean. Document FRI-UW-8507 submitted to the annual meeting of the 

International North Pacific Fisheries Commission, Tokyo, Japan, November, 1985, 

Fisheries Research Institute, University of Washington, Seattle, Washington.

Lindley, S. T., R. S. Schick, A. Agrawal, M. N. Goslin, T. E. Pearson, E. Mora, J. J. Anderson, 

B. P. May, S. Green, C. H. Hanson, A. Low, D. McEwan, R. B. MacFarlane, C. 

Swanson, and J. G. Williams. 2006. Historical population structure of Central Valley 

steelhead and its alterations by dams. San Francisco Estuary and Watershed Science 4:1-

19.

Love, M. S. 1978. Aspects of the life history of the olive rockfish (Sebastes serranoides). 

University of California at Santa Barbara, Santa Barbara, California.

Love, M. S., M. H. Carr, and L. J. Haldorson. 1991. The ecology of substrate-associated 

juveniles of the genus Sebastes. Environmental Biology of Fishes 30:225-243.

Love, M. S., J. E. Caselle, and K. Herbinson. 1998a. Declines in nearshore rockfish recruitment 

and populations in the southern California Bight as measured by impingement rates in 

coastal electrical power generating stations. Fishery Bulletin 96:492-501.

Love, M. S., J. E. Caselle, and W. Van Buskirk. 1998b. A severe decline in the commercial 

passenger fishing vessel rockfish (Sebastes spp.) catch in the Southern California Bight, 

1980-1996. California Cooperative Oceanic Fisheries Investigations Reports 39:180-195.

Love, M. S., D. M. Schroeder, and W. Lenarz. 2005. Distribution of bocaccio (Sebastes 

paucispinis) and cow cod (Sebastes levis) around oil platforms and natural outcrops off 

California with implications for larval production. Bulletin of Marine Science 77:397-

408.

Love, M. S., D. M. Schroeder, W. Lenarz, A. MacCall, A. S. Bull, and L. Thorsteinson. 2006. 

Potential use of offshore marine structures in rebuilding an overfished rockfish species, 

bocaccio (Sebastes paucispinis). Fishery Bulletin 104:383-390.

Love, M. S., and M. Yoklavich. 2008. Habitat characteristics of juvenile cow cod, Sebastes levis 

(Scorpaenidae), in Southern California. Environmental Biology of Fishes 82:195-202.

Love, M. S., M. M. Yoklavich, and L. Thorsteinson. 2002. The Rockfishes of the Northeast 

Pacific. University of California Press, Berkeley, California.

Love, M. S., and A. York. 2005. A comparison of the fish assemblages associated with an oil/gas 

pipeline and adjacent seafloor in the Santa Barbara Channel, southern California bight. 

Bulletin of Marine Science 77:101-117.

Love, M. S., and A. York. 2006. The relationships between fish assemblages and the amount of 

bottom horizontal beam exposed at California oil platforms: fish habitat preferences at 

man-made platforms and (by inference) at natural reefs. Fishery Bulletin 104:542-549.
116

Lower Columbia Fish Recovery Board. 2010. Washington lower Columbia salmon recovery and 

fish and wildlife subbasin plan. Lower Columbia Fish Recovery Board.

Lyubimova, T. G. 1965. Main stages in the life cycle of the rockfish Sebastodes alutus (Gilbert) 

in the Gulf of Alaska. Trudy Vniro 49:85-111.

MacCall, A. D. 1996. Patterns of low frequency variability in fish populations of the California 

Current. California Cooperative Oceanic Fisheries Investigation Report.

MacCall, A. D. 2002a. Status of bocaccio off California in 2002. Pacific Fishery Management 

Council, Portland, Oregon.

MacCall, A. D. 2002b. Use of known-biomass production models to determine productivity of 

west coast groundfish stocks. North American Journal of Fisheries Management 22:272-

279.

MacCall, A. D. 2003. Status of bocaccio off California in 2003. Pacific Fishery Management 

Council, Portland, Oregon.

MacCall, A. D. 2008. Bocaccio rebuilding analysis for 2007. NMFS, SWFSC, Fish Ecology 

Division.

MacCall, A. D., and X. He. 2002a. Bocaccio rebuilding analysis for 2002. Pacific Fishery 

Management Council, Portland, Oregon.

MacCall, A. D., and X. He. 2002b. Status review of the southern stock of bocaccio (Sebastes 

paucispinis). National Oceanic and Atmospheric Administration, National Marine 

Fisheries Service, Southwest Fisheries Science Center, Santa Cruz Laboratory, Santa 

Cruz, California.

MacFarlane, R. B., S. Hayes, and B. Wells. 2008. Coho and Chinook salmon decline in 

California during the spawning seasons of 2007/08. Unpublished report.

MacGregor, J. S. 1970. Fecundity, multiple spawning, and description of the gonads in 

Sebastodes. United States Fish and Wildlife Service, Washington, D. C. .

Mason Jr., W. T., and J. P. Clugston. 1993. Foods of the gulf sturgeon in the Suwannee River, 

Florida. Transactions of the American Fisheries Society 122:378-385.

Matala, A. P., A. K.Gray, and A. J. Gharrett. 2004. Microsatellite variation indicates population 

genetics structure of bocaccio. North American Journal of Fisheries Management 

24:1189-1202.

Matarese, A. C., A. W. Kendall, D. M. Blood, and B. M. Vinter. 1989. Laboratory guide to early 

life history stages of northeast Pacific fishes. NOAA.

Matthews, G. M., and R. S. Waples. 1991. Status review for Snake River spring and summer 

Chinook salmon. NOAA Techical Memo NMFS F/NWC-200, NMFS, NOAA, U.S. 

Department of Commerce.

McAvoy, A. 2012. Hawaii Hit by Number of Endangered Seal Killings. Associated Press. ABC 

News.

McElhany, P., T. Backman, C. Busack, S. Heppell, S. Kolmes, A. Maule, J. Myers, D. Rawding, 

D. Shively, E. A. Steel, C. R. Steward, and T. Whitesel. 2003. Interim report on viability 

criteria for Willamette and Lower Columbia basin Pacific salmonids. Willamette/Lower 

Columbia Technical Recovery Team.

McElhany, P., M. Chilcote, J. Myers, and R. Beamesderfer. 2007. Viability status of Oregon 

salmon and steelhead populations in the Willamette and lower Columbia basins. Report 

prepared by the Willamette/Lower Columbia Technical Recovery Team for the Oregon 

Department of Fish and Wildlife and NMFS, NOAA, Department of Commerce.
117

McEwan, D., and T. A. Jackson. 1996. Steelhead restoration and management plan for 

California. California Department of Fish and Game, Sacramento, California.

McEwan, D. R. 2001. Central Valley steelhead. Pages 1-43 in R. L. Brown, editor. Contributions 

to the biology of the Central Valley salmonids. California Department of Fish and Game, 

Sacramento, California.

McLean, J. E., D. E. Hay, and E. B. Taylor. 1999. Marine population structure in an anadromous 

fish: Life history influences patterns of mitochondrial DNA variation in the eulachon, 

Thaleichthys pacificus. Molecular Ecology 8:S143-S158.

McLean, J. E., and E. B. Taylor. 2001. Resolution of population structure in a species with high 

gene flow: Microsatellite variation in the eulachon (Osmeridae: Thaleichthys pacificus). 

Marine Biology 139:411-420.

Meengs, C. C., and R. T. Lackey. 2005. Estimating the size of historical Oregon salmon runs. 

Reviews in Fisheries Science 13:51-66.

Merz, J. E. 2002. Seasonal feeding habits, growth, and movement of steelhead trout in the lower 

Moklumne River, California. California Fish and Game 88:95-111.

Methot, R. D., and J. J. Stewart. 2005. Status of the U.S. canary rockfish resource in 2005. 

National Marine Fisheries Service, NWFSC, Seattle, Washington.

Meylan, A. M., B. Schroeder, and A. Mosier. 1994. Marine Turtle Nesting Activity in the State 

of Florida, 1979-1992. Page 83 in Proceedings of the Fourteenth Annual Symposium on 

Sea Turtle Biology and Conservation. NOAA Technical Memorandum NMFS-SEFSC351. National Malrine Fisheries Service, Southeast Fisheries Science Center, Hilton 

Head, SC.

Miller, B. A., and S. Sadro. 2003. Residence time and seasonal movements of juvenile coho 

salmon in the ecotone and lower estuary of Winchester Creek, South Slough, Oregon. 

Transactions of the American Fisheries Society 132:546-559.

Miller, B. S., and S. F. Borton. 1980. Geographical distribution of Puget Sound fishes: Maps and 

data source sheets. University of Washington Fisheries Research Institute.

Miller, D. J., and J. J. Geibel. 1973. Summary of blue rockfish and lingcod life histories; a reef 

ecology study; and giant kelp, Macrocystis pyrifera, experiments in Monterey Bay, 

California. Fishery Bulletin 137.

Miller, D. J., and R. N. Lea. 1972. Guide to the coastal marine fishes of California. Fishery 

Bulletin 157:1-249.

Miller, R. J., and E. L. Brannon. 1982. The origin and development of life history patterns in 

Pacific salmonids. Pages 296-309 in E. L. Brannon and E. O. Salo, editors. Proceedings 

of the salmon and trout migratory behavior synposium. School of Fisheries, University of 

Washington, Seattle, Washington.

Minckley, W. L., D. A. Hendrickson, and C. E. Bond. 1986. Geography of western North 

American freshwater fishes: Description and relationship to intercontinental tectonism. 

Pages 519-613 in C. H. Hocutt and E. O. Wiley, editors. The Zoogeography of North 

American Freshwater Fishes. John Wiley and Sons, New York, New York.

Mobley Jr, J. R. 2001. Results of 2001 aerial surveys of humpback whales north of Kauai. North 

Pacific Acoustic Laboratory (NPAL) Program, Scripps Institution of Oceanography.

Mobley Jr., J. R. 2003. Results of 2003 aerial surveys of humpback whales north of Kauai., 

North Pacific Acoustic Laboratory (NPAL) Program, Scripps Oceanographic Institution.

Mobley Jr., J. R. 2004. Results of marine mammal surveys on US Navy underwater ranges in 

Hawaii and Bahamas. Office of Naval Research.
118

Mobley Jr., J. R. 2005. Results of 2005 aerial surveys of humpback whales north of Kauai. 

Scripps Oceanographic Institution, North Pacific Acoustic Laboratory (NPAL) Program.

Moody, M. F. 2008. Eulachon past and present. The University of British Columbia, Vancouver, 

British Columbia, Canada.

Moser, H. G. 1967. Reproduction and development of Sebastodes paucispinis and comparison 

with other rockfishes off southern California. Copeia 4:773-797.

Moser, H. G. 1996a. The early life stages of fishes in the California current region. National 

Oceanic and Atmospheric Administration, National Marine Fisheries Service, La Jolla, 

California.

Moser, H. G. 1996b. Scorpaenidae: scorpionfishes and rockfishes. Pages 733-795 in H. G. 

Moser, editor. The early life stages of fishes in the California current region. Allen Press, 

Lawrence, Kansas.

Moser, H. G., and G. W. Boehlert. 1991. Ecology of pelagic larvae and juveniles of the genus 

Sebastes. Environmental Biology of Fishes 30:203-224.

Moser, H. G., R. L. Charter, W. Watson, D. A. Ambrose, J. L. Butler, S. R. Charter, and E. M. 

Sandknop. 2000. Abundance and distribution of rockfish (Sebastes) larvae in the 

Southern California Bight in relation to environmental conditions and fishery 

exploitation. California Cooperative Oceanic Fisheries Investigations Reports 41:132-

147.

Moulton, L. L., and B. S. Miller. 1987. Characterization of Puget Sound marine fishes: survey of 

available data. Final report FRI-UW-8716 for Washington Sea Grant Program in 

Cooperation with U.S. Environmental Protection Agency, Puget Sound Estuary Program, 

EPA Interagency Agreement No. DW13932556-01-0, Fisheries Research Institute, 

School of Fisheries, University of Washington, Seattle, Washington.

Moyle, P. B. 1976. Inland fishes of California. University of California Press, Berkeley, 

California.

Moyle, P. B., R. M. Yoshiyama, J. E. Williams, and E. D. Wikramanayake. 1995. Fish species of 

special concern in California. California Department of Fish and Game, Inland Fisheries 

Division.

Munk, K. 2001. Maximum ages of groundfishes in waters off Alaska and British Columbia and 

consideration of age determination. Alaska Fisheries Research Bulletin 8:12-21.

Musick, J. A., M. M. Harbin, S. A. Berkeley, G. H. Burgess, A. M. Eklund, L. Findley, R. G. 

Gilmore, J. T. Golden, D. S. Ha, G. R. Huntsman, J. C. McGovern, S. J. Parker, S. G. 

Poss, E. Sala, T. W. Schmidt, G. R. Sedbeny, H. Weeks, and S. G. Wright. 2000. Marine, 

estuarine, and diadromous fish stocks at risk of extinction in North America (exclusive of 

Pacific salmonids). Fisheries 25:6-30.

Myers, J., C. Busack, A. Rawding, A. Marshall, D. J. Teel, D. M. Van Doornik, and M. T. 

Maher. 2006. Historical population structure of Pacific salmonids in the Willamette River 

and Columbia River basins. NOAA Technical Memo NMFS-NWFSC-73, NMFS, 

NOAA, U.S. Department of Commerce.

Natural Resources Council of Maine. 2014. Edwards Dam and Kennebec restoration. 

http://www.nrcm.org/projects-hot-issues/healthy-waters/edwards-dam-and-kennebecrestoration/.

Neuman, M., B. Tissot, and G. Vanblaricom. 2010. Overall status and threats assessment of 

black abalone (Haliotis cracherodii Leach, 1814) populations in California. Journal of 

Shellfish Research 29:577-586.
119

Nickelson, T. E., J. W. Nicholas, A. M. McGie, R. B. Lindsay, D. L. Bottom, R. J. Kaiser, and S. 

E. Jacobs. 1992. Status of anadromous salmonids in Oregon coastal basins. Oregon 

Department of Fish and Wildlife, Corvallis, Oregon.

NMFS. 1991. Final recovery plan for the humpback whale (Megaptera novaeangliae). NMFS, 

NOAA, U.S. Department of Commerce, Silver Spring, Maryland.

NMFS. 1998a. Final recovery plan for the shortnose sturgeon Acipenser brevirostrum. National 

Oceanic and Atmospheric Administration, National Marine Fisheries Service, Silver 

Spring, Maryland.

NMFS. 1998b. Recovery plan for the blue whale (Balaenoptera musculus). National Oceanic 

and Atmospheric Administration, National Marine Fisheries Service, Silver Spring, 

Maryland.

NMFS. 1998c. Status review of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus). National 

Oceanic and Atmospheric Administration, National Marine Fisheries Service.

NMFS. 2005a. Green sturgeon (Acipenser medirostris) status review update. Biological Review 

Team, Southwest Fisheries Science Center, NMFS, NOAA, U.S. Department of 

Commerce.

NMFS. 2005b. Status review update for Puget Sound steelhead, 26 July 2005. NMFS, NOAA, 

U.S. Department of Commerce.

NMFS. 2007a. 2007 Federal recovery outline for the distinct population segment of Central 

California Coast steelhead. NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2007b. 2007 Federal recovery outline for the distinct population segment of Northern 

California steelhead. NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2007c. Endangered Species Act 5-year review: Johnson's seagrass (Halophila johnsonii

Eiseman). National Oceanic and Atmospheric Administration, National Marine Fisheries 

Service, Silver Spring, Maryland.

NMFS. 2007d. Hawaiian monk seal (Monachus schauinslandi). 5-year review: Summary and 

evaluation. National Oceanic and Atmospheric Administration, National Marine Fisheries 

Service.

NMFS. 2007e. Status review of Puget Sound steelhead (Oncorhynchus mykiss). NOAA 

Technical Memorandum NMFS-NWFSC-81, NMFS, NOAA, U.S. Department of 

Commerce.

NMFS. 2008a. Biological opinion for water supply, flood control operations, and channel 

maintenance conducted by the U.S. Army Corps of Engineers, the Sonoma County Water 

Agency, and the Mendocino County Russian River Flood Control and Water 

Conservation Improvement District in the Russian River watershed. Report Tracking 

Number F/SWR/2006/07316, NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2008b. Endangered Species Act section 7(a)(2) consultation biological opinion and 

Magnuson-Stevens Fishery Conservation and Management Act essential fish habitat 

consultation consultation on remand for operation of the Federal Columbia River Power 

System, 11 Bureau of Reclamation projects in the Columbia Basin and ESA section 

10(a)(I)(A) permit for Juvenile Fish Transportation Program (revised and reissued 

pursuant to court order, NWF v. NMFS, Civ. No. CV 01-640-RE (D. Oregon)). Report 

Tracking Number F/NWR/2005/05883, NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2008c. Final white abalone recovery plan (Haliotis sorenseni). NMFS, NOAA, U.S. 

Department of Commerce, Long Beach, California.
120

NMFS. 2008d. Preliminary scientific conclusions of the review of the status of 5 species of 

rockfish: bocaccio (Sebastes paucispinis), canary rockfish (Sebastes pinniger), yelloweye 

rockfish (Sebastes ruberrimus), greenstriped rockfish (Sebastes elongatus) and redstripe 

rockfish (Sebastes proriger) in Puget Sound, Washington. NMFS, NWFSC, Seattle, 

Washignton.

NMFS. 2009a. An assessment of loggerhead sea turtles to estimate impacts of mortality 

reductions on population dynamics. National Oceanic and Atmospheric Administration, 

National Marine Fisheries Service.

NMFS. 2009b. Middle Columbia River steelhead distinct population segment ESA recovery 

plan. NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2009c. Public draft recovery plan for the Evolutionarily Significant Units of Sacramento 

River winter‐run Chinook salmon and Central Valley spring‐run Chinook salmon and the 

Distinct Population Segment of Central Valley steelhead. NMFS, NOAA, U.S. 

Department of Commerce.

NMFS. 2009d. Recovery plan for Lake Ozette sockeye salmon (Oncorhynchus nerka). NMFS, 

NOAA, U.S. Department of Commerce.

NMFS. 2009e. Smalltooth sawfish recovery plan (Pristis pectinata). Report prepared by the 

Smalltooth Sawfish Recovery Team for NMFS, NOAA, U.S. Department of Commerce, 

Silver Spring, Maryland.

NMFS. 2010a. Federal recovery outline: North American green sturgeon, southern distinct 

population segment. Southwest Region, NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2010b. Final recovery plan for the fin whale (Balaenoptera physalus). NMFS, NOAA, 

U.S. Department of Commerce, Silver Spring, Maryland.

NMFS. 2010c. Smalltooth sawfish (Pristis pectinata Latham), 5-year review: summary and 

evaluation NMFS, NOAA, U.S. Department of Commerce, St. Petersburg, Florida.

NMFS. 2011a. 5-year review: summary and evaluation of California Coastal Chinook salmon 

ESU, Central California coast coho salmon ESU. NMFS, NOAA, U.S. Department of 

Commerce.

NMFS. 2011b. 5-year review: summary and evaluation of Central California Coastal steelhead 

DPS and Northern California steelhead DPS. NMFS, NOAA, U.S. Department of 

Commerce.

NMFS. 2011c. 5-year review: summary and evaluation of Central Valley steelhead DPS. NMFS, 

NOAA, U.S. Department of Commerce.

NMFS. 2011d. 5-year review: summary and evaluation of lower Columbia River Chinook, 

Columbia River chum, lower Columbia River coho, and lower Columbia River steelhead. 

NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2011e. 5-year review: summary and evaluation of Middle Columbia River steelhead. 

NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2011f. 5-year review: summary and evaluation of Ozette Lake sockeye. NMFS, NOAA, 

U.S. Department of Commerce.

NMFS. 2011g. 5-year review: summary and evaluation of Puget Sound Chinook, Hood Canal 

summer chum, Puget Sound steelhead. NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2011h. 5-year review: summary and evaluation of Sacramento River winter-run Chinook 

salmon ESU. NMFS, NOAA, U.S. Department of Commerce.
121

NMFS. 2011i. 5-year review: summary and evaluation of Snake River sockeye, Snake River 

spring-summer Chinook, Snake River fall-run Chinook, Snake River Basin steelhead. 

NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2011j. 5-year review: summary and evaluation of South-central California Coast 

steelhead distinct population segment. NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2011k. 5-year review: summary and evaluation of Southern California Coast steelhead 

distinct population segment. NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2011l. 5-year review: summary and evaluation of Southern Oregon/Northern California 

coast coho salmon ESU. NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2011m. 5-year review: summary and evaluation of Upper Columbia River steelhead and 

Upper Columbia River spring-run Chinook NMFS, NOAA, U.S. Department of 

Commerce.

NMFS. 2011n. 5-year review: summary and evaluation of Upper Willamette River steelhead and 

Upper Willamette River Chinook. NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2011o. 5-year review: summary and evaluation, fin whale (Balaenoptera physalus). 

NMFS, NOAA, U.S. Department of Commerce, Silver Spring, Maryland.

NMFS. 2011p. 5-year review: summary and evaluation, Southern Resident killer whales 

(Orcinus orca) NMFS, NOAA, U.S. Department of Commerce, Seattle, Washington.

NMFS. 2011q. Final recovery plan for the sei whale (Balaenoptera borealis). NMFS, NOAA, 

U.S. Department of Commerce, Silver Spring, Maryland.

NMFS. 2012a. 5-year review: summary and evaluation, North Atlantic right whale (Eubalaena 

glacialis). NMFS, NOAA, U.S. Department of Commerce, Gloucester, Massachusetts.

NMFS. 2012b. Biological opinion for registration of pesticides Oryzalin, Pendimethalin, and 

Trifluralin by the Environmental Protection Agency. NMFS, NOAA, U.S. Department of 

Commerce.

NMFS. 2012c. Five-year review: summary and evaluation, North Pacific right whale (Eubalaena 

japonica) NMFS, NOAA, U.S. Department of Commerce, Silver Spring, Maryland.

NMFS. 2012d. Public draft recovery plan for Southern Oregon/Northern California coast coho 

salmon (Oncorhynchus kisutch). NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2012e. Sei whale (Balaenoptera borealis). 5-year review: Summary and evaluation. 

National Oceanic and Atmospheric Administration, National Marine Fisheries Service, 

Office of Protected Resources.

NMFS. 2012f. Southern California steelhead recovery plan. NMFS, NOAA, U.S. Department of 

Commerce.

NMFS. 2013a. Biological opinion for the Carmel River reroute and San Clemente Dam removal 

project at the San Clemente Dam on the Carmel River by the U.S. Army Corps of 

Engineers, San Francisco District. NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2013b. Biological opinion for the operation and maintenance of the U.S. Army Corps of 

Engineers Santa Paula Creek flood control project. NMFS, NOAA, U.S. Department of 

Commerce.

NMFS. 2013c. ESA recovery plan for Lower Columbia River coho salmon, Lower Columbia 

River Chinook salmon, Columbia River chum salmon, and Lower Columbia River 

steelhead. NMFS, NOAA, U.S. Department of Commerce.

NMFS. 2013d. Federal recovery outline: Puget Sound steelhead distinct population segment. 

NMFS, NOAA, U.S. Department of Commerce.
122

NMFS. 2013e. Hawksbill sea turtle (Eremochelys imbricata) 5-year review: Summary and 

evaluation. National Marine Fisheries Service and U.S. Fish and Wildlife Service.

NMFS. 2013f. South-central California steelhead recovery plan. NMFS, NOAA, U.S. 

Department of Commerce.

NMFS. 2014. Programmatic environmental impact statement: final PEIS for Hawaiian monk seal 

recovery actions NMFS, NOAA, U.S. Department of Commerce, Silver Spring, 

Maryland.

NMFS, and USFWS. 2007a. 5-year review: summary and evaluation, green sea turtle (Chelonia 

mydas). NMFS, NOAA, U.S. Department of Commerce and USFWS, U.S. Department 

of the Interior.

NMFS, and USFWS. 2007b. Hawksbill sea turtle (Eretmochelys imbricata) 5-year review: 

Summary and evaluation National Marine Fisheries Service and U.S. Fish and Wildlife 

Service, Silver Spring, Maryland.

NMFS, and USFWS. 2007c. Leatherback sea turtle (Dermochelys coriacea) 5-year review: 

Summary and evaluation. National Marine Fisheries Service and U.S. Fish and Wildlife 

Service, Silver Spring, Maryland.

NMFS, and USFWS. 2007d. Olive ridley sea turtle (Lepidochelys olivacea) 5-year review:

Summary and evaluation. National Marine Fisheries Service and U.S. Fish and Wildlife 

Service, Silver Spring, Maryland.

NMFS, and USFWS. 2013. Hawksbill sea turtle (Eremochelys imbricata) 5-year review: 

Summary and evaluation. National Marine Fisheries Service and U.S. Fish and Wildlife 

Service.

NMFS, USFWS, and SEMARNAT. 2011. Bi-national recovery plan for the Kemp’s ridley sea 

turtle (Lepidochelys kempii), second revision. Silver Spring, Maryland.

O'Connell, V., and D. W. Carlisle. 1993. Habitat-specific density of adult yelloweye rockfish 

Sebastes ruberrimus in the eastern Gulf of Alaska. Fishery Bulletin 91:304-309.

O'Connell, V. M. 1987. Reproductive seasons for some Sebastes species in southeastern Alaska.

Oakley, N. C. 2003. Status of shortnose sturgeon, Acipenser brevirostrum, in the Neuse River, 

North Carolina. North Carolina State University, Raleigh, North Carolina.

Odemar, M. W. 1964. Southern range extension of the eulachon, Thaleichthys pacificus. 

California Fish and Game 50:305-307.

Olander, D. 1991. Northwest coastal fishing guide. Frank Amato Publications, Portland, Oregon.

Olegario, A. O. 2006. Over-wintering diet, growth, and prey availability to juvenile coho salmon 

(Onchorhynchus kisutch) in the West Fork Smith River, Oregon. Master Thesis, Master 

of Science in Fisheries Science. Oregon State University, Corvallis, Oregon.

Oleson, E. M., C. H. Boggs, K. A. Forney, M. B. Hanson, D. R. Kobayashi, B. L. Taylor, P. R. 

Wade, and G. M. Ylitalo. 2010. Status Review of Hawaiian Insular False Killer Whales 

(Pseudorca crassidens) under the Endangered Species Act. Pacific Islands Fisheries 

Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric 

Administration, U.S. Department of Commerce.

Oregon Department of Fish and Wildlife. 2010. Lower Columbia River conservation and 

recovery plan for Oregon populations of salmon and steelhead.

Oregon Department of Fish and Wildlife. 2013. Table: estimated total population, ocean harvest 

impact rate, and spawning population of naturally produced coho. 

http://oregonstate.edu/dept/ODFW/spawn/pdf%20files/coho/CoastalCohoESUSpawnHar

vestSummary.pdf.
123

Oregon Department of Fish and Wildlife, and NMFS. 2011. Upper Willamette River 

conservation and recovery plan for Chinook salmon and steelhead.

Palsson, W. A., T.-S. Tsou, G. G. Bargmann, R. M. Buckley, J. E. West, M. L. Mills, Y. W. 

Cheng, and R. E. Pacunski. 2009. The biology and assessment of rockfishes in Puget 

Sound. FPT 09-04, Fish Management Division, Fish Program, Washington Department 

of Fish and Wildlife.

Parrish, F. A. 2009. Do monk seals exert top-down pressure in subphotic ecosystems? Marine 

Mammal Science 25:91-106.

Parsons, K. M., K. C. B. III, J. K. B. Ford, and J. W. Durban. 2009. The social dynamics of 

southern resident killer whales and conservation implications for this endangered 

population. (Orcinus orca). Animal Behaviour 77:963-971.

Penobscot River Restoration Trust. 2014. Veazie Dam Removal. 

http://www.penobscotriver.org/content/5012/veazie-dam-removal.

Pert, H. A. 1993. Winter food habits of coastal juvenile steelhead and coho salmon in Pudding 

Creek, Northern California. Master Thesis, Master of Science in Wildland Resource 

Science. University of California at Berkeley, Berkeley, California.

Peterson, D. L., M. B. Bain, and N. Haley. 2000. Evidence of declining recruitment of Atlantic 

sturgeon in the Hudson River. North American Journal of Fisheries Management 20:231-

238.

Peterson, D. L., P. Schueller, R. DeVries, J. Fleming, C. Grunwald, and I. Wirgin. 2008. Annual 

run size and genetic characteristics of Atlantic sturgeon in the Altamaha River, Georgia. 

Transactions of the American Fisheries Society 137:393-401.

Phillips, J. B. 1960. Canary rockfish. California Department of Fish and Game.

Pilot, M., M. E. Dahlheim, and A. R. Hoelzel. 2010. Social cohesion among kin, gene flow 

without dispersal and the evolution of population genetic structure in the killer whale 

(Orcinus orca). J Evol Biol 23:20-31.

Piner, K. R., J. R. Wallace, O. S. Hamel, and R. Mikus. 2006. Evaluation of ageing accuracy of 

bocaccio (Sebastes paucispinis) rockfish using bomb radiocarbon. Fisheries Research 

77:200-206.

Pitcher, T. J. 1986. Functions of shoaling behaviour in teleosts. Pages 294-337 in T. J. Pitcher, 

editor. The behavior of teleost fishes. Johns Hopkins University Press, Baltimore, 

Maryland.

Poulakis, G. R., and J. C. Seitz. 2004. Recent occurrence of the smalltooth sawfish, Pristis 

pectinata (Elasmobranchiomorphi: Pristidae), in Florida Bay and the Florida Keys, with 

comments on sawfish ecology. Florida Scientist 67:27-35.

Price, E. R., B. P. Wallace, R. D. Reina, J. R. Spotila, F. V. Paladino, R. Piedra, and E. Velez. 

2004. Size, growth, and reproductive output of adult female leatherback turtles 

Dermochelys coriacea. Endangered Species Research 5:1-8.

Pritchard, P. C. H. 1982. Nesting of the leatherback turtle, Dermochelys coriacea in Pacific 

Mexico, with a new estimate of the world population status. Copeia 4:741-747.

Ragen, T. J. 1999. Human activities affecting the population trends of the Hawaiian monk seal. 

American Fisheries Society Symposium 23:183 - 194.

Ralston, S., and J. N. Ianelli. 1998. When lengths are better than ages: The complex case of 

bocaccio. University of Alaska, Fairbanks, Alaska.
124

Randall, M. T., and K. J. Sulak. 2012. Evidence of autumn spawning in Suwannee River gulf 

sturgeon, Acipenser oxyrinchus desotoi (Vladykov, 1955). Journal of Applied 

Ichthyology 28:489-495.

Rawson, K., N. J. Sands, K. P. Currens, W. H. Graeber, M. H. Ruckelshaus, R. R. Fuerstenberg, 

and J. B. Scott. 2009. Viability criteria for the Lake Ozette sockeye salmon evolutionarily 

significant unit. NOAA Technical Memorandum NMFS-NWFSC-99, NMFS, NOAA, 

U.S. Department of Commerce.

Reeves, R. R., S. Leatherwood, and R. W. Baird. 2009. Evidence of a possible decline since 

1989 in false killer whales (Pseudorca crassidens) around the main Hawaiian Islands. 

Pacific Science 63:253-261.

Reilly, C. A., T. W. Echeverria, and S. Ralston. 1992. Interannual variation and overlap in the 

diets of pelagic juvenile rockfish (genus Sebastes) off central California. Fishery Bulletin 

90:505-515.

Reilly, S. B., J. L. Bannister, P. B. Best, M. Brown, R. L. Brownell Jr., D. S. Butterworth, P. J. 

Clapham, J. Cooke, G. P. Donovan, J. Urbán, and A. N. Zerbini. 2008. Megaptera 

novaeangliae.in I. 2011, editor. IUCN Red List of Threatened Species. .

Reina, R. D., P. A. Mayor, J. R. Spotila, R. Piedra, and F. V. Paladino. 2002. Nesting ecology of 

the leatherback turtle, Dermochelys coriacea, at Parque Nacional Marino Las Baulas, 

Costa Rica: 1988-1989 to 1999-2000. Copeia 2002:653-664.

Richards, L. J. 1986. Depth and habitat distributions of three species of rockfish (Sebastes) in 

British Columbia: Observations from the submersible PISCES IV. Environmental 

Biology of Fishes 17:13-21.

Richards, L. J., J. Paul, A. J. Cass, L. Fitzpatrick, R. v. d. Broek, and C. Lauridsen. 1985. 

SCUBA survey of rockfish assemblages in the Strait of Georgia, July to October 1984. 

Department of Fisheries and Oceans, Fisheries Research Branch, Pacific Biological 

Station.

Richardson, S. L., and W. A. Laroche. 1979. Development and occurrence of larvae and 

juveniles of the rockfishes Sebastes crameri, Sebastes pinniger, and Sebastes 

helvomaculatus (Family Scorpaenidae) off Oregon. Fishery Bulletin 77:1-46.

Rieman, B. E., D. L. Myers, and R. L. Nielsen. 1994. Use of otolith microchemistry to 

discriminate Oncorhynchus nerka of resident and anadromous origin. Canadian Journal 

of Fisheries and Aquatic Sciences 51:68-77.

Rivalan, P., A. C. Prevot-Julliard, R. Choquet, R. Pradel, B. Jacquemin, and M. Girondot. 2005. 

Trade-off between current reproductive effort and delay to next reproduction in the 

leatherback sea turtle. Oecologia 145:564-574.

Rogers, S. G., and W. Weber. 1995. Status and restoration of Atlantic and shortnose sturgeons in 

Georgia., National Oceanic and Atmospheric Administration, National Marine Fisheries 

Service, Southeast Regional Office, St. Petersburg, Florida.

Rosenthal, R. J., L. Haldorson, L. J. Field, V. Moran-O'Connell, and M. G. LaRiviere. 1982. 

Inshore and shallow offshore bottomfish resources in the southeastern Gulf of Alaska. 

Alaska Coastal Research, Sitka, Alaska.

Rosenthal, R. J., V. Moran-O'Connell, and M. C. Murphy. 1998. Feeding ecology of ten species 

of rockfishes (Scorpaenidae) from the Gulf of Alaska. California Department of Fish and 

Game 74:16-37.

Ruckelshaus, M. H., K. P. Currens, W. H. Graeber, R. R. Fuerstenberg, K. Raswon, N. J. Sands, 

and J. B. Scott. 2006. Independent populations of Chinook salmon in Puget Sound. 
125

Technical Memorandum NMFS-NWFSC-78, NMFS, NOAA, U.S. Department of

Commerce.

Sakuma, K. M., and S. Ralston. 1995. Distributional patterns of late larval groundfish off central 

California in relation to hydrographic features during 1992 and 1993. California 

Cooperative Oceanic Fisheries Investigations Reports 36:179-192.

Salo, E. O. 1991. The life history of chum salmon (Onchorhynchus keta). Pages 233-309 in C. 

Groot and L. Margolis, editors. Pacific salmon life histories. University of British 

Columbia Press, Vancouver, British Columbia, Canada.

Sands, N. J., K. Rawson, K. P. Currens, W. H. Graeber, M. H. Ruckelshaus, R. R. Fuerstenberg, 

and J. Scott. 2007. Dawgz 'n the hood: the Hood Canal summer chum salmon ESU, draft 

TRT report for posting. Puget Sound Technical Recovery Team, Seattle, Washington.

Sarti Martinez, A. 2000. Dermochelys coriacea. IUCN Red List of Threatened Species. IUCN 

2011.

Scheffer, M., S. R. Carpenter, T. M. Lenton, J. Bascompte, W. Brock, V. Dakos, J. van de 

Koppel, I. A. van de Leemput, S. A. Levin, E. H. van Nes, M. Pascual, and J. 

Vandermeer. 2012. Anticipating critical transitions. Science 338:344-348.

Schroder, S. L. 1977. Assessment of production of chum salmon fry from the Big Beef Creek 

spawning channel. FRI-UW-7513, Fisheries Research Institute, University of 

Washington.

Scott, W. B., and E. J. Crossman. 1973. Freshwater fishes of Canada. Bulletin of the Fisheries 

Research Board of Canada 184:1-966.

Secor, D., P. Anders, V. W. Webster, and D. Dixon. 2002. Can we study sturgeon to extinction? 

What we do and don't know about the conservation of North American sturgeon. 

American Fisheries Society Symposium 28:183-189.

Secor, D. H., E. J. Niklitschek, J. T. Stevenson, T. E. Gunderson, S. P. Minkkinen, B. 

Richardson, B. Florence, M. Mangold, J. Skjeveland, and A. Henderson-Arzapalo. 2000. 

Dispersal and growth of yearling Atlantic sturgeon, Acipenser oxyrinchus, released into 

Chesapeake Bay. Fishery Bulletin 98:800-810.

Seitz, J. C., and G. R. Poulakis. 2002. Recent occurrences of sawfishes (Elasmobranchiomorphi: 

Pristidae) along the southwest coast of Florida (USA). Florida Scientist 65:256–266.

Shapovalov, L., and A. C. Taft. 1954. The life histories of the steelhead rainbow trout (Salmo 

gairdneri gairdneri) and silver salmon (Oncorhynchus kisutch) with special reference to 

Waddell Creek, California, and recommendations regarding their management. California 

Department of Fish and Game Bulletin 98.

Sherrill-Mix, S. A., and M. C. James. 2008. Evaluating potential tagging effects on leatherback 

sea turtles. Endangered Species Research 4:187-193.

Shortnose Sturgeon Status Review Team. 2010. A Biological Assessment of shortnose sturgeon 

(Acipenser brevirostrum). Report to Northeast Regional Office, NMFS, NOAA, U.S. 

Department of Commerce.

Simpfendorfer, C. A. 2003. Abundance, movement and habitat use of the smalltooth sawfish. 

NMFS contract number: WC133F-02-SE-0247, Mote Marine Laboratory, Sarasota, Florida.

Simpfendorfer, C. A., and T. R. Wiley. 2004. Determination of the distribution of Florida’s 

remnant sawfish population, and identification of areas critical to their conservation. 

Mote Marine Laboratory, Sarasota, Florida.
126

Skjeveland, J. E., S. A. Welsh, M. F. Mangold, S. M. Eyler, and S. Nachbar. 2000. A report of 

investigations and research on Atlantic and shortnose sturgeon in Maryland waters of 

Chesapeake Bay (1996-2000). U.S. Fish and Wildlife Service, Annapolis, Maryland.

Smith, T. I. J., E. K. Dingley, and E. E. Marchette. 1980. Induced spawning and culture of 

Atlantic sturgeon. Progressive Fish Culturist 42:147-151.

Smith, W. E., and R. W. Saalfeld. 1955. Studies on Columbia River smelt Thaleichthys pacificus

(Richardson). Washington Department of Fisheries, Fisheries Research Paper 1:3-26.

Snelson, F. F., and S. E. Williams. 1981. Notes on the occurrence, distribution, and biology of 

elasmobranch fishes in the Indian River Lagoon System, Florida. Estuaries 4:110-120.

Sogard, S. M., S. A. Berkeley, and R. Fisher. 2008. Maternal effects in rockfishes Sebastes spp.: 

a comparison among species. Marine Ecology-Progress Series 360:227-236.

Sogard, S. M., T. H. Williams, and H. Fish. 2009. Seasonal patterns of abundance, growth, and 

site fidelity of juvenile steelhead in a small coastal california stream. Transactions of the 

American Fisheries Society 138:549-563.

Sonoma County Water Agency. 2008. Chinook salmon in the Russian River. 

http://www.scwa.ca.gov/environment/natural_resources/chinook_salmon.php.

Spence, B. C., E. P. Bjorkstedt, J. C. Garza, J. J. Smith, D. G. Hankin, D. Fuller, W. E. Jones, R. 

Macedo, T. H. Williams, and E. Mora. 2008. A framework for assessing the viability of 

threatened and endangered salmon and steelhead in the north-central California Coast 

recovery domain. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-423, 

NMFS, NOAA, U.S. Department of Commerce.

Spence, B. C., and T. H. Williams. 2011. Status review update for Pacific salmon and steelhead 

listed under the Endangered Species Act: Central California Coast coho salmon ESU. 

NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-475, NMFS, NOAA, U.S. 

Department of Commerce.

Spotila, J. R., A. E. Dunham, A. J. Leslie, A. C. Steyermark, P. T. Plotkin, and F. V. Paladino. 

1996. Worldwide population decline of Dermochelys coriacea: Are leatherback turtles 

going extinct? Chelonian Conservation and Biology 2:209-222.

Squiers, T. S. 2003. Completion report Kennebec River shortnose sturgeon population study 

(1997-2001). National Oceanic and Atmospheric Administration, National Marine 

Fisheries Service.

Stahl-Johnson, K. L. 1985. Descriptive characteristics of reared Sebastes caurinus and S. 

auriculatus larvae. Pages 65-76 in 3rd International Symposium on the Early Life History 

of Fishes & 8th Annual Larval Fish Conference.

Starr, R. M. 1998. Design principles for rockfish reserves on the U. S. West Coast. Marine 

harvest refugia for west coast rockfish: a workshop.

Starr, R. M., J. N. Heine, J. M. Felton, and G. M. Cailliet. 2002. Movements of bocaccio 

(Sebastes paucispinis) and greenspotted (S. chlorostictus) rockfishes in a Monterey 

submarine canyon: implications for the design of marine reserves. Fishery Bulletin 

100:324-337.

STAT. 1999. Status of the canary rockfish resource off Oregon and Washington in 1999. 

National Marine Fisheries Service, Newport, Oregon.

Stevick, P. T., J. Allen, P. J. Clapham, N. Friday, S. K. Katona, F. Larsen, J. Lien, D. K. Mattila, 

P. J. Palsboll, J. Sigurjonsson, T. Smith, N. Oien, and P. S. Hammond. 2003. North 

Atlantic humpback whale abundance and rate of increase four decades after protection 

from whaling. Marine Ecology Progress Series 258:263-273.
127

Stout, H. A., P. W. Lawson, D. L. Bottom, T. D. Cooney, M. J. Ford, C. E. Jordan, R. G. Kope, 

L. M. Kruzic, G. R. Pess, G. H. Reeves, M. D. Scheuerell, T. C. Wainwright, R. S. 

Waples, E. Ward, L. A. Weitkamp, J. G. Williams, and T. H. Williams. 2012. Scientific 

conclusions of the status review for Oregon Coast coho salmon (Oncorhynchus kisutch). 

NOAA Technical Memorandum NMFS-NWFSC-118, NMFS, NOAA, U.S. Department 

of Commerce.

Sturdevant, M. V., T. M. Willette, S. Jewett, and E. Deberec. 1999. Diet composition, diet 

overlap, and size of 14 species of forage fish collected monthly in PWS, Alaska, 1994-

1995.

Thorpe, J. E. 1994. Salmonid fishes and the estuarine environment. Estuaries 17:76-93.

Tissot, B. N., M. A. Hixon, and D. L. Stein. 2007. Habitat-based submersible assessment of 

macro-invertebrate and groundfish assemblages at Heceta Bank, Oregon, from 1988 to 

1990. Journal of Experimental Marine Biology and Ecology 352:50-64.

Tolimieri, N., and P. S. Levin. 2005. The roles of fishing and climate in the population dynamics 

of bocaccio rockfish. Ecological Applications 15:458-468.

Tucker, A. D. 2010. Nest site fidelity and clutch frequency of loggerhead turtles are better 

elucidated by satellite telemetry than by nocturnal tagging efforts: Implications for stock 

estimation. Journal of Experimental Marine Biology and Ecology 383:48-55.

Turtle Expert Working Group. 2007. An assessment of the leatherback turtle population in the 

Atlantic Ocean. National Oceanic and Atmospheric Administration, National Marine 

Fisheries Service, Southeast Fisheries Science Center, Turtle Expert Working Group.

Upper Columbia Salmon Recovery Board. 2007. Upper Columbia spring Chinook salmon and 

steelhead recovery plan.

USFWS, and Gulf States Marine Fisheries Commission. 1995. Gulf sturgeon recovery plan. U.S. 

Fish and Wildlife Service, U.S. Department of the Interior; Gulf States Marine Fisheries 

Commission, Atlanta, Georgia.

USFWS, and NMFS. 2009. Gulf sturgeon (Acipenser oxyrinchus desotoi), 5-year review: 

summary and evaluation. Panama City Ecological Services Field Office, U.S. Fish and 

Wildlife Service, U.S. Department of the Interior and Southeast Region, NMFS, NOAA, 

U.S. Department of Commerce.

USFWS, and U.S. Bureau of Reclamation. 2007. A compilation and analysis of anadromous fish 

monitoring data from the Central Valley of California, 1992-2006. Comprehensive 

Assessment and Monitoring Program, U.S. Department of the Interior, Sacramento, 

California.

Vetter, R. D., and E. A. Lynn. 1997. Bathymetric demography, enzyme activity patterns, and 

bioenergetics of deep-living scorpaenid fishes (genera Sebastes and Sebatolobus): 

Paradigms revisited. Marine Ecology Progress Series 155:173-188.

Waldron, K. D. 1968. Early larvae of the canary rockfish, Sebastodes pinniger. Journal of the 

Fisheries Research Board of Canada 25:801-803.

Wallace, B. P., S. S. Kilham, F. V. Paladino, and J. R. Spotila. 2006. Energy budget calculations 

indicate resource limitation in Eastern Pacific leatherback turtles. Marine Ecology 

Progress Series 318:263-270.

Wallace, B. P., P. R. Sotherland, P. S. Tomillo, R. D. Reina, J. R. Spotila, and F. V. Paladino. 

2007. Maternal investment in reproduction and its consequences in leatherback turtles. 

Oecologia 152:37-47.
128

Wallace, J. R. 2001. Status of the yelloweye rockfish resource in 2001 for northern California 

and Oregon waters. Washignton Department of Fish and Wildlife, Montesano, 

Washignton.

Wallace, J. R. 2007. Update to the status of yelloweye rockfish (Sebastes ruberrimus) off the 

U.S. West Coast in 2007. Pacific Fishery Management Council, Portland, Oregon.

Waring, G. T., E. Josephson, K. Maze-Foley, and P. E. Rosel. 2010. US Atlantic and Gulf of 

Mexico marine mammal stock assessments-2010. National Oceanic and Atmospheric 

Administration, National Marine Fisheries Service, Northeast Fisheries Science Center.

Waring, G. T., E. Josephson, K. Maze-Foley, and P. E. Rosel. 2012. US Atlantic and Gulf of 

Mexico marine mammal stock assessments - 2011. National Oceanic and Atmospheric 

Administration, National Marine Fisheries Service, Northeast Fisheries Science Center.

Waring, G. T., E. Josephson, K. Maze-Foley, and P. E. Rosel. 2013. U.S. Atlantic and Gulf of 

Mexico marine mammal stock assessments - 2012. National Oceanic and Atmospheric 

Administration, National Marine Fisheries Service.

Washington Department of Fisheries, Washington Department of Wildlife, and Western 

Washington Treaty Indian Tribes. 1993. 1992 Washington State salmon and steelhead 

stock inventory. Olympia, Washington.

Washington, P. M., R. Gowan, and D. H. Ito. 1978. A biological report on eight species of 

rockfish (Sebastes spp.) from Puget Sound, Washington. National Oceanic and 

Atmospheric Administration, National Marine Fisheries Service, Seattle, Washington.

WDF. 1975-1986. Washington state sport catch reports. Washington Department of Fisheries.

WDFW, and ODFW. 2001. Washington and Oregon eulachon management plan. Washington 

Department of Fish and Wildlife and Oregon Department of Fish and Wildlife.

Wedemeyer, G. A., R. L. Saunders, and W. C. Clarke. 1980. Environmental factors affecting 

smoltification and early marine survival of anadromous salmonids. Mar.Fish.Rev.:1–14.

Weinberg, K. L. 1994. Rockfish assemblages of the middle shelf and upper slope off Oregon and 

Washington. Fishery Bulletin 92:620-632.

Weishampel, J. F., D. A. Bagley, L. M. Ehrhart, and B. L. Rodenbeck. 2003. Spatiotemporal 

patterns of annual sea turtle nesting behaviors along an East Central Florida beach. 

Biological Conservation 110:295-303.

Weitkamp, L. A., T. C. Wainwright, G. J. Bryant, G. B. Milner, D. J. Teel, R. G. Kope, and R. S. 

Waples. 1995. Status review of coho salmon from Washington, Oregon, and California. 

NOAA Technical Memorandum NMFS-NWFSC-24, NMFS, NOAA, U.S. Department 

of Commerce.

Welsh, S. A., M. F. Mangold, J. E. Skjeveland, and A. J. Spells. 2002. Distribution and 

movement of shortnose sturgeon (Acipenser brevirostrum) in Chesapeake Bay. Estuaries 

25:101-104.

Westrheim, S. J. 1975. Reproduction, maturation, and identification of larvae of some Sebastes

(Scorpaenidae) species in the northeast Pacific Ocean. Journal of the Fisheries Research 

Board of Canada 32:2399-2411.

Westrheim, S. J., and W. R. Harling. 1975. Age-length relationships for 26 scorpaenids in the 

northeast Pacific Ocean. Fisheries and Marine Service Research Division, Nanaimo, 

British Columbia.

Wiley, T. R., and C. A. Simpfendorfer. 2010. Using public encounter data to direct recovery 

efforts for the endangered smalltooth sawfish Pristis pectinata. Endangered Species 

Research 12:179-191.
129

Williams, E. H., S. Ralston, A. D. MacCall, D. Woodbury, and D. E. Pearson. 1999. Stock 

assessment of the canary rockfish resource in the waters off southern Oregon and 

California in 1999. Page 75 Status of the Pacific coast groundfish fishery through 1999 

and recommended acceptable biological catches for 2000 appendix: stock assessments. 

Pacific Fishery Management Council, Portland, Oregon.

Williams, T. H., S. T. Lindley, B. C. Spence, and D. A. Boughton. 2011. Status update for 

Pacific salmon and steelhead listed under the Endangered Species Act: Southwest, 20 

May 2011 – update to 5 January 2011 report. NMFS, NOAA, U.S. Department of 

Commerce.

Willson, M. F., R. H. Armstrong, M. C. Hermans, and K. Koski. 2006. Eulachon: A review of 

biology and an annotated bibliography. Auke Bay Laboratory, Alaska Fisheries Science 

Center, Juneau, Alaska.

Wishard, L. N., F. M. Utter, and D. R. Gunderson. 1980. Stock separation of five rockfish 

species using naturally occurring biochemical genetic markers. Marine Fisheries Review 

42:64-73.

Woodbury, D., and S. Ralston. 1991. Interannual variation in growth rates and back-calculated 

birth-date distributions of pelagic juvenile rockfishes (Sebastes spp.) off the central 

California coast. Fishery Bulletin 89:523-533.

Wright, S. 1999. Petition to list eulachon Thaleichthys pacificus as threatened or endangered 

under the Endangered Species Act.

Wydoski, R. S., and R. R. Whitney. 1979. Inland Fishes of Washington. University of 

Washington Press, Seattle, Washington.

Wyllie Echeverria, T. 1987. Thirty-four species of California rockfishes: maturity and 

seasonality of reproduction. Fisheries Bulletin 85:229-250.

Yamanaka, K. L., and A. R. Kronlund. 1997. Inshore rockfish stock assessment for the west 

coast of Canada in 1996 and recommended yields for 1997.

Yamanaka, K. L., L. C. Lacko, R. Withler, C. Grandin, J. K. Lochead, J. C. Martin, N. Olsen, 

and S. S. Wallace. 2006. A review of yelloweye rockfish Sebastes ruberrimus along the 

Pacific coast of Canada: Biology, distribution, and abundance trends 

Yoklavich, M. M., H. G. Greene, G. M. Cailliet, D. E. Sullivan, R. N. Lea, and M. S. Love. 

2000. Habitat associations of deep-water rockfishes in a submarine canyon: An example 

of a natural refuge. Fishery Bulletin 98:625-641.

Zedonis, P. A. 1992. The biology of steelhead (Onchorynchus mykiss) in the Mattole River 

estuary/lagoon, California. Master Thesis. Humboldt State University, Arcata, California.

Zehfuss, K. P., J. E. Hightower, and K. H. Pollock. 1999. Abundance of Gulf Sturgeon in the 

Apalachicola River, Florida. Transactions of the American Fisheries Society 128:130-

143.
Appendix C

Additional Species Specific Effects Analysis for Species 

Under Jurisdiction of NMFS
1

Table of Contents

Page

1 Cetaceans ................................................................................................................................ 6

1.1 Stressors ........................................................................................................................... 7

1.2 Exposure........................................................................................................................... 7

1.3 Response........................................................................................................................... 8

1.4 Southern Resident Killer Whale....................................................................................... 8

1.5 Cook Inlet Beluga Whale ............................................................................................... 10

1.6 Main Hawaiian Island Insular False Killer Whale ......................................................... 12

1.7 North Atlantic Right Whale ........................................................................................... 12

1.8 North Pacific Right Whale ............................................................................................. 15

1.9 Humpback and Fin Whales............................................................................................ 15

1.10 Sei and Blue Whales ...................................................................................................... 17

1.11 Critical Habitat ............................................................................................................... 17

2 Pinnipeds............................................................................................................................... 18

2.1 Stressors ......................................................................................................................... 20

2.2 Exposure......................................................................................................................... 20

2.3 Response......................................................................................................................... 21

2.4 Hawaiian Monk Seal ...................................................................................................... 22

2.5 Western DPS of Steller Sea Lion ................................................................................... 22

2.6 Critical Habitat ............................................................................................................... 24

3 Sea Turtles ............................................................................................................................ 25

3.1 Stressors ......................................................................................................................... 27

3.2 Exposure......................................................................................................................... 27

3.3 Response......................................................................................................................... 29

3.4 Leatherback Sea Turtles................................................................................................. 34

3.5 Loggerhead Sea Turtles.................................................................................................. 35

3.6 Green Sea Turtles........................................................................................................... 36

3.7 Hawksbill Sea Turtles .................................................................................................... 36

3.8 Kemp’s Ridley Sea Turtles ............................................................................................ 36

3.9 Olive Ridley Sea Turtles................................................................................................ 37

3.10 Critical Habitat ............................................................................................................... 37

4 Salmonids.............................................................................................................................. 38

4.1 Stressors ......................................................................................................................... 38

4.2 Exposure......................................................................................................................... 38

4.3 Response......................................................................................................................... 39

4.4 Population and Species Level Effects............................................................................ 42

4.5 Critical Habitat ............................................................................................................... 42

5 Pacific Eulachon, Southern DPS........................................................................................... 43

5.1 Stressors ......................................................................................................................... 43

5.2 Exposure......................................................................................................................... 44

5.3 Response......................................................................................................................... 44
2

5.4 Population and Species Level Effects............................................................................ 45

5.5 Critical Habitat ............................................................................................................... 45

6 Sturgeon ................................................................................................................................ 46

6.1 Stressors ......................................................................................................................... 46

6.2 Exposure......................................................................................................................... 46

6.3 Response......................................................................................................................... 49

6.4 Shortnose Sturgeon ........................................................................................................ 52

6.5 Atlantic Sturgeon............................................................................................................ 53

6.6 Gulf Sturgeon ................................................................................................................. 55

6.7 Green Sturgeon............................................................................................................... 56

6.8 Critical Habitat ............................................................................................................... 56

7 Sawfish.................................................................................................................................. 59

7.1 Exposure......................................................................................................................... 59

7.2 Response......................................................................................................................... 59

7.3 Critical Habitat ............................................................................................................... 61

8 Rockfish ................................................................................................................................ 62

8.1 Stressors ......................................................................................................................... 62

8.2 Exposure......................................................................................................................... 62

8.3 Response......................................................................................................................... 62

8.4 Population and Species Level Effects............................................................................ 65

8.5 Critical Habitat ............................................................................................................... 65

9 Abalone ................................................................................................................................. 65

9.1 Stressors ......................................................................................................................... 66

9.2 Exposure......................................................................................................................... 66

9.3 Response......................................................................................................................... 66

9.4 Population and Species Level Effects............................................................................ 68

9.5 Critical Habitat ............................................................................................................... 69

10 Corals.................................................................................................................................... 69

10.1 Stressors ......................................................................................................................... 70

10.2 Exposure......................................................................................................................... 70

10.3 Response......................................................................................................................... 71

10.4 Population and Species Level Effects............................................................................ 73

10.5 Critical Habitat ............................................................................................................... 73

11 Johnson’s Seagrass................................................................................................................ 74

11.1 Stressors ......................................................................................................................... 74

11.2 Exposure......................................................................................................................... 74

11.3 Response......................................................................................................................... 74

11.4 Population And Species Level Effects........................................................................... 75

12 Literature Cited ..................................................................................................................... 77
3

Effects of Cooling Water Intake Structures on Threatened and Endangered Species 

under National Marine Fisheries Service Jurisdiction

Under the Endangered Species Act (ESA), “effects of the action” means the direct and indirect 

effects of an action on the species or critical habitat, together with the effects of other activities 

that are interrelated or interdependent with that action, that will be added to the environmental 

baseline (50 CFR 402.02). Indirect effects are those that are caused by the proposed action and 

are later in time, but still are reasonably certain to occur.

We analyze the effects of cooling water intake structures (CWIS) considering only the 

mandatory requirements of the Environmental Protection Agency’s (EPA) regulation, without 

any of the U.S. Fish and Wildlife and National Marine Fisheries Services’ (Services) species and 

habitat protection measures (except where noted). The effects analysis in the Opinion anticipates

that where necessary State and Tribal Directors will incorporate the control measures, 

monitoring, and reporting recommendations provided by the Services through technical 

assistance facilitated by the exchange of information between the Directors and the Services into 

NPDES permits that contain 316(b) requirements. For federal permits issued by EPA, the 

Services will review and evaluate the effects of a facility’s CWIS during consultation with EPA

(where that consultation is required under section 7) for each individual permit. For permits 

issued by States and Tribes, the Services will receive all permit applications for review, will 

evaluate the effects of each facility’s CWIS, identify measures when appropriate and, when 

necessary, work with EPA to implement its oversight procedures.

Appendix C provides an initial evaluation of the direct and indirect effects of the proposed action 

on species and critical habitat. The National Marine Fisheries Services (NMFS) performs our 

effects analysis using a series of steps. 

1) We identify the physical, chemical, or biotic stressors that are likely to result from the 

operation of CWIS, as regulated under the Rule. 

2) We determine whether and how many individuals are likely to be exposed to such 

stressors. 

3) Then, we evaluate the probable responses of individuals to the stressors. If responses are 

likely to reduce the fitness (i.e., survival and/or reproduction) of one or more individual, 

we consider the magnitude of such losses on population viability. 

The ultimate purpose of our assessment is to determine whether the proposed action is likely to 

reduce the species’ likelihood of surviving and recovering in the wild (our “jeopardy” 

determination). 

Our “destruction or adverse modification” determinations must be based on an action’s effects 

on the conservation value of habitat that has been designated as critical to threatened or 

endangered species. If an area encompassed in a critical habitat designation is likely to be 

exposed to the direct or indirect consequences of the proposed action on the natural environment, 

we ask if primary constituent elements included in the designation (if there are any) or physical, 
4

chemical or biotic phenomena that give the designated area conservation value are likely to be 

appreciably diminished. 

The biological evaluation (BE) provides a qualitative assessment of the stressors potentially 

arising from the proposed action and their possible direct or indirect effects on ESA-listed 

species and designated critical habitat. These stressors include; impingement, entrapment, 

entrainment, thermal discharges, chemical discharges, and altered flow regimes (EPA 2013). 

Discharges are not regulated under Section 316(b); however, such discharges are an indirect 

effect of EPA’s action. In the BE, EPA includes thermal and chemical discharges in their 

description of the direct and indirect effects of the action on ESA-listed species and designated 

critical habitat; therefore, we include them in our effects analyses. 

The location of all facilities that may be within the action area of the rule is unknown. From a 

survey that EPA conducted, however, EPA knows the names and location of 575 electric 

generating facilities and 230 manufacturers that may be within action area of the rule. The 

survey was a census of electric generating facilities. For manufacturers, however, a weighted 

sample was collected. For the purpose of analyzing the rule, EPA estimated that 544 electric 

generating facilities and 521 manufacturing facilities, or a total of 1,065 facilities, will be subject 

to the rule (ABT 2014). 

While EPA is confident that in its estimate that there are 1,065 total facilities with one or more 

CWISs, because of the sample of manufacturers, EPA does not know the location of roughly 315 

of these facilities (ABT 2014). Consequently, in order to produce a better sense of 

manufacturers’ locations for the purpose of the Biological Evaluation, EPA developed an upperbound set of manufacturers. This set included all manufacturers that may potentially be within 

the Agency’s action area of the rule, found by searching its permit database for facilities that 

hold a NPDES permit and share a North American Industry Classification code with 

manufacturing facilities that responded to the survey that they had a CWIS. This search 

identified the location of an additional 2,925 manufacturing facilities that may be within action 

area of the rule. EPA added the 2,925 additional manufacturing facilities to the 575 electric 

generating facilities and 230 manufacturers with known locations to estimate that a total of 3,730

facilities may potentially be within the action area of the rule. It is important to note that EPA is 

confident that only 1,065 of these 3,730 facilities have a CWIS (ABT 2014). The set of 3,730 

facilities, which represents an upper bound estimate of the number off facilities that may 

possibly have cooling water intakes, allows the Services to identify the broadest set of species 

that may be affected by CWISs. Of the 3,730 facilities, 3,490 (94 percent) facilities overlap with 

the range of one or more ESA-listed species (EPA 2013) (Table 1). Overall, based on the set of 

3,730 facilities, the EPA estimates 21,039 facility-species overlaps are theoretically possible, 

though many fewer are projected when one looks only at the 1,065 facilities EPA estimates will 

actually be subject to this rule.
5

Table 1. Species under the jurisdiction of NMFS that are protected under the ESA that 

may be affected by the issuance of regulations pursuant to section 3016(b) of the 

Clean Water Act.

Common name (Distinct population segment, 

evolutionarily significant unit, or subspecies) Scientific name Status Critical Habitat

Cetaceans

Blue whale Balaenoptera musculus Endangered No

Bowhead whale Balaena mysticetes Endangered No

Fin whale Balaenoptera physalus Endangered No

Humpback whale Megaptera novaeangliae Endangered No

Killer whale (Southern Resident) Orcinus orca Endangered Yes

North Atlantic right whale Eubalaena glacialis Endangered Yes

Sei whale Balaenoptera borealis Endangered No

Sperm whale Physeter macrocephalus Endangered No

Beluga whale (Cook Inlet) Delphinapterus leucas Endangered Yes

False killer whale (Main Hawaiian insular) Pseudorca crassidens Endangered No

Pinnipeds

Guadalupe fur seal Arctocephalus townsendi Threatened No

Hawaiian monk seal Monachus schauinslandi Endangered Yes, Proposed

Steller sea lion (Western) Eumetopias jubatus Endangered Yes

Bearded seal (Beringia) Erignathus barbatus nauticus Threatened No

Ringed seal (Arctic) Phoca hispida hispida Threatened No

Sea turtles

Green sea turtle (Florida & Mexico’s Pacific coast colonies) Chelonia mydas Endangered No

Green sea turtle (all other areas) Threatened Yes

Hawksbill sea turtle Eretmochelys imbricate Endangered Yes

Kemp’s ridley sea turtle Lepidochelys kempii Endangered No

Leatherback sea turtle Dermochelys coriacea Endangered Yes

Loggerhead sea turtle (North Pacific Ocean) Caretta caretta Endangered No

Loggerhead sea turtle (Northwest Atlantic Ocean) Threatened Proposed

Olive ridley sea turtle (Mexico’s Pacific coast breeding 

colonies)

Lepidochelys olivacea Endangered No

Olive ridley sea turtle (all other areas) Threatened No

Sturgeons

Shortnose sturgeon Acipenser brevirostrum Endangered No

Green sturgeon (southern) Acipenser medirostris Threatened Yes

Gulf sturgeon Acipenser oxyrhynchus desotoi Threatened No

Atlantic sturgeon (Gulf of Maine) Acipenser oxyrhynchus Threatened No

Atlantic sturgeon (New York Bight) Endangered No

Atlantic sturgeon (Chesapeake Bay) Endangered No

Atlantic sturgeon (Carolina) Endangered No

Atlantic sturgeon (South Atlantic) Endangered No

Salmonids

Atlantic salmon (Gulf of Maine) Salmo salar Endangered Yes

Chinook salmon (CA Coastal) Oncorhynchus tschawytscha Threatened Yes

Chinook salmon (Central Valley Spring-run) Threatened Yes

Chinook salmon (Lower Columbia River) Threatened Yes

Chinook salmon (Upper Columbia River Spring-run) Endangered Yes

Chinook salmon (Puget Sound) Threatened Yes

Chinook salmon (Sacramento River Winter-run) Endangered Yes

Chinook salmon (Snake River Fall-run) Threatened Yes

Chinook salmon (Snake River Spring/Summer-run) Threatened Yes

Chinook salmon (Upper Willamette River) Threatened Yes

Chum salmon (Columbia River) Oncorhynchus keta Threatened Yes

Chum salmon (Hood Canal Summer-run) Threatened Yes

Coho salmon (Central CA Coast) Oncorhynchus kisutch Endangered Yes

Coho salmon (Lower Columbia River) Threatened Proposed

Coho salmon (Southern Oregon & Northern California 

Coast)

Threatened Yes

Coho salmon (Oregon Coast) Yes

Sockeye salmon (Ozette Lake) Oncorhynchus nerka Threatened Yes

Sockeye salmon (Snake River) Endangered Yes

Steelhead (Central California Coast) Oncorhynchus mykiss Threatened Yes

Steelhead (California Central Valley) Threatened Yes

Steelhead (Lower Columbia River) Threatened Yes

Steelhead (Middle Columbia River) Threatened Yes

Steelhead (Northern California) Threatened Yes
6

Steelhead (Puget Sound) Threatened No

Steelhead (Snake River) Threatened Yes

Steelhead (South-Central California Coast) Threatened Yes

Steelhead (Southern California) Threatened Yes

Steelhead (Upper Columbia River) Threatened Yes

Steelhead (Upper Willamette River) Threatened Yes

Other fishes

Pacific eulachon Thaleichthys pacificus Threatened Yes

Bocaccio (Georgia Basin) Sebastes paucispinis Endangered Proposed

Yelloweye rockfish (Georgia Basin) Sebastes pinniger Threatened Proposed

Canary rockfish (Georgia Basin) Sebastes ruberrimus Threatened Proposed

Smalltooth sawfish Pristis pectinata Endangered Yes

Marine invertebrates

Elkhorn coral Acropora palmata Threatened1 Yes

Staghorn coral Acropora cervicornis Threatened1 Yes

White abalone Haliotis sorenseni Endangered

Black abalone Haliotis cracherodii Endangered Yes

Marine plants

Johnson’s seagrass Halophilia johnsonii Threatened Yes

Because EPA did not provide facility monitoring data or information on aggregate effects, we 

searched for information describing the effects of CWIS on listed species. We found the 

following, which represents the best available information: recent biological opinions, often on 

the Nuclear Regulatory Commission’s (NRC) licensing of a CWIS facility; ESA section 10 

permits or permit applications for incidental take at CWIS facilities; facility reports; government 

reports; peer-reviewed literature; and published design criteria for fish screens. We begin each 

species-group section with a discussion of the best available information. We describe the 

information and explain whether this information reflects the effects of typical CWIS, as 

regulated under the Rule. For example, when considering information from biological opinions, 

we note that such facilities have been the subject of a section 7 consultation and operate under an 

incidental take statement (ITS), which requires minimization of take, monitoring, and reporting 

under 50 CFR 402.14(i). 

1 Cetaceans

To determine the effects of CWIS on cetaceans, the best information would ideally consist of 

daily impingement and entrainment monitoring data, quantifying the number of prey items killed 

at each CWIS facility that overlaps with the ranges of the species, plus daily environmental 

monitoring data from each facility to determine the effects of thermal and chemical discharges 

on cetaceans and their prey. In the BE, EPA explains that this information is not available. EPA 

concludes that data are insufficient to evaluate whether cetaceans have been adversely affected 

by existing CWIS and associated discharges (EPA 2013). We agree that data are limited but 

identified the following as the best available information. We were unable to locate information 

describing the effects of CWIS on Cook Inlet beluga whales, Southern Resident killer whales, or 

Main Hawaiian Island Insular false killer whales, but we identified government reports and peerreviewed scientific literature detailing the importance of piscine prey for these species. A NOAA 

 

1

Proposed endangered
7

Technical Memorandum describes the potential biological impacts of the Kahe Point Ocean 

Thermal Energy Conversion Facility in Hawaii (Harrison 1987). In a letter dated May 17, 2012, 

from the NMFS Northeast Region to the NRC, NMFS concurred that the Pilgrim Nuclear Power 

Station, located in Plymouth, MA, was not likely to adversely affect sei, fin, humpback, or North 

Atlantic right whales and was not likely to adversely affect North Atlantic right whale critical 

habitat (NMFS 2012). 

1.1 Stressors

Whales are too large to be impinged or entrained by CWIS, and we are not aware of any such 

occurrences. Thermal discharges, however, may affect individuals. In addition, cetaceans may be 

indirectly affected by the effects of CWIS facilities on their prey (e.g., fish, invertebrates, and/or 

zooplankton). Prey availability is likely to be reduced by impingement, entrainment, thermal 

discharges, and chemical discharges of CWIS facilities regulated under the Rule.

1.2 Exposure

In the BE, EPA estimates the number of facilities that overlap with cetacean species (Table 2). In 

addition, we used ArcGIS (a geographic information system) to map the list of facilities 

potentially regulated under the Rule (EPA 2013) to identify overlap with ranges of listed species 

and their designated critical habitat. As regulated under the Rule, CWIS facilities are likely to 

result in prey reductions. Prey reductions are likely to affect all individuals within a species or 

DPS, especially in the following species, which have small population sizes and restricted 

ranges: North Atlantic right whale, North Pacific right whale, Southern Resident killer whale, 

Cook Inlet beluga whale, and Main Hawaiian Island insular false killer whale). Prey reductions 

are likely to affect males and females of all age groups.

Table 2. Facilities overlapping with ESA-listed cetacean species as identified by EPA (EPA 2013). 

Our mapping results shown in parentheses.

Species Overlapping facilities Exposed individuals

North Atlantic Right Whale 77 (21) 396

North Pacific Right Whale (15) 1,000

Humpback Whale 14 (66) 40,000

Fin Whale (62) 12,000

Blue Whale (66) 3,000

Sei Whale (62) 500

Southern Resident Killer Whale 6 (5) 87

Cook Inlet Beluga Whale (3) 345

Main Hawaiian Island Insular False Killer 

Whale (1) 170
8

1.3 Response

Stressors that may affect cetacean species are indirect effects from thermal discharges and 

indirect effects to prey species which are discussed in general and then for each ESA-listed 

cetacean species below.

1.3.1 Thermal Discharges

Right whales have been recorded at sea surface temperatures of 0.0 to 21.8°C (Kenney 2007), 

humpback whales at sea surface temperatures up to 32°C (NMFS 1991), and fin whales at sea 

surface temperatures up to 28°C (NMFS 2010). Whales exhibit some tolerance for changing 

temperatures, as reflected by movements through varied water temperatures over periods of 

minutes to weeks (Kenney 2007). In response to thermal discharges, whales are likely to avoid 

the area of the plume. Depending on the temperature, duration, and size of the plume, such 

avoidance may result in changes to foraging or migration behavior. We do not have any 

information on whether such changes result in fitness reductions for individuals. We expect the 

risk to be higher in areas with multiple CWIS facilities, which would make plume avoidance 

more difficult. Therefore, the aggregate effects of thermal discharges from CWIS facilities are 

likely to adversely affect cetaceans, both directly and indirectly (through the reduction of prey). 

1.3.2 Effects to Prey Species

Cetacean prey species are likely to be impinged or entrained by CWIS or adversely affected by 

the thermal and chemical discharges. Planktonic prey items are likely to be entrained; larger prey 

items, such as adult fish, are likely to be impinged. Entrainment and impingement of many 

individuals, at multiple facilities (i.e., aggregate effects), could reduce the amount of prey 

available to cetaceans. Thermal and chemical discharges have the potential to result in even 

greater reductions of prey because more individuals are likely to be exposed to the plume, which 

covers a larger area than the intake structure itself. Cetaceans are likely to respond to prey 

limitation by increasing foraging time and effort. Some individuals of ESA-listed species could 

experience fitness loss as a consequence of reduced prey availability, which often results in 

slower growth and maturity, less reproductive, and possible emaciation (Ward et al. 2009, Ford 

et al. 2010). Below, we consider the effects of reduced prey availability, as a result of 

impingement and entrainment authorized by the Rule, on the fitness of individuals and the 

viability of populations and species. 

1.4 Southern Resident Killer Whale

Mapping the facilities that may be regulated under the Rule (EPA 2013) to the range of the 

species, we find five facilities that overlap with the Southern resident killer whale DPS (Table 2). 

As with all of the ESA-listed cetaceans, Southern resident killer whales are too large to be 

impinged or entrained by CWIS. However, they may be affected by thermal discharges and 

indirect effects to prey species.

Hormone analyses indicate that the Southern Resident killer whale is prey-limited (Ayres et al. 

2012). However, a more thorough review of all available info on prey limitation is available in 

Hilborn et al. (2012). Their review is not this clear cut and they had concerns about some of the 
9

info presented regarding the hormone analysis. The population has a highly specialized diet, 

which is primarily comprised of Chinook salmon (80 percent of total diet) plus steelhead trout 

and chum, sockeye, and coho salmon in lesser amounts (Hanson et al. 2010). The whales prefer 

the larger and fattier but less abundant Chinook salmon, as opposed to the more abundant 

species, such as pink and sockeye salmon (Ford and Ellis 2006). Canadian and U.S. Chinook 

salmon populations occur within the range of the Southern Resident killer whale, including nine 

ESA-listed Chinook salmon ESUs. In inland marine waters, during the summer months, 

Southern Resident killer whales prey upon Fraser River Chinook salmon (31 to 94 percent of 

their diet). Fraser River stocks are the most abundant Chinook salmon populations that migrate 

through the area starting in June; however, they are rare in May. In May, the whales rely more 

heavily on Chinook salmon from the North Puget Sound, South Puget Sound, and the Central 

Valley (47 percent of their diet; Hanson et al. 2010). Though Southern Resident killer whales 

likely consume Chinook and other salmonid species during the fall, winter, and spring and in 

outer coastal waters, the source populations of these salmon remains unknown (Hanson et al. 

2010). 

In the salmonid section below, we describe the effects of CWIS on salmon based on the best 

available information provided by EPA (EPA 2013). As described in the BE and follow up 

conversations, EPA used data obtained from the Pittsburgh Power Station in Pittsburgh, CA, and 

Contra Costa Power Station in Antioch, CA (now called Gateway Generating Station), to 

estimate an annual impingement and entrainment mortality rate of 609 Chinook salmon in total 

for all facilities per year. Information regarding the life stage (i.e., eggs, fry, parr, smolt, 

juveniles or adults) of these mortalities was not provided. We consider this to be a minimum 

estimate because these facilities incorporated multiple control measures to minimize the 

impingement and entrainment of salmonids (e.g., seasonal operation reductions to avoid peak 

larval/egg present, reduced intake velocity, operation of a cooler, and reduced intake volumes); 

whereas the Rule only requires facilities to implement one of the seven Best Technology 

Available (BTA) Standards for Impingement Mortality. 

EPA estimates that 126 CWIS facilities overlap with Chinook salmon (EPA 2013). Multiplying 

this number by the minimum impingement and entrainment mortality rate (609 

salmon/year/facility), we estimate a minimum total impingement and entrainment mortality of 

76,734 Chinook salmon per year. Thermal and chemical discharges (as described in the salmonid 

section below) are likely to result in higher levels of mortality of Chinook salmon, as a result of 

CWIS regulated under the Rule. We do not have information regarding the life stage of Chinook 

salmon mortalities. In Washington, Oregon, Idaho, and California, pre-fishing abundance of 

Chinook salmon is estimated at 960,788 (NMFS 2008). Hilborn et al. (2012) and Ward et al. 

(2013) have more recently estimated adult abundance using several different Chinook abundance 

indices at approximately 1.2 million salmon (Ward et al. 2013) .

The DPS consists of one small population consisting of 87 whales (Carretta et al. 2013), which is 

almost half of its likely previous size (140 to as many as 400 whales; Carretta et al. 2013; Krahn 
10

et al. 2004). Prey limitation may have led to a 20 percent decline in the population’s abundance 

from 1995 to 2001(Ayres et al. 2012). Because of this population’s small size, it is susceptible to 

demographic stochasticity. This population has a variable growth rate (28-year mean=0.3% ± 

3.2% s.d), and risk of quasi extinction that ranges from 1 percent to as high as 66 percent over a 

100-year horizon, depending on the population’s survival rate and the probability and magnitude 

of catastrophic events (Krahn et al. 2004, Carretta et al. 2013). The effective population size (i.e., 

the number of breeders under ideal genetic conditions) of 26 whales is very small, and this in 

combination with the absence of gene flow from other populations may elevate the risk of 

inbreeding and other issues associated with low genetic diversity (Ford et al. 2011). The 

influences of demographic stochasticity and potential genetic issues in combination with other 

sources of random variation combine to amplify the probability of extinction, known as the 

extinction vortex (Gilpin and Soule 1986, Melbourne and Hastings 2008). 

In summary, Southern resident killer whales are not expected to be directly affected by CWIS; 

they may be indirectly affected due to impacts to prey species, primarily Chinook salmon. 

1.5 Cook Inlet Beluga Whale

Mapping the facilities that may be regulated under the Rule (EPA 2013) to the range of the 

species, we find three facilities that overlap with the Cook Inlet beluga whale DPS (Table 2). As 

with all of the ESA-listed cetaceans, Cook Inlet beluga whales are too large to be impinged or 

entrained by CWIS. However, they may be affected by thermal discharges and indirect effects to 

prey species. 

Cook Inlet beluga whales are opportunistic feeders for which eulachon and salmon form the bulk 

of the prey when they are seasonally abundant (Hobbs et al. 2008). In the northwestern Cook 

Inlet, eulachon spawning migration occurs in May (several hundred thousand fish) and June 

(several million fish; Calkins 1989). The fat content of eulachon (up to 15 percent of total body 

weight; Payne et al. 1999) is significant source of energy for beluga whales, especially for 

pregnant and lactating females (Calkins 1989). Native hunters in Cook Inlet have stated that 

beluga whale blubber is thicker after the whales have fed on eulachon (1 ft) as compared to the 

early spring prior to eulachon runs (2 to 3 inches; Huntington, 2000).(Hobbs et al. 2008). In the 

northwestern Cook Inlet, eulachon spawning migration occur in May (several hundred thousand 

fish) and June (several million fish; Calkins 1989). The fat content of eulachon (up to 15 percent

of total body weight) (Payne et al. 1999) is significant source of energy for beluga whales, 

especially for pregnant and lactating females (Calkins 1989). Native hunters in Cook Inlet have 

stated that beluga whale blubber is thicker after the whales have fed on eulachon (1 ft) as 

compared to the early spring prior to eulachon runs (2 to 3 inches) (Huntington 2000). 

Alaska Department of Fish and Game has conducted limited research on eulachon but substantial 

research on salmon in the Cook Inlet watershed. They report that biomass estimates for eulachon 

in Cook Inlet streams are unavailable, but eulachon biomass in the central Gulf of Alaska has 

increased since the early 1980’s (CIBWRP 2010). Eulachon are anadromous fish(Willette 2010). 

Eulachon are anadromous that spawn and hatch in fresh water streams, then quickly move into 
11

salt water to grow and mature in the ocean (Barlett 2012). Eulachon escapement is estimated at 

several million fish (Calkins 1989) and was the fourth most abundance species found in surveys 

conducted in northern Cook Inlet in June, July, and September of 1993 (Moulton 1997). Based 

on the assumption that the CWIS locations overlap with eulachon spawning areas, then during 

spawning and egg/larval migration to the ocean, some mortality of eulachon is expected. 

In the summer, as eulachon runs diminish, belugas rely heavily on five species of salmon. Like 

eulachon, salmon are another source of lipid-rich prey for the beluga whale and represent the 

greatest percent frequency of occurrence of the prey species found in Cook Inlet beluga whale 

stomachs (Hobbs et al. 2008). Eulachon and salmon may be vital for beluga sustenance 

throughout the year (Abookire and Piatt 2005, Litzow et al. 2006). Eating such fatty prey and 

building up fat reserves throughout spring and summer allows beluga whales to sustain 

themselves during periods of reduced prey availability (e.g., winter) or other adverse impacts by 

using the energy stored in their blubber to meet metabolic needs. Mature females have additional 

energy requirements. The known presence of pregnant females in late March, April, and June 

(Mahoney and Shelden 2000, Vos and Shelden 2005) suggests breeding may be occurring in late 

spring into early summer. Calves depend on their mother’s milk as their sole source of nutrition 

for at least a year (Burns and Seaman 1986), and lactation lasts up to 23 months. Thus, eulachon 

and salmon are critical prey for Cook Inlet beluga whales. 

Descriptions of fish abundance and distribution for the Cook Inlet area are generally lacking 

(Goetz et al. 2007), and summertime prey availability is difficult to quantify. Since 1970, 

sockeye and coho salmon abundances have generally increased in Cook Inlet while chum salmon 

abundances have decreased (Willette 2010). Salmon catches in northern Cook Inlet have 

generally declined due largely to declining fishing effort (Willette 2010). Shields and Dupuis 

(2013) report a total harvest of 3.1 million salmon (5 species). 

Small reductions in salmon populations are not likely to reduce the fitness of any individual. 

Several animals exhibited a thin blubber layer in the late summer (Hobbs et al. 2008). We found 

one example of an emaciated Cook Inlet beluga whale, a pregnant female whose death may have 

been caused by her poor body condition (thin, with vertebrae showing through the skin; Vos and 

Shelden 2005). We could not find any information linking these whales to reduced prey 

availability. Similarly, we did not find any information linking the low growth rate of the DPS to 

prey limitation or nutritional stress. Samples of harvested and stranded beluga whales have 

shown consistent summer blubber thicknesses, a possible indication that the species is not prey 

limited. Weighing both sides of the admittedly limited data, we tentatively conclude that prey 

reductions as a result of CWIS are not likely to reduce the fitness of Cook Inlet beluga whales. 

In summary, Cook Inlet beluga whales are not expected to be directly affected by CWIS; they 

may be indirectly affected due to impacts to prey species, primarily eulachon and secondarily 

Chinook salmon.
12

1.6 Main Hawaiian Island Insular False Killer Whale

Mapping the facilities that may be regulated under the Rule (EPA 2013) to the range of the 

species, we find one facility that overlaps with the Main Hawaiian Island insular false killer 

whale DPS (Table 2). As with all of the ESA-listed cetaceans, Main Hawaiian Island insular

false killer whales are too large to be impinged or entrained by CWIS. However, they may be 

affected by thermal discharges and indirect effects to prey species.

The Main Hawaiian Island insular false killer whale has been observed feeding on a wide variety 

of large pelagic fish, including tunas, swordfish, and mahimahi. These fishes are not likely to be 

impinged by CWIS; however their eggs or larvae may be entrained. To evaluate the indirect 

effects of CWIS on Main Hawaiian Island insular false killer whales, we consider the 

information provided by Harrison (1987), which describes the possible environmental effects of 

the construction and operation of a proposed Ocean Thermal Energy Conversion facility at Kahe 

Point in Hawaii. This information is applicable to this consultation because an existing 

conventional power plant currently operates at this site and is regulated under the Rule (EPA 

2013). The Kahe Power Plant withdraws ambient surface water (25°C) to cool its six generating 

units and discharges the effluent at 31 to 32°C. Kahe Point appears to be an important location 

for large fish densities and high concentrations of eggs and larvae (Harrison 1987). Based on the 

limited information available we are not able to conduct site specific analysis. Entrainment 

mortality of prey is also likely and may result in a greater impact on local fish populations than 

impingement (Harrison 1987). Reduced prey biomass is a medium level threat to Main Hawaiian 

Island insular false killer whales, whose range overlaps with five facilities (Oleson et al. 2010). 

In summary, Main Hawaiian Island insular false killer whales are expected to be directly and

indirectly affected by CWIS. 

1.7 North Atlantic Right Whale

The BE indicated that 77 CWIS overlap the range of the North Atlantic right whale DPS. NMFS 

mapping suggested that 21 CWIS that may be regulated under the Rule (EPA 2013) overlap with 

the range of the species (Table 2). As with all of the ESA-listed cetaceans, North Atlantic right 

whales are too large to be impinged or entrained by CWIS. However, they may be affected by 

thermal discharges and indirect effects to prey species.

The best available information on CWIS effects on the North Atlantic right whale is provided in 

the May 17, 2012 concurrence letter, from the NMFS Northeast Region to the NRC (NMFS 

2012), regarding the Pilgrim Nuclear Power Station, which uses a single pass CWIS that would

be regulated under the Rule. The cooling system uses two pipes with an intake capacity of 224 

MGD. The intake structure consists of wing walls, a skimmer wall, vertical bar racks, and 

vertical traveling screens to remove aquatic organisms and small debris. The intake approach 

velocity just before the screens is 1 ft/sec (ENSR Corporation 2000). EPA issued the current 

National Pollutant Discharge Elimination Permit (NPDES) permit in 1991; the permit expired in 

1996 but has been administratively extended for the past 18 years. It is unknown whether 

impingement and entrainment of prey species would be reduced under the Rule, or whether EPA 
13

would determine that the facility meets the proposed impingement and entrainment best 

technology available standards. The Pilgrim Nuclear Power Plant was the subject of an informal 

section 7 consultation on the NRC renewal of its 20-year operating license. In preparation, NRC 

prepared an environmental impact statement and a biological assessment. The facility conducts 

impingement monitoring three times per week and entrainment sampling 6 to 12 times per 

month; as a condition of their NRC license, the facility must report impingement or entrainment 

of listed species to NRC. Cetacean prey species have been impinged or entrained at the facility. 

The facility appears to be typical of facilities regulated under the Rule, with the exception of 

impingement monitoring, entrainment sampling, and reporting, which is required by the NRC, 

but is not required by EPA in the Rule. The following information is based upon the data 

described in the NMFS concurrence letter as well as results in published government reports and 

peer-reviewed scientific papers. 

Right whales forage on high-density concentrations of copepods, including Calanus 

finmarchicus, Pseudocalanus spp., and Centropages spp. (Baumgartner et al. 2007, Pace and 

Merrick 2008). Because of their small size, copepods are likely to be entrained in CWIS; they 

may also be adversely affected by thermal and chemical discharges. Despite its required 

entrainment monitoring, NRC was not able to provide data on the number of copepods entrained 

at the Pilgrim Nuclear Power Station. Overall zooplankton entrainment mortality rates at the 

facility average 5 percent, with an additional loss of 8.3 percent mortality after exposure to 

chlorine (Bridges and Anderson 1984). A study of freshwater entrainment reveals that calanoid 

copepods are the most sensitive to entrainment, with discharge mortalities nearly 10 percent 

higher than intake mortalities, which ranged from four to 35 percent (Evans et al. 1986). Using 

an entrainment mimic unit, Bamber and Seaby (2004) report that while the majority of adult 

copepods (Acartia tonsa) survive entrainment (overall 20 percent mortality under standard 

operating conditions), individuals die as a result of pressure (11 percent mortality), unusually 

high temperatures (increases of 7.6 to 11.5 ̊C resulted in 12 percent mortality), and chlorine (23 

percent mortality). Carpenter et al. (1974) estimate that about 70 percent of copepods entering 

the CWIS of a facility on Long Island Sound are not returned to the Sound in the effluent. In 

summary, 4 to70 percent of copepods exposed to entrainment, thermal, and chemical discharges 

are likely to die as a result of the exposure. Therefore, we consider how such levels of copepod 

mortality affect the concentrations of prey available to whales. 

As explained in NMFS’s concurrence letter, a two-year study was conducted to evaluate the

effect of the Pilgrim Nuclear Power Station on zooplankton concentrations (ENSR Corporation 

2000). Monthly water samples were taken at intake, discharge, and offshore (i.e., control) 

locations. Copepods were found in moderate abundance in all samples, and there were no 

statistically significant differences among mean densities of copepods (ENSR 2000, ENSR 

Corporation 2000). This study is corroborated by a similar study performed at the Seabrook 

Nuclear Power Station, located in Seabrook, NH, where CWIS have not reduced zooplankton 

densities in more than 20 years of operation. As a result of 70 percent copepod mortality rates, 

Carpenter et al. (1974) estimate a 0.1 percent reduction in annual copepod production in the area 
14

immediately surrounding the Long Island Sound facility. Two additional studies indicate that 

there have been no changes in the zooplankton community and no evidence for decline in 

copepods in Cape Cod Bay (Stamieszkin et al. 2010, Werme et al. 2011), despite the operation of 

the Pilgrim facility. Based on these data, NMFS concluded that while the entrainment of 

copepods at the Pilgrim Nuclear Power Station is likely to reduce the amount of prey available to 

right whales, such reductions are likely to be insignificant and undetectable from natural 

variability.

While a single facility may not adversely affect North Atlantic right whales, we must consider 

the aggregate effects of multiple facilities. In the BE, EPA identifies 77 facilities with CWIS

within the habitat of the North Atlantic right whale (i.e., “facility overlap,” EPA 2013). Mapping 

the list of 3,730 facilities, which represent an upper bound estimate of the number of facilities 

that may possibly have cooling water intakes (ABT 2014), we identify 21 facilities that overlap 

with the range of the North Atlantic right whale. Extrapolating the estimated 0.1 percent 

reduction in annual copepod production as a result of losses at one facility (Carpenter et al. 

1974), we estimate that CWIS facilities within the range of the species are likely to reduce 

annual copepod production by 2.1 to 7.7 percent. 

North Atlantic right whales require an estimated prey concentration of 7.57 to 2,394 kcal/m3

(Kenney et al. 1986). Therefore, individuals must seek out and exploit extremely dense patches 

of copepods. Whales are likely to respond to small reductions in prey available by increasing the 

time and effort spent foraging. This is not beyond their normal behavior. North Atlantic right 

whales have been shown to expend more energy to forage at depths, where copepods are more 

abundant, of higher caloric content, and less able to avoid capture (Baumgartner et al. 2003). 

Ingestion rates appear to exceed estimated daily metabolic requirements for most of the 26 North 

Atlantic right whales studied in the Bay of Fundy; however, there are large uncertainties in 

estimating metabolic rates and requirements (Baumgartner and Mate 2003). Baumgartner and 

Mate (2003) conclude that all individuals meet the daily metabolic requirements for survival 

because no emaciated individuals were observed; however, the data do not allow the authors to 

determine whether there is sufficient prey availability to support reproduction for the population. 

Given these data, we do not expect small reductions in copepod concentrations to reduce the 

survival of any right whales; however, it is unknown whether reproductive potential may be 

reduced. Given the small magnitude of reduction in prey availability (2.1 to 7.7 percent), 

however, we would expect reductions in reproductive potential to be small. Therefore, we 

conclude that reductions in fitness as a result of CWIS facilities regulated under the Rule are 

possible, but are likely to be small. We do not expect population level effects as a result of these 

small reductions in fitness. 

In summary, North Atlantic right whales are not expected to be directly affected by CWIS; they 

may be indirectly affected due to impacts to prey species.
15

1.8 North Pacific Right Whale

The BE did not identify any CWIS overlap with the range of the North Pacific right whale DPS. 

NMFS mapping suggested that 15 CWIS that may be regulated under the Rule (EPA 2013)

overlap with the range of the species (Table 2). As with all of the ESA-listed cetaceans, North 

Pacific right whales are too large to be impinged or entrained by CWIS. However, they may be 

affected by thermal discharges and indirect effects to prey species.

Like North Atlantic right whales, individuals require exceptionally high densities of prey for 

survival and reproduction (Baumgartner et al. 2003, Baumgartner and Mate 2003, Baumgartner 

et al. 2011). North Pacific right whales forage on copepods in shelf, slope and oceanic areas 

within the Bering Sea and Gulf of Alaska (Shelden et al. 2005). Though not described in the BE, 

we used the associated list of CWIS facilities that may be regulated under the Rule to identify 15 

CWIS facilities that overlap with the range of the North Pacific right whale DPS. These facilities 

are likely to reduce copepod concentrations, as a result of entrainment and thermal and chemical 

discharges, as described above. 

As compared to North Atlantic right whales, however, these whales appear to have a greater 

pelagic distribution, possibly related to a wider distribution of larger copepods across shelf, slope 

and oceanic regions of the southeastern Bering Sea and the Gulf of Alaska. Therefore, prey 

reductions, and resulting reductions in reproductive rates, are expected to be even smaller than 

described for the North Atlantic right whale. Thus, we do not expect the issuance and 

implementation of the Rule to result appreciable reductions in fitness for individual North Pacific 

right whales. 

In summary, North Pacific right whales are not expected to be directly or indirectly affected by 

CWIS.

1.9 Humpback and Fin Whales

The BE indicated that 14 CWIS overlap the range of the humpback whale but did not identify 

any CWIS that overlap the range of fin whales. NMFS mapping suggested that 66 and 62 CWIS

that may be regulated under the Rule (EPA 2013) overlap with the range of humpback and fin 

whales, respectively (Table 2). As with all of the ESA-listed cetaceans, humpback and fin whales

are too large to be impinged or entrained by CWIS. However, they may be affected by indirect 

effects to prey species.

Humpback and fin whales feed on krill and small schooling fish, primarily Atlantic herring, 

mackerel, and sand lance; humpback whales may also feed on capelin, Pollock, and haddock. 

These prey species are likely to be impinged as juveniles or adults and entrained as eggs or larval 

fishes. To evaluate the indirect effects of CWIS on humpback and fin whales, we use the 

impingement and entrainment data gathered at the Pilgrim Nuclear Power Station (Table 3).

Table 3. Impingement and entrainment rates of cetacean prey at the Pilgrim Nuclear Power Station 

(Normandeau Associates 2011).

Impingement 

study years

Mean annual 

impingement

Entrainment 

study year

Mean annual 

entrainment

Population size or 

recruitment estimate
16

Atlantic 

herring 1990-2004 2,069 0.01% spawning biomass 3.3 billion age-one fish

Atlantic 

mackerel 1980-2010 7 2010 316 age-one fish 566 million age-one fish

Sand 

lance NA NA 2010 3,854 larvae 500,000 metric tons

Pollock 1980-2010 65 1989-1998 26,044 eggs 

47-364 larvae 196,000 metric tons

Haddock 2007 15 1989-1998 0-89,926 eggs 

0-178,892 larvae 120,000 metric tons

As described in the letter of concurrence, the impingement and entrainment rates of cetacean 

prey items are small relative to annual recruitment or population estimates. Humpback and fin 

whales are foraging generalists and are not likely to be prey limited, as their populations are 

somewhat large and growing. Based on these data, NMFS concluded that the Pilgrim Nuclear 

Power Station is not likely to adversely affect humpback and fin whales. We must consider the 

aggregate effects of multiple facilities. In the BE, EPA estimates that 14 facilities overlap with 

the range of the humpback whale (EPA does not include fin whales). Mapping the list of 3,730 

facilities, which represent an upper bound estimate of the number of facilities that may possibly 

have cooling water intakes, we identify 66 and 62 facilities that overlap with the ranges of the 

humpback and fin whale, respectively. Extrapolating from the Pilgrim facility data to 66 

facilities, we expect CWIS regulated under the Rule to result in the impingement of 

approximately 126,554 herring, 462 mackerel, 4,290 pollock, and 990 haddock. Extrapolating 

from the Pilgrim facility data to 66 facilities, we expect CWIS regulated under the Rule to result 

in the entrainment of 0.66 percent of herring spawning biomass, 20,856 mackeral age-one 

equivalents, 254,354 sand lance larvae, over 1.7 million pollock eggs and up to 24,024 pollock 

larvae, and up to 5.9 million haddock eggs and up to 11.8 million haddock larvae. As described 

above, we do not know whether the Rule will reduce the impingement or entrainment of cetacean 

prey species because of the variable efficacy among the seven alternatives for the BTA Standards 

for Impingement Mortality and because the Rule does not establish an entrainment best 

technology available standard but instead relies on Director discretion. Therefore, we evaluate 

the effects of current levels of impingement and entrainment on cetacean prey.

Humpback and fin whales depend on large, dense prey aggregations to build up energy stores 

prior to travel to less productive waters; this is especially important for females, who expend 

considerable energy nursing calves (Brodie 1975, Dolphin 1987). Humpback whales, for 

example, spend approximately 80 percent of daylight hours between the months of July and 

September foraging (Dolphin 1987). Fin whales may require higher concentrations of prey than 

humpback whales (Piatt and Methven 1992), but both species need large amounts of prey. 

Kenney et al. (1997) estimated that cetaceans on the Northeast Shelf consume approximately 1.3 

million tons of fish and 244,000 tons of zooplankton. Faced with reductions in prey availability, 
17

humpback and fin whales are likely to exert more time and effort into feeding or to shift their 

distribution (Weinrich 1998). Examples of emaciated sei and humpback whales exist (Clapham 

and Mayo 1987) but are generally associated with entanglement. The reproductive rates of 

humpback and sei whales do not appear to be limited by prey availability. 

In summary, humpback and fin whales are not expected to be directly or indirectly affected by 

CWIS. 

1.10 Sei and Blue Whales

The BE does not indicated any overlap of CWIS with sei and blue whale ranges. NMFS mapping 

suggested that 62 and 66 CWIS that may be regulated under the Rule (EPA 2013) overlap with 

the range of sei and blue whales, respectively (Table 2). As with all of the ESA-listed cetaceans, 

sei and blue whales are too large to be impinged or entrained by CWIS. However, they may be 

affected indirectly by direct effects to prey species.

The effects of CWIS on planktonic prey concentrations are likely to diminish with distance from 

the facility. Sei whales eat copepods, and blue whales eat krill, but these cetaceans mainly forage 

in areas off the continental shelf and other offshore waters. Therefore, CWIS are likely to have 

minor effects on the availability of their prey. We do not expect any fitness reductions to sei or 

blue whales as a result of CWIS regulated under the Rule. 

In summary, sei and blue whales are not expected to be directly or indirectly affected by CWIS.

1.11 Critical Habitat

Designated critical habitat overlaps with CWIS likely to be regulated under the Rule for two 

cetacean species: Southern Resident killer whales and Cook Inlet beluga whales. Designated 

critical habitat for the Southern Resident killer whale DPS includes: the Summer Core Area in 

Haro Strait and waters around the San Juan Islands; Puget Sound; and the Strait of Juan de Fuca 

(71 FR 69054). Fish are the major dietary component of the DPS, with salmon the clearly 

preferred prey, consumed in large amounts. The designated critical habitat includes the 

biological feature of prey species of sufficient quantity, quality and availability to support 

individual growth, reproduction and development, as well as overall population growth. As 

described above and below (for salmonids), CWIS, as regulated under the Rule, are likely to 

reduce prey availability through impingement, entrainment, and thermal discharges. Though 

EPA determined that no facilities overlap with Southern Resident killer whale critical habitat, 

our mapping revealed overlap with seven facilities within a one kilometer diameter (and one 

facility directly overlapping). We believe that the thermal, chemical and indirect effects of CWIS

may occur within one kilometer of the CWIS. 

Designated critical habitat for the Cook Inlet beluga whale includes 7,800 km2of marine and 

estuarine area in Cook Inlet, Alaska. There are two specified areas: Cook Inlet northeast of a 

line from the mouth of Threemile Creek to Point Possession (bounded by the Municipality of 

Anchorage, the Matanuska-Susitna Borough, and the Kenai Peninsula borough); and the area 

south of the former area, including nearshore areas along the west side of the Inlet and 
18

Kachemak Bay on the east side of the lower inlet (76 FR 20180). Fish are the primary prey 

species of the Cook Inlet beluga whale, especially salmon and Pacific eulachon, which have very 

high fat content and occur in large concentrations at or near the mouths of tributary streams. The 

designated critical habitat includes the biological feature of primary prey species consisting of 

four species of Pacific salmon (Chinook, sockeye, chum, and coho), Pacific eulachon, Pacific 

cod, walleye pollock, saffron cod, and yellowfin sole. As described above and below (for 

salmonids), CWIS may reduce prey availability. Though EPA determined that no facilities 

overlap with Cook Inlet beluga whale critical habitat, our mapping revealed overlap with one 

facility within a one kilometer diameter.

2 Pinnipeds

The Rule establishes Best Technology Available Standards for Impingement And Entrainment.

While one alternative of the Best Technology Available Standards for Impingement Mortality 

(i.e., offshore velocity cap) is defined to exclude marine mammals, it is one of seven alternatives, 

and we have no way of determining the proportion of facilities that may select this alternative.

To determine the effects of CWIS on pinnipeds, the best information would consist of daily 

impingement and entrainment monitoring data, quantifying the number of prey items killed at 

each CWIS facility that overlaps with the ranges of the species, plus daily environmental 

monitoring data from each facility to determine the effects of thermal and chemical discharges 

on pinnipeds and their prey. In the BE, EPA states that this information is not available and that 

EPA does not have sufficient data to evaluate whether these species have been affected by 

existing CWIS and associated discharges. EPA concludes that ESA-listed pinniped species, due 

to their large size, high mobility, and broad habitat ranges, would not be directly affected by 

entrainment or impingement in CWIS regulated under the Rule; however, pinnipeds are likely to 

be indirect affected by reduced prey availability as a result of impingement or entrainment of 

prey items in CWIS (EPA 2013). EPA explains that their proposed action may affect the general 

aquatic habitat, which may change fish community composition (including forage fish and prey 

species upon which mammals may depend for a high quality diet).

We agree that data are limited, but we do not agree that pinnipeds are not likely to be directly

affected by CWIS regulated under the Rule because many pinnipeds have been entrapped in 

CWIS. The best available information includes NMFS’s 1999 Letter of Authorization under the 

Marine Mammal Protection Act to the Seabrook Station nuclear power plant (64 FR 28114) and 

2008 Marine Mammal Protection Act permit applications from 11 power generating stations in 

California (73 FR 9299). 

In 1999, NMFS issued a Letter of Authorization to the Seabrook Station in New Hampshire (64 

FR 28114). This letter describes the impacts of the CWIS on seals in the area. From 1993 to 

1998, 56 habor, gray, harp, and hooded seals were entrapped and died in the holding bays at the 

terminus of the intake tunnels (Table 4). NMFS determined that the taking of up to 20 harbor 
19

seals and four of any combination of gray, harp, and hooded seals, annually would have no more 

than a negligible impact on these stocks of marine mammals (64 FR 28114). 

In 2008, NMFS received Marine Mammal Protection Act permit applications from 11 power 

generating stations in California (73 FR 9299). These permit applications contain biological 

monitoring data, which describe and quantify the effects of the CWIS on pinnipeds (MBC 

Applied Environmental Sciences 2001). Such data are available because these 11 facilities 

monitored and reported on the annual number of pinnipeds entrapped in their CWIS and the 

number of pinnipeds found dead in their CWIS (Table 4). Many facilities reported that pinnipeds 

were found decomposed and may have died before becoming entrapped within the CWIS. The 

entrapped pinnipeds include: California sea lions, harbor seals, and one northern elephant seal. 

Table 4. Entrapped pinnipeds at facilities with CWIS (64 FR 28114) (MBC Applied Environmental 

Sciences 2001).

Facility Years (N) Total 

pinnipeds

Min-max 

annual 

pinnipeds

Mean (SD) 

annual 

pinnipeds

Total 

dead

Mean (SD) 

annual 

dead

Proportion 

dead 

pinnipeds

Seabrook 1993 – 1998 (6) 56 2-17 9.3(5.5) 56 9.3(5.5) 1.00

San Onofre 1978-2000 (23) 385 0-64 17(15) 217 9.9(18.8) 0.56

Diablo Canyon 1995-2000 (6) 0 0 0 0 0

El Segundo 1979-2000 (22) 15 NA 0.7(NA) 10 NA 0.67

Scattergood 1989-2000 (12) 40 0-8 3.3(3.0) 35 4.4(2.2) 0.88

Encina 1978-2000 (23) 4 0-2 0.2(0.5) 3 1.0(0.0) 0.75

Huntington 

Beach

1977-2000 (24) 13 0-3 0.5(0.9) 9 1.5(0.6) 0.70

Ormond Beach 1977-2000 (24) 75 0-8 3.2(3.0) 41 3.2(1.6) 0.55

Redondo Beach 1976-2000 (25) 37 0-7 1.5 (1.9) 19* 1.9(1.2) 0.51

Moss Landing 1992-1999 (8) 8 0-3 1.0(1.1) 8** 1.6(0.9) 1.00

Mandalay 1977-2000 (24) 1 0-1 (NA) 1 (NA) 1.00

Long Beach 1977-2000 (24) 0 0 0 0 0

TOTAL (221) 634 0-64 2.9 (7.2) 399 5.3 (6.4) 0.63

*We considered four “fate unknown” pinnipeds as dead.

**We considered eight seriously injured pinnipeds as dead.

Table 4 summarizes the data reported from the 12 CWIS facilities (64 FR 28114) (MBC Applied 

Environmental Sciences 2001). The number of pinnipeds entrapped annually at each facility 

ranges from 0 to 64; the annual number of deaths at each facility ranges from 0 to 37 pinnipeds 

(data not shown). The proportion of entrapped pinnipeds that are found dead annually ranges 

from zero to 100 percent. Over all facilities during all years, a total of 634 pinnipeds were 

entrapped, an average of 2.9 per year. Over all facilities during all years, a total of 399 pinnipeds 

were found dead in the CWIS. Over all facilities, during all years, the average proportion of 
20

entrapped pinnipeds that were found dead was 63 percent. For each facility, we calculated the 

mean and standard deviation of the annual number of pinniped entrapments for all monitoring 

years. For each facility, we calculated the mean and standard deviation of the annual number of 

pinnipeds found dead for all monitoring years in which pinnipeds were entrapped. For each 

facility, we also calculated the mean proportion of entrapped pinnipeds that were found dead. We 

recognize the large variation among facilities (e.g., annual take ranges from 0 to 64) and attribute 

these to differences in facility locations, CWIS characteristics, and implementation of control 

measures (e.g., more or less monitoring). 

These 12 facilities have implemented control measures to minimize adverse effects on pinnipeds. 

The Seabrook Station’s three CWIS consist of a velocity cap and vertical bars, spaced 16 inches

apart, covering the intake openings; twice daily monitoring and reporting (within 30 days of take 

and annually) are required (64 FR 28114). The 11 facilities in California also have velocity caps 

and large organism excluder bars, spaced 18 inches apart; the facilities utilize marine mammal 

rescue cages to remove the pinnipeds from the CWIS, and unhealthy or injured pinnipeds are 

transferred to a marine mammal rehabilitation center. If not removed and rehabilitated, we would 

expect entrapped individuals to die as a result of injuries or starvation. It is our understanding 

that these facilities are the only CWIS facilities likely to be regulated under the Rule that have 

applied for a Marine Mammal Protection Act permit, which is required of any facility that 

entraps or otherwise harms or harasses marine mammals. These facilities are not representative 

of facilities regulated under the Rule, which does not require large organism excluder bars and 

velocity caps as well as monitoring, removal of entrapped individuals, and monitoring and 

reporting. Instead, the Rule requires the owner or operator of an existing facility to comply with 

one of seven alternatives under the Best Technology Available Standards for Impingement 

Mortality. One of these alternatives is an “offshore velocity cap,” which is defined in the Rule as 

“a velocity cap located a minimum of 800 feet from the shoreline and outside of the littoral zone. 

A velocity cap is an open intake designed to change the direction of water withdraw from 

vertical to horizontal, thereby creating horizontal velocity patterns that result in avoidance of the 

intake by fish and other aquatic organisms. For purposes of this subpart, the velocity cap must 

use bar screens or otherwise exclude marine mammals, sea turtles, and other large aquatic 

organisms. 

2.1 Stressors

Pinnipeds may be directly affected by CWIS by entrapment. In addition, indirect effects could

occur because pinniped prey (e.g., fish and invertebrates) are likely to be impinged, entrained or 

otherwise affected by flow reduction and thermal and chemical discharges.

2.2 Exposure

In the BE, EPA estimates the number of facilities that overlap with listed pinniped species (Table 

5). In addition, we used ArcGIS to map the list of facilities potentially regulated under the Rule 

(EPA 2013) to identify overlap with ranges of listed species and their designated critical habitat 

(Table 5). As observed at the 12 facilities described above, pinnipeds of all ages and both sexes 

may be exposed to entrapment or the indirect effects to their prey species. 
21

Table 5. Facilities overlapping with the Steller sea lion and Hawaiian monk seal as identified by 

EPA (EPA 2013). NMFS mapping results shown in parentheses.

Species Overlapping facilities Expected exposure

Steller sea lion (Western DPS) 16 (3) ~50,000

Hawaiian monk seal (5) ~1,000

2.3 Response

Stressors that may affect ESA-listed pinniped species are entrapment and thermal discharges; 

indirect effects to prey species may also affect ESA-listed pinnipeds. General responses to these 

stressors are discussed below followed by subsequent species specific discussions.

2.3.1 Entrapment

The 12 facilities described above do not overlap with ESA-listed pinnipeds, and we do not have 

any information from facilities that overlap with ESA-listed pinnipeds in Hawaii and Alaska. 

Pinnipeds are likely to encounter CWIS because they forage at nearshore and offshore locations, 

where CWIS may be located. Pinnipeds are opportunistic predators that are attracted to CWIS, 

which concentrate and impinge prey (MBC Applied Environmental Sciences 2001). Pinnipeds 

are also curious and bold, often leading to fishery interactions, entanglements, and use of manmade structures. Steller sea lions and Hawaiian monk seals exhibit these same behavioral 

characteristics that have likely led to the entrapment of California sea lions, harbor seals, 

northern elephant seals, gray seals, harp seals, and hooded seals. Therefore, where CWIS

facilities and listed pinnipeds overlap, entrapment is likely. 

The species entrapped in the 12 facilities are not listed under the ESA and may be more abundant 

than listed species. Estimated abundances of these species are as follows (64 FR 28114, MBC 

Applied Environmental Sciences 2001):

 North Atlantic harbor seals: minimum 30,990

 Gray seal regional population: minimum 2,010

 Harp seal: minimum 4.8 million

 Hooded seal: minimum 400,000

 California sea lions: approximately 200,000

 California harbor seals (local): approximately 30,000

The western Steller sea lion DPS has an estimated abundance of approximately 50,000 

individuals. The total abundance of Hawaiian monk seals is approximately 1,212 seals (Carretta 

et al. 2013). The abundances of listed species that potentially could be affected by CWIS (1,000 

– 50,000) are similar in magnitude to the abundances of species previously entrapped in CWIS

(2,010 – 4.8 million). 

2.3.2 Indirect Effects

Pinnipeds are foraging generalists, preying on a variety of fish and invertebrates. Impingement 

and entrainment of prey is likely to result in the death of hundreds of millions or billions of 
22

individuals at a single facility (EPA 2011). Flow reduction, thermal discharges, and chemical 

discharges are likely to kill individuals of prey species. Such impacts are likely to affect aquatic 

habitats and alter fish community composition (EPA 2013). Therefore, CWIS are likely to result 

in prey reduction, which may result in fitness reductions for individuals. 

2.4 Hawaiian Monk Seal

The BE did not identify any CWIS overlap with the range of the Hawaiian monk seal. NMFS 

mapping suggested that five CWIS that may be regulated under the Rule (EPA 2013) overlap 

with the range of the species (Table 5). Hawaiian monk seals would be directly exposed to 

entrapment and thermal discharges and indirectly to potential effects on prey species. 

Prior to the 1990s, monk seals were rarely observed in the main Hawaiian Islands (Baker and 

Johanos 2004); however, this population has since grown to 152 individuals (Baker et al. 2011). 

Seals have been observed at Kahe Point, which hosts large fish densities and high concentrations 

of eggs and larvae and is also the site of the Kahe Generating Station. We were not able to find 

information in our literature search indicating monk seal entrapment, or the lack thereof, at this 

or other CWIS facilities in Hawaii. However, we contacted a Hawaiian monk seal researcher

who was not aware of any occurrences of monk seal entrapment (C. Littnan, NMFS PIFSC, pers. 

comm. to K. Petersen, NMFS, May 5, 2014).

At the Kahe Generating Station, 165 species of fishes and 55 invertebrate species have been 

impinged (Harrison 1987). Extrapolated estimates of impingement range from 18,976 to 125,279 

individuals (161 to 1,237 kg) annually (Harrison 1987). Extrapolating to five facilities in Hawaii, 

we expect an impingement rate of 94,880 to 626,395 individuals (805 to 6,185 kg) per year. 

Entrainment may result in a larger impact on local fish populations than impingement (Harrison 

1987). Total reef fish biomass in the main Hawaiian Islands is approximately 16,600,000 kg 

(Sprague et al. 2013). The main Hawaiian Islands population of monk seals consumes an 

estimated 1,300 kg/day, which is a maximum of 0.009 percent of the estimated available prey 

biomass (Sprague et al. 2013). Therefore, we do not expect the loss of 0.0003 percent of the 

estimated available prey biomass to result in fitness reductions for any individual.

The Hawaiian monk seal is an endangered species that continues to decline in abundance. The 

species is steadily declining at a rate of four percent per year (Carretta et al. 2013), which makes 

the small (N = 152) but growing (6.5 percent annually) subpopulation in the main Hawaiian 

Islands essential to the survival and recovery of the species (Baker et al. 2011). 

In summary, Hawaiian monk seals may be directly and indirectly affected by CWIS.

2.5 Western DPS of Steller Sea Lion

EPA identified 16 CWIS that overlap the range of the Western DPS of Steller sea lions. NMFS 

mapping suggested that three CWIS that may be regulated under the Rule (EPA 2013) overlap 

with the range of the species (Table 5). The Western DPS of Steller sea lions would be directly 

exposed to entrapment and thermal discharges and indirectly to potential effects on prey species. 
23

We were not able to any find information on Steller sea lion entrapment or the lack thereof at 

CWIS facilities. Therefore, we rely on the data from the 12 facilities described above. Pinniped 

entrapment rates vary from 0 to 64 individuals per facility per year, with an average of three 

individuals per facility per year. Extrapolating to the range of the Steller sea lion (Western DPS), 

where 3 - 16 facilities may be regulated under the Rule, we find an annual entrapment rate of 0 to 

192 individuals, with an average of 9 (for three facilities) and 0 to 1,024, with an average of 48 

(for 16 facilities). It is possible that EPA included both DPSs when determining overlap of the 

species; therefore, we consider our estimate of three facilities to be more accurate. Because of 

the low abundance of the species, actual entrapment rates are likely to be at the lower end of the 

range (0 to 3 individuals/facility/year), such that 0 to 9 individuals may be entrapped in CWIS

annually. 

Steller sea lions forage on a wide variety of invertebrates and fish, including: capelin, cod, 

herring, mackerel, pollock, rockfish, salmon, and eulachon. Seasonally available, energy-rich 

prey, such as herring, eulachon and salmon, are important to Steller sea lions (Sigler et al. 2004). 

As described above for cetaceans, impingement, entrainment, and other adverse environmental 

effects of CWIS are likely to result in prey reductions. We could not find information on the 

impingement and entrainment rates of Pacific herring. Using the data described for the Cook 

Inlet beluga whale, we estimate a minimum impingement and entrainment mortality rate of 9,135 

salmon/year (3 facilities x 5 salmon species x 609 salmon/year) and 74,757 to 187,578 

eulachon/year. In comparison, Alaska fisheries reported a preliminary harvest of 272 million 

salmon (476,000 metric tons or 524,700 tons) in 2013 (Sustainable Fisheries Partnership 2014), 

and eulachon escapement is estimated at several million fish (Calkins 1989). Therefore, salmon 

and eulachon losses as a result of CWIS are likely to reduce prey availability by less than one 

percent and 2 to 6 percent, respectively. We expect herring losses as a result of CWIS to fall 

within a similar range. Sigler et al. (2009) estimate that 500 to 1700 tons of prey are needed near 

a terrestrial location where 500 Steller sea lions haul out. Converting individuals to tons, we 

estimate that three CWIS facilities would take a minimum of 17 tons of salmon and 6 to 15 tons 

of eulachon annually. These estimates are small compared to fishery losses (e.g., up to 100 tons 

of eulachon are harvested annually; Shields and Dupuis 2013). 

Prey reduction has led to nutritional stress in Steller sea lions of the Western DPS, which exhibit 

reduced body size, reduced productivity, and high mortality of pups and juveniles (Trites and 

Donnelly 2003). The dramatic decline in population size may have been caused by reduced 

abundance of high quality prey, including herring and eulachon (Trites and Donnelly 2003), due 

to a regime shift in ocean climate (i.e., the Pacific Decadal Oscillation; Trites et al. 2007; 

Guenette et al. 2006). However, Steller sea lions have a broad range and move between areas as 

prey become available (Sinclair and Zeppelin 2002, Sigler et al. 2009), resulting in a much larger 

prey base. Adults can likely meet their daily energy needs eating exclusively low energy prey 

(Sigler et al. 2009). Furthermore, Steller sea lions exhibit a flexible foraging strategy, allowing 

them to take advantage of seasonal prey aggregations that presumably are easier to capture due 

to high prey density and choose prey with higher energy content (Sinclair and Zeppelin 2002). 
24

This strategy buffers Steller sea lions against seasonally varying energetic requirements as a 

result of pregnancy, lactation and fasting during the breeding period (Winship et al. 2002). Sigler 

et al. (2009) conclude that a flexible foraging strategy and diverse diet allows Steller sea lions to 

compensate for less nutritious prey. 

In summary, CWIS are likely directly and indirectly affect Steller sea lions.

2.6 Critical Habitat

Steller sea lion (Western DPS) critical habitat does not overlap with facilities that are likely to be 

regulated under the Rule. Hawaiian monk seal proposed critical habitat is likely to overlap with 

five CWIS regulated under the Rule. The proposed designation for the Hawaiian monk seal 

includes six areas in the main Hawaiian Islands, including: terrestrial and marine habitat from 5 

miles inland from the shoreline extending seaward to the 500-meter depth contour around: Kaula 

Island, Niihau, Kauai, Oahu, Maui Nui (including Kahoolawe, Lanai, Maui, and Molokai), and 

Hawaii. Food limitation is identified in the recovery plan as a critical threat to the Hawaiian 

monk seal; therefore, prey quantity and quality within the marine foraging habitat is an essential 

component in the recovery and conservation of the species. The proposed critical habitat includes 

the biological feature of marine areas with adequate prey quantity and quality. As described 

above, CWIS as regulated under the Rule are likely to reduce the availability of prey. The effects 

of energy projects are further considered in the Draft Economic Analysis of Critical Habitat 

Designation for the Hawaiian Monk Seal (ECONorthwest 2011), as follows: 

“NMFS has determined that energy projects may alter ecosystem dynamics and 

affect the proposed critical habitat. In general, the anticipated energy projects 

pose a potential threat to the essential features of critical habitat for the Hawaiian 

monk seal in several ways, similar to those associated with other in-water and 

coastal construction projects. Energy projects may have additional effects, but 

little is known about these projects and how their effects differ from those of other 

types of projects. Depending on their location and scope, future energy projects 

may impact the essential features of the proposed Hawaiian monk seal critical 

habitat in these ways: 1) in-water construction may reduce the numbers of 

available prey, by reducing available prey habitat or by reducing the quality of 

prey habitat; 2) inwater construction may reduce the amount or value of available 

shallow, sheltered marine habitat adjacent to preferred pupping areas utilized by 

moms and pups; and 3) activities associated with construction and related 

activities may increase the potential for anthropogenic disturbance, thus making 

monk seals avoid or abandon preferred haul-out areas or pupping areas. While it 

is clear that the structures and activities associated with these projects may have 

an impact on the essential features of the proposed critical habitat, variation in 

project design, anticipated energy production, and environmental conditions at a 

specific location will all play a role in defining the scope of these impacts. 

Uncertainties regarding the variation between projects, designs, locations, and 
25

structure make it difficult to define the potential impacts, or to determine the 

specific, potential project modifications that might be necessary to avoid the 

impacts. Consequently, NMFS has determined that it most likely will address the 

nature of the potential threat on a project-specific basis.”

The indirect effects of CWIS are likely to overlap with proposed critical habitat and reduce prey 

availability at those sites. However, the losses are not expected to substantially reduce the 

estimated available prey biomass. Therefore, as regulated under the Rule, CWIS are not likely to 

appreciably reduce the conservation value of the proposed critical habitat of Hawaiian monk 

seals. 

3 Sea Turtles

The Rule establishes Best Technology Available standards for impingement and entrainment.

While one alternative of the Best Technology Available Standards for Impingement Mortality 

(i.e., offshore velocity cap) is defined to exclude sea turtles, it is one of seven alternatives, and 

we have no way of determining the proportion of facilities that may select this alternative.

To determine the effects of CWIS on sea turtles, the best information would consist of an 

evaluation of all daily impingement and entrainment monitoring data, quantifying the number of 

prey items killed at each CWIS facility that overlaps with the ranges of the species, plus daily 

environmental monitoring data from each facility to determine the effects of thermal and 

chemical discharges on pinnipeds and their prey. Using this information, EPA could estimate the 

aggregate effects of CWIS on sea turtles. As described in the BE, EPA was unable to locate and 

evaluate this information; however, EPA provided annual take data from 13 power generating 

stations. Seven facilities were the subject of ESA section 7 consultations and six applied for 

incidental take permits. We identified similar data in another consultation that was not included 

in the BE on the Port Everglades facility. We used the data available in the following biological 

opinions to describe the effects of CWIS on sea turtles: 

 Operation of the Cooling Water Intake System at the Brunswick Steam Electric Plant, 

Carolina Power and Light Company, 2000 (NRC) (NMFS 2000a)

 Greenhouse Gas Permit to Florida Power & Light for proposed improvements at the Port 

Everglades Next Generation Clean Energy Center, 2013 (EPA) (NMFS 2013b)

 Cooling Water Intake System at the Crystal River Energy Complex [Florida], 2002 

(NRC) (NMFS 2002)

 Continued Operation of the St. Lucie Nuclear Power Plant’s Circulating Seawater 

Cooling System, Jensen Beach, Hutchinson Island, Florida, 2001 (NRC) (NMFS 2001)

 Reinitiation of a Consultation in accordance with Section 7(a) of the ESA regarding 

Continued Operation of the Salem and Hope Creek Nuclear Generating Stations on the 

Eastern Shore of the Delaware River in New Jersey, 1993 (NRC) (NMFS 1992)
26

 Reinitiation - Continued Operation of Oyster Creek Nuclear Generating Station [New 

Jersey] pursuant to a License issued by the NRC in April 2009, 2011 (NRC) (NMFS 

2011)

 Formal Consultation on the Continued Operation of the Diablo Canyon Nuclear Power 

Plant and San Onofre Nuclear Generating Station [California], 2006 (NRC) (NMFS 

2006b)

These biological opinions resulted from section 7(a)(2) consultations. In most instances, NRC 

was the action agency; EPA consulted on the issuance of a Greenhouse Gas Permit. The 

consultation on the issuance of ESA section 10 permits to seven power plants in California has 

yet to be completed (the permits have yet to be issued). These biological opinions evaluate 

biological monitoring data, describing and quantifying the effects of CWIS on sea turtles. Such 

data are available because this small subset of facilities (N = 14) monitored and reported on the 

annual number of sea turtles entrapped in their CWIS and the number of sea turtles that died as a 

result of entrapment; some facilities gathered information on the non-lethal effects as well. For 

specific details on each facility, please refer to the original biological opinions. 

Eight of the 14 facilities worked with NMFS to receive take exemption through ITSs. These 

facilities implemented control measures to minimize adverse effects on ESA-listed species and 

designated critical habitat, including: large organism excluder bars and sea turtle response 

programs. The reasonable and prudent measures generally require trained staff at the facility to 

contact turtle recovery experts at NMFS or rehabilitation centers, remove/release/transfer the 

turtle, and complete a report for each incident of entrapment. These facilities are also required to 

conduct biological monitoring (inspections of the intake structure for entrapped sea turtles) at 

least daily and up to 24 hours per day. The facilities sent annual reports to the action agency 

and/or NMFS. 

Six of the 14 facilities are working with NMFS to receive section 10 incidental take permits. 

These facilities are located in California, where State regulations require large organism excluder 

bars spaced nine inches apart. These facilities provided 25 years of data on sea turtle entrapment 

in their incidental take permit applications. 

This subset of 14 facilities does not represent a random sample of the possible 3,730 facilities

that represent an upper bound estimate of the number of facilities that may possibly have cooling 

water intakes (ABT 2014). Most of the facilities potentially authorized under the Rule have not 

been the subject of section 7(a)(2) consultation and have not worked with the Services to receive 

an ITS or ESA section 10 permit. The Rule does not require Directors to establish permit 

requirements to protect sea turtles from entrapment, and Directors are not likely to require such 

measures (EPA 2013). As described in the BE, the subset of 14 facilities do not provide an 

unbiased sample, suitable for extrapolation to all facilities regulated under the Rule (EPA 2013). 

Still, the information from the relevant biological opinions represents the best available data and, 

though not a representative sample of the regulated universe, provides insight into the minimum 

adverse effects on sea turtles and critical habitat to be expected.
27

Table 6 summarizes the data analyzed in the biological opinions on the 14 facilities. The annual 

entrapment at each facility ranges from 0 to 949 turtles. Over all facilities during all years, a total 

of 15,595 turtles were entrapped, an average of 46 turtles per facility per year (standard deviation 

= 165). The annual number of deaths at each facility ranges from 0 to 28 turtles. Over all 

facilities during all years, a total of 385 entrapped turtles died. At individual facilities, the 

proportion of entrapped turtles that die ranges from 0 to 100 percent annually and 0 to 67 percent 

over all years. On average, 23 percent of entrapped turtles die annually at each facility (standard 

deviation = 0.33). 

3.1 Stressors

In the BE, EPA identified numerous stressors that are produced as a result of CWIS. These 

include entrapment and indirect effects from thermal discharges, chemical discharges and of prey 

reduction. 

3.2 Exposure

Large variation among the 14 facilities (e.g., annual take ranges from 0 to 949 turtles) is a result 

of the differences in facility locations, CWIS characteristics, and control measures. We expect at 

least this much variation in the 3,370 facilities that may be regulated under the Rule, attributed to 

differences in facility locations, CWIS characteristics, and control measures or lack thereof. The 

14 facilities are required to minimize incidental take of sea turtles by implementing protective 

measures, such as excluder bars; even so, these facilities entrap 0 to 949 sea turtles annually. 

Infrequent monitoring increases the likelihood of death by drowning, starvation, predation, 

stress-related injuries and illnesses, or diminished overall condition. A large proportion (75 - 100 

percent) of entrapped sea turtles are injured (see Response section, under injury). Without proper

removal and handling, even minor injuries are likely to result in death. Prolonged entrapment is 

likely to interrupt or delay normal migrating, foraging, nesting, and mating behaviors. 

Table 6. Sea turtle entrapment at 14 cooling water intake structures (data from biological opinions, 

see above).

Facility Years (N)

Total 

turtle 

take

Annual 

turtle 

take

Total 

dead 

turtles

Annual 

dead 

turtles

Annual 

proportion dead 

turtles

Brunswick* 1986-1999 

(14) 203 Unknown 31 Unknown Unknown

Brunswick 2003-2012 

(10) 104 4 – 23 24 0 – 9 0 – 0.39

Crystal River 2002-2011 

(10) 87 3 – 21 9 0 – 2 0 – 0.25

Port 

Everglades

1991-2012 

(22) 32 0 – 4 12 0 – 3 0 – 0.75

St. Lucie* 1976-1982 (7) 851 Unknown 76 Unknown Unknown

St. Lucie 1983-2011 

(29) 14,103 122 – 949 176 0 – 28 0 – 0.11

Salem 1978-2010 

(33) 71 0 – 24 26 0 – 6 0 – 1.00

Oyster Creek 1992-2011 77 0 – 11 23 0 – 4 0 – 1.00
28

(20)

San Onofre 2083-2012 

(30) 40 0 – 7 4 0 – 1 0 – 0.50

Diablo Canyon 1988-2012 

(25) 11 0 – 2 0 0 0

El Segundo 1982-2006 

(24) 3 0 – 1 1 0 – 1 0 – 1.00

Scattergood 1982-2006 

(24) 6 0 – 2 0 0 0

Encino 1982-2006 

(24) 3 0 – 1 2 0 – 1 0 – 1.00

Huntington 

Beach

1982-2006 

(24) 0 0 – 0 0 0 0

Ormond Beach 1982-2006 

(24) 1 0 – 1 0 0 – 1 0

Redondo 

Beach

1982-2006 

(24) 3 0 – 1 1 0 – 1 0 – 1.00

TOTAL (344) 15,595 129-1,047 385 0 – 57 0 – 1.00

*Annual data not available.

When analyzing the data from the 14 facilities, we did not analyze the data by species, but 

instead combined all turtle data because facility location and individual CWIS characteristics 

determine which sea turtles may be exposed. For example, in some locations, we might expect a 

facility to entrap primarily loggerheads sea turtles, whereas in another location, we may expect 

the entrapment of Kemp’s ridley sea turtles. Similarly, we did not analyze the data by turtle size 

or age because the facility location and CWIS characteristics likely play a large role in 

determining whether adult, juvenile, or hatchling turtles are entrapped. Gender data was not 

available from the majority of facilities; however, when it was available, the sex ratio varied 

from 1:1 to 6:1 favoring females. The skew likely reflects nesting females, which migrate to 

inshore waters when returning to their natal beaches. These nesting females are the most 

valuable individuals in terms of a species’ survival and recovery. For our exposure analyses, we 

will assume that up to 85 percent of exposed turtles are female.

In the BE, EPA estimates the number of facilities that overlap with the range of each species 

(Table 7). In addition, we used ArcGIS to map the list of facilities potentially regulated under the 

Rule (EPA 2013) to identify overlap with ranges of listed species. There is a large discrepancy 

between EPA’s and our estimates of the number of facilities overlapping with sea turtle ranges. 

We used the same list of 3,730 facilities provided by EPA that represent an upper bound estimate 

of the number of facilities that may possibly have cooling water intake structures (ABT 2014). 

EPA estimated that more of these facilities would fall within the range of sea turtles. It is 

possible that our mapping of turtle ranges was more precise than that used by EPA. Therefore, 

we consider our estimate to be more likely. Even so, the high range of the estimates is large and 

in some cases exceeds the total abundance of the species (e.g., leatherback, Kemp’s ridley, and 

hawksbill sea turtles). The reason for this is because of the large number of sea turtles taken one 

year at the St. Lucie Nuclear Power Plant Facility (N = 949). EPA did not provide us data on the 

location or characteristics of CWIS; therefore, we cannot determine how each facility is likely to 

impact sea turtles. However, it is unlikely that all facilities overlap with sea turtle nesting 
29

beaches. Therefore, the maximum mortality estimate (based on entrapment of 949 sea turtles at 

each facility) is unlikely but can be considered the absolute maximum mortality we expect from 

all CWIS as regulated under the Rule. Mean entrapment based on the information available is 46 

sea turtles per year. This average is based on facilities that implement control measures to 

minimize take (i.e., entrapment). 

Table 7. Estimated exposure and minimum estimated annual mortality of sea turtles as a result of 

entrapment based on limited, non-site specific information.

Species Overlapping 

facilities Total mortality * Female mortality

Loggerhead 61 (260) 2,806 – 57,889 2,386 – 49,206

Green 59 (192) 2,714 – 55,991 2,307 – 47,593

Leatherback 62 (164) 2,852 – 58,838 2,425 – 50,013

Kemp's 42 (164) 1,932 – 39,858 1,643 – 33,880

Hawksbill 36 (124) 1,656 – 34,164 1,408 – 29,040

Olive ridley 14 (23) 644 – 13,286 548 – 11,294

TOTAL 14 – 62 (23 – 260) 12,604 – 260,026 10,717 – 221,026

* Total mortality estimated by multiplying the number of facilities overlapping with species’ ranges (EPA estimates in parentheses) 

by 46 – 949 (average and maximum annual mortality per facility due to entrapment at 14 facilities that minimize take). We estimated 

female mortality by multiplying total mortality by 85 percent and rounding to the next whole number. 

3.3 Response

Stressors that may affect sea turtles are entrapment, and indirect effects from thermal and 

chemical discharges and to prey species which are discussed in general and then for each ESAlisted sea turtle species below.

3.3.1 Entrapment

As described in the BE, power plants are known to entrap all six species of sea turtles found in 

U.S. waters (Norem 2005), with more than 730 occurrences of overlap between species ranges 

and CWIS (EPA 2013). Incidences of mortality have been reported at facilities in California, 

Texas, Florida, South Carolina, North Carolina, and New Jersey (National Research Council 

1990, Plotkin 1995). These facilities span a wide range of intake flows (fewer than 30 million to 

more than 1,400 million gallons per day average intake flow), suggesting that sea turtle mortality 

or injury is not limited to large intakes. According to EPA, high-quality data on sea turtle 

impingement or entrainment is available from only one source, the St. Lucie Nuclear Power 

Plant, at Hutchinson Island, FL (EPA 2013). Therefore, most instances of entrapment, and 

resulting injury or mortality, are likely to go undetected and unreported. In the BE, EPA 

concludes that the cumulative impact of entrapment of sea turtles is unclear because sufficient 

data do not exist to estimate baseline sea turtle mortality due to entrapment at regional or 

national scales. Since all entrapment constitute incidental take (i.e., via entrapment or 

harassment), we conclude that the majority of incidental take has not been exempted by the 
30

Services through an ITS or an ESA section 10 permit and that EPA has not structured its Rule to 

provide this information in the future. 

The entrapment of sea turtles is caused by a voluntary or involuntary approach to the CWIS. Sea 

turtles may voluntarily approach the CWIS out of curiosity, in pursuit of prey, or in search of 

shelter. Some facilities appear to attract sea turtles, possibly because their CWIS concentrate 

prey (on screens or at returns) or heat surrounding waters. Smaller turtles or those with 

compromised swimming ability which cannot overcome the intake velocity may be involuntarily 

drawn toward the CWIS. Once inside the CWIS, the turtle may become entrapped, entangled, 

disoriented, submerged, or otherwise encumbered and unable to escape. Below we summarize 

the potential responses that sea turtles may exhibit as a result of exposure to entrapment. All 

responses are dependent upon several factors, including: 

 Turtle species, size, and condition (health or reproductive status)

 Swimming efficiency, relative to intake velocity

 CWIS location, characteristics, and control measures

 Water temperature and other environmental characteristics

 Biological and environmental monitoring

 Response, experience, and knowledge of facility staff

 Mortality

 In reviewing the eight biological opinions described above, we have identified many 

sources of mortality as a result of entrapment in a CWIS:

 Drowning due to forced, prolonged submergence in the intake structure

 Drowning as a result of entanglement in barrier nets, screens, or other control measures

 Drowning as a result of entanglement in debris on improperly maintained trash bars

 Death as a result of injuries sustained in intake pipes or canal 

 Starvation or otherwise debilitation of condition due to long periods of entrapment

 Exposure to predators 

 Death as a result of drowning, entanglement, injury and stress sustained during capture

 Death due to previous injury or illness compounded by stress and exhaustion caused by 

entrapment

 Unknown causes

Drowning is a common cause of death for entrapped sea turtles. In natural situations, turtles may 

remain submerged for several hours; however stress decreases the amount of time a turtle can 

remain submerged and not drown (National Research Council 1990). For example, trawl times 

for shrimpers in the Southeast are limited by regulation to 55 minutes in the summer months and 

75 minutes in the winter months, due to the fact that there is a strong positive correlation 

between tow time (i.e., forced submergence) and incidence of sea turtle death(Henwood and 

Stuntz 1987). A forcibly submerged sea turtle may suffer from a "wet" or "dry" drowning. 

During a wet drowning, water enters the lungs, causing damage to the organs and asphyxiation. 
31

In a dry drowning, a reflex spasm seals lungs off from air and water (National Research Council 

1990). Typically before drowning, a turtle becomes comatose or unconscious. During a forcible 

submergence, a turtle maintains a high level of energy consumption and rapidly depletes its 

oxygen store, resulting in potentially harmful conditions (Magnuson et al. 1990). One such 

condition is metabolic acidosis, when blood lactate levels get too high as a result of the 

submergence. Other conditions that may result from forced submergence include an increase in 

carbon dioxide in the blood and increases in epinephrine and other hormones associated with 

stress. The severity of the metabolic stress response is related to the size of the turtle, water 

temperature, and biological and behavioral differences among species. For example, Kemp’s 

ridleys cannot survive underwater as long as other species and have been found to drown faster 

in trawl nets (Magnuson et al. 1990). Larger sea turtles are capable of longer voluntary dives and 

thus may be more able to survive a forced submergence for a longer period of time (Gregory et 

al. 1996). Additionally, Gregory et al. (1996) note that routine metabolic rates of turtles are 

higher during the warmer months, so the impacts of stress may be magnified. It is likely that 

entrapped sea turtles are already stressed; these conditions may increase the turtles’ susceptibility 

to drowning.

Death as a result of entrapment clearly eliminates an individual’s survival, but it also eliminates 

the individual’s reproductive contribution to the population. Because sea turtles found in nearshore environments may be females returning to their natal beaches to nest, such deaths are 

likely to have devastating impacts on populations and species. 

Injury

Injury, as a result of entrapment, is also a cause for concern. Sustained injuries may result in 

death after a turtle has been released. Injuries may prevent reproduction, reducing an individual’s 

fitness to zero. Or injuries may prevent or reduce the normal development, growth, and 

behaviors of sea turtles. We have identified many sources of injury as a result of entrapment:

 Physiological changes, as a result of forced submergence in the intake structure

 Entanglement in barrier nets, screens, or other control measures

 Entanglement in heavy debris load of improperly maintained trash bars

 Abrasion or pinching resulting from entrapment in intake pipes, canal, or well

 Emaciation or otherwise debilitation of condition due to long periods of entrapment

 Exposure to predators 

 Stress and injuries sustained during capture

 Exacerbation of previous injury or illness compounded by stress and exhaustion caused 

by entrapment

 Unknown causes

Many of the causes of injury are likely to result in death if severe or prolonged. One example is 

the physiological impacts of submergence. In addition to the stress-inducing effects of 

submergence, described above, sea turtles may also exhibit dynamic endocrine responses to 
32

submergence. Plasma hormone responses to the capture and restraint of male green turtles result 

in the abandonment of breeding behavior; female green turtles also exhibit a limited 

adrenocortical stress response during capture and restraint (Jessop et al. 2002). The submergence 

of loggerhead sea turtles produces severe metabolic and respiratory acidosis; though the acidbase imbalance is reduced during successive submergences, changes in blood pH, dissolved 

CO2, and lactate are significant (Stabenau and Vietti 1999). 

In our review of relevant biological opinions, some facilities indicated that entrapped sea turtles 

were released without injury; however, we generally found that the majority of impinged or 

entrained sea turtles exhibited injury. For example, at St. Lucie, which EPA identified as the only 

high-quality data source, approximately 85 percent of turtles show evidence of injury as a result 

of entrainment (Norem 2005). Our analyses indicate that 75 percent of all impinged or entrained 

sea turtles at Port Everglades were injured or killed. The Northeast Region reports that nearly all 

of the sea turtles recovered from the Oyster Creek facility have evidence of injury from sustained 

contact with the trash bars. The injuries included abrasions, bruises, scrapes, and even puncture 

wounds, likely caused by the tines of the trash rake. It is important to note that the large 

incidence of injury occurs despite frequent monitoring and conscientious turtle response 

programs, as implemented at the 14 facilities.

It is easy to estimate the fitness costs of mortality (100 percent); it is more difficult to estimate 

the fitness costs of injury. Injuries that are likely to result in latent mortality or prevent 

reproduction will reduce fitness 100 percent. Other injuries may temporarily prevent or delay 

reproduction; and yet others may delay growth or development. Some injuries may not have any 

fitness costs whatsoever; however, even minor injuries may result in major costs to fitness if the 

turtle is not released. 

Reduced Foraging

As a result of impingement or entrainment, some sea turtles may be unable to locate and capture 

prey. For example, green sea turtles may not have access to their normal food sources, which 

include sea grasses and algae. Foraging specialists, such as the leatherback or hawksbill sea 

turtles, may not encounter adequate amounts of prey within the CWIS. This reduced prey 

availability could delay growth and development, prolong inter-nesting periods, or result in 

reduced condition. All responses are expected to reduce an individual’s overall fitness. The 

severity would increase proportionately to the length of entrapment. Because the Rule does not 

require facilities to monitor or remove turtles from CWIS, we expect prolonged entrapment, and 

thus greater fitness costs, to occur at the majority of facilities regulated by the Rule. 

Delayed or Interrupted Migration or Reproduction

As described above, entrapment is likely to cause stress to sea turtles. The release of stress 

hormones may result in reduced or delayed reproduction (Jessop et al. 2002). We are also 

concerned with the physical disruption of the turtle’s behavior. Turtles may be entrapped while 

attempting to migrate, forage, nest, or mate. Their entrapment in a CWIS interrupts or delays 

these activities. Leatherbacks are probably more sensitive to interruption of migration than the 
33

other species of sea turtle because their spring migrations seem to be closely synchronized with 

the presence of prey species. The ridley turtles nest in large arribadas that are time- and locationsensitive. The availability of mates may also be time sensitive (Pearse and Avise 2001). The loss 

of nesting opportunities has been documented at the St. Lucie facility, where an entrapped 

female sea turtle was forced to nest on the canal bank. Several of the resulting hatchlings died, 

despite the frequent monitoring. The delay or interruption of normal behaviors is likely to result 

in negative fitness consequences. 

Indirect Effects

In the preceding paragraphs, we described how sea turtles are likely to respond to the direct 

effects of CWIS, which include entrapment of sea turtles or exposure of sea turtles to thermal or 

chemical discharges. Here, we consider the impingement or entrainment of sea turtle prey, or the 

exposure of sea turtles and their prey to thermal or chemical discharges. In our review of relevant 

biological opinions, we found that each CWIS impinged or entrained a large number of potential 

sea turtle prey items annually. For example, at the Oyster Creek facility, the equivalent of 59,000 

adult hard clams and 10,400 blue crabs are lost to impingement and entrainment each year. EPA 

estimates that CWIS, as regulated under the Rule, will impinge or entrain over a trillion aquatic 

organisms in waters of the U.S. each year, with most impacts to early life stages of fish and 

shellfish (EPA 2011). Such losses reduce prey availability for all sea turtle species. Thermal and 

chemical discharges may also reduce the availability of prey. Cold and heat shock mortalities of 

fish have been documented at the Oyster Creek facility, for example. The chlorine discharge may 

also have an effect on sea turtle prey. Thus, CWIS are likely to reduce prey availability to sea 

turtles, potentially resulting in fitness losses. 

Thermal Discharges

In the BE, EPA identifies thermal discharges as likely stressor resulting from the operation of 

regulated CWIS. For example, the Oyster Creek facility has a daily maximum “end-of-pipe” 

temperature of 41.1°C, though the maximum temperature recorded was 38°C. Environmental 

temperatures above 40°C can result in stress for green sea turtles (Spotila et al. 1997). Excessive 

heat exposure (hyperthermia) is a known stress to sea turtles, but it is a rare phenomenon when 

sea turtles are in the ocean (Milton and Lutz 2003). As such, limited information is available on 

the impacts of hyperthermia on sea turtles. 

While sea turtles may not be killed by the elevated temperatures, thermal plumes may affect 

normal distribution and foraging patterns. For example, green sea turtles have been found to 

aggregate in the warm water effluent discharged from the San Diego Gas and Electric Company's 

power generating facility. This is the only area on the west coast of the United States where the 

green sea turtles are known to aggregate (Stinson 1984). 

Thermal effluent discharges may attract sea turtles or allow them to stay in an area longer than 

usual. Sea turtles may remain in areas late enough into the fall to become cold stunned when they 

finally begin their southern migration. Cold stunning occurs when water temperatures drop 

quickly and turtles become incapacitated, losing their ability to swim or dive (Spotila et al. 
34

1997). Stranding reports from the NMFS Southwest Region document the cold stunning of olive 

ridley turtles from Los Angeles County and north to San Francisco County (NMFS 2006a).

Cold stunning is likely to have fitness reductions on sea turtles. Other thermal effects are likely 

to reduce the fitness of turtles by altering their normal reproductive behaviors. We do not have 

data on the thermal discharges of all facilities, but it is likely that thermal discharges will reduce 

the fitness of sea turtles. 

Chemical Discharges

In the BE, EPA identifies chemical discharges as a likely stressor resulting from the operation of 

regulated CWIS. Our review of relevant biological opinions revealed two potential concerns: 

sponge balls and chlorine. 

The St. Lucie facility releases sponge balls (maximum = 3/day) as a byproduct of the condenser 

cleaning system. The sponge balls are made of vulcanized natural rubber and could be mistaken 

for prey items by turtles. The effects of ingestion are unknown but are likely to include 

poisoning, choking, or blockages.

Other facilities use low level, intermittent chlorination to control biofouling in their CWIS. 

Though not specified in the Rule, we found maximum daily concentration of chlorine discharge 

values of 0.2 mg/L or a maximum daily chlorine usage of 41.7 kg/day, at one facility, and a 

maximum total residual oxidant concentration of 200 ppb, at another facility. For the former, the 

anticipated total residual chlorine level at the point of discharge is significantly higher than 

EPA’s ambient water quality criteria and higher than chlorine levels known to be protective of 

aquatic life (maximum = 0.019 mg/L). 

Chemical contaminants have been found in the tissues of sea turtles from certain geographical 

areas. While the effects of chemical contaminants on turtles are relatively unclear, they may have 

an effect on sea turtle reproduction and survival. Chemical contaminants may also affect the 

immune system, making sea turtles more susceptible to disease and other stresses. There is no 

information available on the effects of chlorination on sea turtles. 

It is assumed that the chlorination is quickly diluted within the water body; however, this 

assumption has not been tested, and the effects on turtles remain unclear. Therefore, we must 

allow that chemical discharges may result in adverse effects to sea turtles.

3.4 Leatherback Sea Turtles

The global population of adult females has declined over 70 percent in less than one generation, 

from an estimated 115,000 adult females in 1980 to 34,500 adult females in 1995 (Pritchard 

1982, Spotila et al. 1996). However, the most recent population size estimate for the North 

Atlantic alone is a range of 34,000-94,000 adult leatherbacks (NMFS USFWS 2013). Our 

analysis based on available information, without site specific data suggests that substantial 

numbers of leatherback sea turtles could die each year, as a result of entrapment in CWIS. 

Leatherback sea turtles migrate long, transoceanic distances between their tropical nesting 

beaches and the highly productive temperate waters, where they forage, primarily on jellyfish 
35

and tunicates. These gelatinous prey are relatively nutrient-poor, such that leatherbacks must 

consume large quantities to support their body weight. Jellyfish are impinged and entrained in 

CWIS in very large quantities, to the point of leading to the shutdown of power plants 

(Masilamoni et al. 2000). Such losses reduce the availability of jellyfish prey for leatherback sea 

turtles. 

Leatherbacks are constrained to a tight metabolic budget (Wallace and Jones 2008) and must 

meet a reproductive energy threshold before returning to nesting beaches to reproduce (Benson 

et al. 2007, Benson et al. 2011); if they do not, their remigration intervals (the time between 

breeding seasons) increases, without a corresponding increase in clutch size the next season 

(Hays 2000, Price et al. 2004, Wallace et al. 2006). Females lay up to seven clutches per year, 

with more than 65 eggs per clutch (Reina et al. 2002, Wallace et al. 2007). The loss of a single 

breeding season would result in a cost of 455 eggs per individual. Due to the great variance in 

hatchling success and the unknown lifetime reproductive success of leatherbacks, we are unable 

to accurately estimate the loss of reproductive potential in terms of offspring that survive to 

reproduce; however, the loss of a breeding season is likely to diminish lifetime reproductive 

success and reduced fitness. The loss of jellyfish prey, as a result of impingement and 

entrainment in CWIS, is likely to reduce the reproductive potential of many leatherback sea 

turtles, causing a decline in annual population productivity. 

In summary, leatherback sea turtles are expected to be directly and indirectly affected by CWIS.

3.5 Loggerhead Sea Turtles

The North Pacific Ocean DPS has a small nesting population of a few thousand females that 

produces 7,000 to 8,000 nests annually. The female population size of the Northwest Atlantic 

DPS is estimated at 20,000 to 40,000 females. 

Loggerhead sea turtles are susceptible to cold stunning (Witherington and Ehrhart 1989), such 

that thermal discharges could result effects to loggerhead sea turtles. Juveniles are omnivorous 

and forage on crabs, mollusks, jellyfish and vegetation at or near the surface (Dodd 1988). Subadult and adult loggerheads prey on benthic invertebrates such as mollusks and decapod 

crustaceans in hard bottom, coastal habitats. These species and/or their larval stages are likely to 

be impinged and entrained by CWIS. Therefore, we expect that CWIS are likely to result in 

additional losses, beyond the minimum entrapment of 2,386 females annually.

The North Pacific DPS has a small population size that is not resilient to further perturbation. 

Though the Northwest Atlantic DPS has a relatively large abundance, however it continues to 

face significant threats from fishing bycatch throughout their range in the Atlantic Ocean and 

Gulf of Mexico. The Northwest DPS appears to be declining largely driven by fishery bycatch 

throughout the Pacific Ocean (76 FR 58943). 

In summary, loggerhead sea turtles will be directly and indirectly affected by CWIS.
36

3.6 Green Sea Turtles

Along the central and southeast coast of Florida, an estimated 200 to 1,100 females nest each 

year (Meylan et al. 1994, Weishampel et al. 2003). 

Green sea turtles are susceptible to cold stunning (Witherington and Ehrhart 1989). As described 

above, green sea turtles aggregate in the warm water effluent of CWIS (Stinson 1984). These 

waters provide a warm water refuge as surrounding water temperatures decrease. If the turtles 

leave the warm water plume to begin their migration, cold stunning is likely to occur. Turtles that 

do not leave the warm water plume are unable to migrate and reproduce at natal nesting beaches. 

Furthermore, increases in water temperatures to 30°C increase the induction and severity of 

lesions associated with herpes virus infection (Haines and Kleese 1977), which reduces fitness in 

green sea turtles. Therefore, thermal effluent is likely to lead to reductions in survival and 

reproduction. 

Entrapment of females CWIS, are likely to reduce the survival and recovery of the green sea 

turtle, Florida breeding colony. For all other areas, entrapment is likely to result in the loss of 

green turtles. Additional losses, as a result of thermal discharges, are likely to further reduce the 

viability of green sea turtle populations. Apparent increases in abundance in recent years are 

optimistic but must be viewed cautiously, as the datasets represent a fraction of a green sea turtle 

generation, which is up to 50 years. Green sea turtles exist at a fraction of their historical 

abundance, which combined with the high variance in abundance, reduces their resilience to 

population collapse (Dai et al. 2012, Scheffer et al. 2012). 

In summary, green sea turtles will be directly and indirectly affected by CWIS.

3.7 Hawksbill Sea Turtles

Globally, 22,004 to 29,035 females nest annually. The loss of at least 1,408 females annually, as 

a result of entrapment in CWIS (Table 7), represents a minimum of 5 to 6 percent annual loss to 

the species. Thermal and chemical discharges are likely result in additional losses, further 

reducing the viability of hawksbill sea turtle populations. Long-term data on the hawksbill sea 

turtle indicate declines at nesting sites over the past 20 to 100 years. The species’ resilience to 

further perturbations is low. 

In summary, hawksbill sea turtles will be directly and indirectly affected by CWIS.

3.8 Kemp’s Ridley Sea Turtles

The best estimate of Kemp’s ridley abundance is 8,000 nesting females. The loss of sea turtles of 

both sexes as a result of entrapment in CWIS is likely based on the information available. 

Kemp’s ridleys sea turtles are susceptible to cold stunning (Meylan and Sadove 1986), such that 

thermal discharges are likely to result in additional losses. Kemp’s ridleys forage on swimming 

crabs, fish, jellyfish, mollusks, and tunicates, all of which are likely to be impinged or entrained 

in CWIS. Therefore, we expect that CWIS are likely to result in additional losses of sea turtles.

Among all sea turtle species, the Kemp’s ridley has declined to the lowest population level. 

Though it has increased in abundance in recent years, the species’ limited range and small 
37

population size make it vulnerable to population collapses as a result of demographic and 

environmental stochasticity vortex (Gilpin and Soule 1986, Melbourne and Hastings 2008). 

In summary, individual Kemp’s ridley sea turtles will be directly and indirectly affected by 

CWIS.

3.9 Olive Ridley Sea Turtles

The total estimate of olive ridley sea turtles exceeds 1.39 million individuals. The minimum loss 

of 644 sea turtles annually represents 0.05 percent of the total abundance, and the maximum loss 

of 13,286 represents one percent of the total abundance. Nesting estimates appear to be 

increasing or stable. 

In summary, olive ridley sea turtles will be directly and indirectly affected by CWIS.

3.10 Critical Habitat

We have determined that CWIS are likely to overlap with designated and proposed critical 

habitat of sea turtles. There are no CWIS on the islands where designated critical habitat occurs 

for green and hawksbill sea turtles; however, we determined that the effects of CWIS (within 1 

km of the CWIS) are likely to overlap with leatherback designated critical habitat and Northwest 

Atlantic loggerhead proposed critical habitat. 

Leatherback designated critical habitat includes a 43,798 km2area stretching along the California 

coast from Point Arena to Point Arguello and a 64,760 km2area stretching from Cape Flattery, 

Washington to Cape Blanco, Oregon (77 FR 4170). The designated habitat includes marine 

waters from the ocean surface down to a maximum depth of 80 m. The designation includes one 

primary constituent element, which is essential for the conservation of leatherbacks in marine 

waters off the U.S. West Coast: the occurrence of prey species, primarily scyphomedusae of the 

order Semaeostomeae (e.g., Chrysaora, Aurelia, Phacellophora, and Cyanea), of sufficient 

condition, distribution, diversity, abundance and density necessary to support individual as well 

as population growth, reproduction, and development of leatherbacks. Three facilities are likely 

to overlap with leatherback critical habitat. As described above, the indirect effects of CWIS

could reduce the prey availability for leatherback sea turtles. 

Northwest Atlantic loggerhead proposed critical habitat includes nearshore reproductive habitat, 

winter area, breeding areas, and migratory corridors (78 FR 43005). The proposed critical habitat 

includes physical and biological features that are essential to the recovery of the DPS, including: 

waters with minimal manmade structures that could promote predators (i.e., nearshore predator 

concentration caused by submerged and emergent offshore structures), disrupt wave patterns 

necessary for orientation, and/or create excessive longshore currents; and sufficient prey 

availability and quality, such as benthic invertebrates, including crabs (spider, rock, lady, hermit, 

blue, horseshoe), mollusks, echinoderms and sea pens. Four facilities are likely to overlap with 

the proposed critical habitat. We have described above how CWIS are likely to reduce the prey 

availability for all sea turtle species. In addition, large withdrawals of water are likely to alter 

currents, disrupt wave patterns, or attract predators. 
38

4 Salmonids

In the BE, EPA describes the likely adverse effects of CWIS on ESA-listed Atlantic and Pacific 

salmonids, and steelhead trout (i.e., salmonids). To estimate the extent of these effects, EPA 

evaluated the NPDES permits of eight facilities (Abt 2012). Three of these facilities overlapped 

with salmonid ranges: Portland General Electric Beaver Generating Facility in Clatskanie, OR; 

Port Townsend Paper Corporation in Townsend, WA; and Columbia Generating Station in 

Benton Co., WA. As described in their report, none of the NPDES permits had special conditions 

or requirements to protect ESA-listed species or to minimize impingement and entrainment of 

ESA-listed species. 

As described in the BE and follow up conversations, EPA used data obtained from the Pittsburgh 

Power Station in Pittsburgh, CA, and Contra Costa Power Station in Antioch, CA (now called 

Gateway Generating Station), to calculate the annual loss of salmon per facility, as a result of 

impingement and entrainment. These facilities observed impingement and entrainment mortality 

of the following species: Atlantic salmon, Chinook salmon, Coho salmon, and steelhead trout. 

Quantitative data were only available for Chinook salmon. To estimate annual impingement and 

entrainment mortality per facility: 

“EPA calculated an average annual loss rate for each facility reporting losses. 

These facility-specific raw loss rates were corrected to account for any technology 

installed to reduce [impingement mortality and entrainment] between the 

sampling year and present, and summed to estimate reported annual losses. In no 

cases were [ESA-listed] species observed in [impingement mortality and 

entrainment] studies in more than three facilities, and in no case were these 

observations more recent than 1992” (EPA 2013). 

Hanson et al. (1977) provide an overview of the entrapment and impingement of fishes by power 

plant cooling water intakes. The authors evaluate various measures for minimizing impingement 

and impingement mortality of fishes. They explain that several power plants have documented 

impingement mortalities approaching or exceeding one million fish annually. Their entrainment 

estimates (Hanson et al. 1977) include the Connecticut Yankee Power Plant (179 million fish 

larvae and juveniles annually) and the Oyster Creek Power Plant (150 million eggs and 100 

million larvae). The variance among control measures and individual CWIS makes it difficult to 

predict the magnitude losses and their impact on aquatic resources (Hanson et al. 1977).

4.1 Stressors

CWIS have the potential to result in the following stressors for salmonids: impingement; 

entrainment; thermal discharges; chemical discharges; flow alteration; and indirect effects as a 

result of reduced prey availability or increased predation.

4.2 Exposure

Salmonids of multiple life stages and both sexes are likely to be exposed to the adverse effects of 

CWIS. Thermal and chemical discharges, flow alteration, and indirect effects are likely to reduce 

the fitness of a large proportion of salmonid populations. In addition, some salmonids are likely 
39

to be impinged or entrained in CWIS. We used ArcGIS to map the list of facilities potentially 

regulated under the Rule (EPA 2013) to identify overlap with ranges of listed species(Table 8).

Table 8. Estimated number of CWIS that overlap the range of salmonid species (EPA estimated 

number of facilities in parentheses). 

Species Overlapping facilities

Atlantic salmon 21 (147)

Chinook 71 (126)

Chum salmon 28 (81)

Coho salmon 37 (109)

Sockeye salmon (77)

Steelhead trout 129 (190)

4.3 Response

Stressors that may affect ESA-listed salmon species are impingement, entrainment, thermal

discharges, chemical discharges, and flow alterations; indirect effects to prey species may also 

affect ESA-listed pinnipeds. General responses to these stressors are discussed below followed 

by subsequent species specific discussions.

4.3.1 Impingement

Without screens and bypass systems, impingement (and resulting mortality) is more likely.

Automatically cleaned screens with low approach velocity (less than 0.4 ft/s), small screen face 

openings (3/32" circular or square, or 1.75 mm continuous slots or rectangular openings) and 

bypass systems designed for fish swimming ability and behavioral traits, typically avoid most 

juvenile salmonid fish impingement or entrainment, and should be used anywhere juvenile 

salmonids could be present. With inadequate screen submergence, the water velocity directly 

between the water surface and the top of the screen can exceed the juvenile salmon swimming 

ability, potentially capturing fish above the screens until they fatigue or become prey. Even with 

a closed-cycle recirculating system, screens, and reduced intake velocity, the Columbia 

Generating Station is likely to impinge salmonids. 

Sublethal effects are also a concern because they are likely to reduce fitness. Hanson et al. (1977)

describes the relationship between water velocity and impingement time on physiological stress 

and survival. In general, the degree of oxygen stress observed in juvenile salmon increased with 

both increasing water velocity and increasing impingement time. For example, oxygen stress and 

a loss of equilibrium were evident in fish impinged 15 min at a water velocity of 61 cm/sec. 

Reduced activity was evident in fishes 48 hour after impingement of 9 minutes or longer at a 

velocity of 61 cm/sec. Survival decreased as the duration of impingement and water velocity 

increased. Prentice and Ossiander (1974) reported internal hemorrhaging in impinged salmonids 

and found the minimal velocity at which hemorrhaging occurred was approximately 46 cm/sec. 

At 61 cm/sec hemorrhaging occurred in approximately 10 percent of the fish tested after a 30-
40

second impingement, increasing to 33 percent after impingement for 60 seconds. Bell (1974)

observed internal hemorrhaging, eye loss, and bent gill opercula in fish as a result of 

impingement. Impingement may also result in fish being partially descaled. Loss of scales 

destroys the integrity of the protective body covering causing disruption of essential osmotic 

differentiation between fish body fluids and their environment and increasing susceptibility to 

disease and parasitism. The injury rate resulting from scale loss was inversely proportional to 

fish size (i.e., small fish are affected greatly by scale loss). They reported that delayed mortality 

following partial descaling was a significant problem; studying salmon less than 30 cm in length, 

death occurred 3-18 hours after 30-50 percent scale loss. In addition, fish behavior after scale 

loss was observed to change markedly. One hour after descaling, juvenile salmon were 

noticeably less active and less alert to visual stimuli than were controls. Loss of equilibrium 

occurred approximately 3 hours after descaling, followed by a decrease in respiration and 

activity. In general, death occurred approximately 4 hours after descaling. The time sequence 

varied with the severity of scale loss. Loss of body weight followed descaling in marine species, 

presumably as the result of osmotic removal of water and body fluid through the injured skin 

surface and the gills. Delayed mortality resulting from scale loss may arise from an osmotic 

imbalance and an increased susceptibility to infection and disease. In addition, physiological 

stress due to scale loss may substantially decrease the ability of a fish to avoid predators.

Mortality resulting from mechanical abrasion may increase in areas characterized by high silt 

and debris loading. High debris densities and algal mats have been reported to trap and impinge 

fish on intake screens. Accumulation of debris on trash racks and intake screens not only serves 

to entrap and entangle fish, resulting in increased mechanical damage, but also effectively alters 

the hydraulic flow field and approach velocities associated with each intake structure. High 

concentrations of suspended sediment abrade the eyes, gills, and epidermal tissue of impinged 

fish. From the literature it appears that mechanical damage may be a significant factor in survival 

of entrapped and impinged organisms. 

4.3.2 Entrainment

Salmonids that are entrained within a CWIS could be exposed to pressure and high temperatures, 

which kill them. Very young organisms, usually at the egg or larvae stage, are most susceptible 

to death by entrainment (EPA 2011).

The intake, condenser cooling, and heated water discharge systems of a thermal power plant 

could have an adverse effect on reproduction, depending on the proximity to important spawning 

areas and the life history pattern of the species (Craddock 1976). Gravid females and their eggs 

could be damaged by the intake system or by entrainment in discharge waters; spawning time 

could be altered. Eggs and larvae passed through a condenser cooling system would almost 

surely be damaged or killed (Craddock 1976). Salmon fingerlings, especially chum salmon, are 

vulnerable to entrainment because they migrate in dense schools near shore, where intakes may 

be located (Craddock 1976). 
41

4.3.3 Flow Alteration

Female salmonids lay eggs in a “redd,” covered by gravel or cobble. The depth of a redd is 

partially dependent on water velocity. Survival of eggs depends on intragravel flow rates. Upon 

hatching, alevins move deeper into the gravel. As fry, they emerge from the gravel and orient 

themselves into the water current. As described in the BE, CWIS alter patterns of flow within 

receiving waters by withdrawing a substantial amount of water and by changing flow velocities 

and turbulence. Such withdrawals and changes are likely to disrupt the gravel deposits and 

intragravel flow rates, reducing the viability of eggs and fry.

4.3.4 Indirect Effects

Fish may be attracted to CWIS. For example, at the Columbia Generating Station, the support 

and riprap around the intake structure provides shelter for fish species that consume other fish, 

including salmonid fry (NRC 2011). Predators selectively prey on thermally shocked salmonids 

(Coutant 1973) and are likely to prey on salmonids stressed by impingement, flow alteration, and 

chemical discharges as well. Juvenile salmonids feed on zooplankton and larvae, which are 

entrained by CWIS. 

Thermal Discharges 

Thermal discharges from CWIS could result in damage or death to fishes from temperatures 

higher or lower than their normal temperature range (Craddock 1976). As temperatures rise, an 

animals’ respiration rate increases along with the heartbeat rate, which consequently increases 

the demand for oxygen. At higher temperatures the hemoglobin of the blood has reduced 

carrying capacity for oxygen. The combination of increased demand for oxygen and decreased 

efficiency for obtaining it causes a severe stress on the organism. This may eventually cause 

death or one or more of the many sublethal effects (Craddock 1976). Sublethal effects to 

exposure to increased temperatures, especially for juvenile fish, include increased susceptibility 

to predation (Sylvester 1972, Coutant 1973). 

Other sublethal effects of entrainment in CWIS include physical shock and abrasion, the effects 

of chemicals used as biocides, and the effects of temperature increases and pressure changes that 

cause gas embolisms. Gas embolism may either kill the fish directly or render it susceptible to 

predation (Craddock 1976). A review of the literature revealed that increased temperature was an 

important factor in most fish diseases (Ordal and Pacha 1963). Studies with juvenile salmon and 

trout demonstrated that increased water temperatures intensified the effects of vibrio disease, 

kidney disease, furunculosis, and columnaris. Columnaris disease has been found to be 

exceptionally virulent during periods of high temperature. Elevated temperatures can increase 

predation rate on juveniles, which cannot swim effectively at high temperatures and low 

dissolved oxygen concentrations. They can result in inadequate food supplies. Elevated 

temperatures also increase the toxicity of chemical substances and the susceptibility to diseases. 

Prolonged exposure to elevated temperatures results in a stress response that further reduces 

body condition, survival rates, and reproductive success. Miara et al. (2013) report that elevated 

temperatures have altered, and are likely to continue altering, the migration of Atlantic salmon. 
42

Chemical Discharges

Chlorination is often used as a biocide for antifouling of CWIS, with residual chlorine 

concentrations of 0.05 to 0.5 mg/L (Brungs 1973). For coho salmon, the maximum nonlethal 

concentration of residual chlorine is 0.05 mg/L. At concentrations of 0.083 mg/L for seven days, 

50 percent of coho salmon survive (TL50); at concentrations greater than 0.13, 100 percent of 

cohol salmon die within 1 to 2 days (Brungs 1973). Brungs (1973) recommends limiting 

chlorination to 30 min/day with a maximum concentration of 0.01 mg/L. Durations and 

concentrations above such levels are likely to result in the mortality of salmonids.

Return of fish to non-source waters

The Rule allows the Director to approve the return of fish to non-source waters. Salmon return to 

their natal streams to spawn. The return of salmon to non-source waters is likely to interrupt their 

spawning migration. It is likely to result in the loss of reproductive potential, either through lack 

of spawning or fertilization. Introgression, gene flow among isolated gene pools, may also occur. 

The removal and introduction of other species to salmon habitat is likely to result in changes in 

predation, prey availability, and competition for salmon. It is also likely to result in the 

introduction of novel diseases and aquatic invasive species to salmonids. 

4.4 Population and Species Level Effects

Anadromous salmonid populations have experienced dramatic declines in abundance during the 

past several decades as a result of various human-induced and natural factors, resulting in their 

threatened and endangered status. In recent years, some populations may not be able to withstand 

substantial losses fry, parr, or smolt salmon as a result of impingement and entrainment, or other 

adverse impacts from CWISs. 

Numerous DPSs have shown encouraging increases in population size. Other populations within 

salmonid ESUs and DPSs have been extirpated, indicating that populations are susceptible to 

collapse. The adverse environmental impacts of thermal discharges, chemical discharges, flow 

alteration, introduction of aquatic invasive species, and the spread of disease have the potential to 

contribute to the decline of salmon and steelhead.

In summary, salmonids will be directly and indirectly affected by CWIS. 

4.5 Critical Habitat

Critical habitat has been designated or proposed for most listed “salmonid” species and DPSs, 

including: Atlantic salmon, coho salmon, Chinook salmon, chum salmon, sockeye salmon, and 

steelhead trout. We summarize information on these critical habitats under the Status of the 

Species section, and detailed information is provided in the listings (64 FR 24049, 65 FR 7764, 

70 FR 52488, 70 FR 52630, 73 FR 7816, 76 FR 65324, and 78 FR 2725). Because there are so 

many listed DPSs, we will not describe the physical and biological features essential to the 

conservation of each DPS. Instead, we provide a summary of all features, which are similar 

across all taxa:

 Sites for spawning, rearing, and migration;
43

 Food, areas with juvenile and adult forage items, foraging habitat;

 Substrate;

 Space, areas free from obstruction;

 Safe passage conditions;

 Water quality, quantity, temperature, and velocity; and

 Cover/shelter, riparian vegetation.

CWIS have the potential to alter flow regimes (including velocity and turbidity), increase water 

temperatures, reduce water quality (through the introduction of chlorine), reduce prey 

availability, and obstruct movement of salmon. In the BE, EPA estimates: 55 facilities will 

overlap with Chinook salmon critical habitat; 44 facilities will overlap with steelhead trout 

critical habitat; 13 facilities will overlap with chum salmon critical habitat; and three facilities 

overlap with coho salmon critical habitat. Using ArcGIS, we estimate that 13 facilities overlap 

with Atlantic salmon critical habitat; 54 facilities overlap with Chinook salmon critical habitat 

(within 1 km of the facility); 15 facilities overlap with chum salmon critical habitat (within 1 km 

of the facility); 85 facilities overlap with steelhead trout critical habitat (within 1 km of the 

facility); and 3 facilities overlap with coho salmon critical habitat (within 1 km of the facility). 

5 Pacific Eulachon, Southern DPS

In the BE, EPA does not estimate how many Pacific eulachon (southern DPS) are likely to be 

impinged and entrained at a single facility annually; however, they provide estimates of the 

impingement and entrainment mortality of other smelt species in different genera (EPA 2013). 

EPA estimates the annual impingement and entrainment mortality rate for delta smelt at 

62,526/year and longfin smelt 24,919/year (EPA 2013). 

We were unable to find additional information on the effects of CWIS on Pacific eulachon 

(southern DPS). However, we found annual impingement and entrainment estimates of rainbow 

smelt at the Bay Shore Power Plant: 536,265,835 larvae entrained (10.9 percent of river 

population of larval rainbow smelt), 4,365,674 juvenile entrained, and 11,472 individuals 

impinged (Ager et al. 2008). This facility is located near Oregon, Ohio; cooling water is obtained 

from the Maumee River and Maumee Bay via an open intake channel. The design intake 

capacity is 810 mgd, and the design through screen velocity is 2.58 ft/sec. The facility has nine 

travelling screens (3/8 in openings) with bar racks. This facility is likely to be regulated under 

the Rule. 

5.1 Stressors

Pacific eulachon (southern DPS) are likely to be adversely affected by the following stressors: 

impingement, entrainment, thermal discharges, chemical discharges, indirect effects, and the 

stressors associated with releasing fish at non-source water bodies. 
44

5.2 Exposure

Mapping the facilities that may be regulated under the Rule (EPA 2013) to the range of the 

species, we find that 123 CWIS facilities overlap with Pacific eulachon (Southern DPS). 

Eulachon are likely to be exposed to the adverse effects of CWIS as larvae, juvenile, and adults. 

5.3 Response

Stressors that may affect the ESA-listed Southern DPS of Pacific eulachon are entrapment and 

thermal discharges; indirect effects to prey species may also affect ESA-listed Pacific eulachon. 

5.3.1 Impingement and Entrainment

Impingement survival appears to be linked to season, temperature, and screen type. McLaren and 

Tuttle Jr. (2000) estimated impingement survival rates of 1.5 to 94.9 percent for rainbow smelt. 

Because the Rule does not require facilities to use screens, and because the Rule does not require 

screens to be designed to minimize eulachon mortality, low survival rates (i.e., high mortality 

rates) are expected. Entrainment results in “heavy losses” for smelt larvae (Craddock 1976), and 

the high temperatures associated with entrainment are likely to result in 100 percent mortality 

(McLaren and Tuttle Jr. 2000). 

5.3.2 Thermal Discharge

Pacific eulachon exhibit a preference for a narrow range of water temperature, entering the 

Columbia River and its tributaries at temperatures of 4 to 10°C. They are sensitive to changes in 

water temperature, which affects prey availability, spawning, and rearing success. In addition, 

some marine species do not spawn when exposed to higher than normal temperatures (Craddock 

1976). Temperature treated female eulachon of the Columbia River retained their eggs where the 

control group spawned normally (Blahm and McConnell 1971). In a series of experiments, 

Blahm and McConnell (1971) exposed to elevated water temperatures. They found:

 100 percent of fish died after 8 days of exposure to 11°C water

 50 percent of fish died after 1 hour of exposure to 18°C water

 100 percent of fish died after 1 hour of exposure to 24°C water

5.3.3 Chemical Discharge

We expect Pacific eulachon responses to chemical discharges to be similar as those described for 

salmonids. 

5.3.4 Indirect Effects

Larval and post larval eulachon prey upon phytoplankton, copepods, copepod eggs, mysids, 

barnacle larvae, worm larvae, and other eulachon larvae until they reach adult size (WDFW and 

ODFW 2001). The primary prey of adult eulachon are copepods and euphausiids, malacostracans 

and cumaceans (Smith and Saalfeld 1955, Barraclough 1964, Drake and Wilson 1991, 

Sturdevant et al. 1999, Hay and McCarter 2000). The prey of eulachon are likely to be entrained 

in CWIS.
45

5.3.5 Flow Alteration

Eulachon eggs adhere to the river bottom in areas of gravel and course sand. Flow alteration and 

turbidity, as a result of CWIS, is likely to interfere with the settlement and adherence of eggs to 

the river bottom. In addition, flow alteration may interfere with the downstream transport of 

larvae to estuarine and marine habitat.

5.3.6 Return of Fish to Non-Source Waters

The Rule allows the Director to approve the return of fish to non-source waters. Eulachon return 

to their natal streams to spawn. Most adults die after spawning. The return of Pacific eulachon to 

non-source waters is likely to interrupt their spawning migration. It is likely to result in the loss 

of reproductive potential, either through lack of spawning or fertilization. Introgression, gene 

flow among isolated gene pools, may also occur. The removal and introduction of other species 

to eulachon habitat is likely to result in changes in predation, prey availability, and competition 

for eulachon. It is also likely to result in the introduction of novel diseases and aquatic invasive 

species to the DPS. 

5.4 Population and Species Level Effects

Impingement and entrainment has the potential to effect more than three million eulachon and 

various life stages. Also of concern are potential losses due to thermal and chemical discharges, 

flow alteration, and the release of impinged fish into non-source waters. These adverse 

environmental impacts have the potential to affect large numbers of fish. Spawning is strongly 

influenced by water temperatures, and increased temperatures as a result of CWIS may interfere 

with spawning in areas near CWIS discharges. Females lay eggs over sand, course gravel or 

detritial substrate and incubate for 30 to 40 days, after which larvae drift to estuaries and coastal 

marine waters. Flow alteration is likely to interfere with the attachment and incubation of eggs 

and the movement of larvae.

In summary, Pacific eulachon (Southern DPS) will be directly and indirectly affected by CWIS.

5.5 Critical Habitat

No CWIS overlap directly with Pacific eulachon (southern DPS) critical habitat, however 11 

facilities are located with 11 km of Pacific eulachon (southern DPS) critical habitat. Pacific 

eulachon (southern DPS) critical habitat consists of 16 specific areas in California, Oregon, and 

Washington. The designated areas are a combination of freshwater creeks and rivers and their 

associated estuaries, comprising approximately 539 km of habitat (76 FR 65323). The 

designation identifies three categories of physical or biological features essential to the 

conservation of the southern DPS:

(1) Freshwater spawning and incubation sites with water flow, quality and temperature 

conditions and substrate supporting spawning and incubation, and with migratory access 

for adults and juveniles. These features are essential to conservation because without 

them the species cannot successfully spawn and produce offspring.
46

(2) Freshwater and estuarine migration corridors associated with spawning and 

incubation sites that are free of obstruction and with water flow, quality and temperature 

conditions supporting larval and adult mobility, and with abundant prey items supporting 

larval feeding after the yolk sac is depleted. These features are essential to conservation 

because they allow adult fish to swim upstream to reach spawning areas and they allow 

larval fish to proceed downstream and reach the ocean.

(3) Nearshore and offshore marine foraging habitat with water quality and available prey, 

supporting juveniles and adult survival. Eulachon prey on a wide variety of crustacean 

species. These features are essential to conservation because they allow juvenile fish to 

survive, grow, and reach maturity, and they allow adult fish to survive and return to 

freshwater systems to spawn.

6 Sturgeon

As described in the BE, EPA was unable to locate data on all facilities, their CWIS, and the 

likely effects of those structures on ESA-listed species or designated critical habitat. It is difficult 

for us to predict such parameters because the Rule does not establish impingement and 

entrainment standards required of all facilities. For example, we have determined that closedcycle recirculating systems at some facilities (e.g., Vogtle Electric Generating Plant in Georgia) 

are not likely to adversely affect ESA-listed sturgeon; however, owners or operators may choose 

to implement less protective alternatives, such as the Director-determined systems of technology. 

We cannot predict which of the alternatives an owner or operator may select or how that 

selection is likely to affect impingement or entrainment. Without such data, we cannot accurately 

quantify the effect of the action on sturgeon or their designated critical habitat. Instead, we 

estimate the likely effects of the action, as supported by the best available data, found in the BE, 

biological opinions, and scientific literature.

6.1 Stressors

CWIS are likely to cause impingement or entrainment, thermal discharges, chemical discharges,

and the indirect effect of prey and habitat reduction

6.2 Exposure

To best estimate the possible take, we gathered information on all of the 7(a)(2) consultations 

that have considered take of sturgeon or their critical habitat. NMFS (2013c) anticipates three 

CWIS will kill 562 shortnose sturgeon and 414 Atlantic sturgeon (92 percent New York Bay, 6 

percent Gulf of Mexico, 2 percent Chesapeake Bay) in the next 23 years. Data from 1972 to 

1998 for the other four CWIS on Hudson River power plants killed 212 shortnose sturgeon over 

those 27 years (NMFS 2000b). NMFS anticipates no mortality of shortnose or Atlantic sturgeon 

from CWIS associated with the Yadkin-Pee Dee project (NMFS 2013a). NMFS (2000a)

estimated no mortality of shortnose or Atlantic sturgeon from CWIS in the Cape Fear River, 

North Carolina. No take of Atlantic or shortnose sturgeon was projected from the four CWIS at 

the Vogtle Electric Generating Plant. There were no projects considering Gulf or green sturgeon 
47

or their critical habitat and only two of the above projects considered Atlantic sturgeon, which

were not listed until 2012. Other CWIS in the Delaware River (NRC 1979) have also been 

shown to impinge and entrain shortnose sturgeon (and possibly Atlantic sturgeon, though they 

were not listed at the time monitoring took place), however without long-term monitoring and an 

estimate of the annual shortnose sturgeon impingement and entrainment, we cannot use these 

individual points in this analysis.

Based on the above information from 13 CWIS, the average anticipated annual mortality of 

shortnose sturgeon is approximately 2.49 per facility that overlaps with shortnose sturgeon range. 

Shortnose sturgeon range from Maine to Florida, but only one shortnose sturgeon has been 

captured in Virginia recently, so CWIS in Virginia will not be considered. And based on 

information from eight CWIS (the assessments on the other five structures were before Atlantic 

sturgeon were listed), the average anticipated annual mortality of Atlantic sturgeon is 

approximately 2.26 per facility that overlaps with Atlantic sturgeon range. 

The data above are annual take estimates from 13 CWIS of a total of at least 557 CWIS that 

overlap with shortnose, Atlantic, Gulf, and green sturgeon nursery habitat. While this is the best 

available information for this exposure analysis, this represents meaningful data from just 2.25 

percent of the CWIS that may affect listed sturgeon species and their critical habitat, highlighting 

the need for increased oversight associated with 316(b) permits. Furthermore, there are 

apparently no consultations for the effects of CWIS on Gulf or green sturgeon, despite 

indications that green sturgeon are very vulnerable to impingement and entrainment of all U.S. 

sturgeon species (Poletto et al. 2014). Additionally, the seven CWIS with documented take are 

on the Hudson River. On the one hand, these facilities proactively applied for a Conservation 

Plan and take permit, in the process, minimizing and mitigating their effects to listed species to 

the maximum extent practicable as required under ESA section 10(a)(2)(B)(ii), likely reducing 

the amount of impingement and entrainment more so than the other approximately 544 CWIS

affecting sturgeon. On the other hand, the impingement and entrainment documented in these 

consultations comes from the Hudson River, which has the largest populations of both shortnose 

and Atlantic sturgeon along the coast, increasing the probability of sturgeon becoming impinged 

or entrained. NMFS believes that because these impingement and entrainment estimates 

represent the maximum amount of mitigation in the largest population of both shortnose and 

Atlantic sturgeon that it is reasonable to use those numbers to estimate the probable level of take 

for facilities that are not meeting the strict criteria established under ESA section 10(a)(2)(B)(ii) 

but are also operating in rivers with smaller Atlantic and shortnose populations.

Because there is no impingement or entrainment data for Gulf sturgeon or green sturgeon, we are 

forced to use the only information available. Shortnose sturgeon are impinged and entrained at 

approximately 2.49 fish per facility and Atlantic sturgeon are impinged and entrained at 

approximately 2.26 fish per facility. To estimate green sturgeon impingement and entrainment 

rates, it is appropriate to use at least 2.49 fish per facility because they are entrained at a higher 
48

rate than other Acipenserids (Poletto et al. 2014). But to estimate Gulf sturgeon, a sub-species of 

Atlantic sturgeon, it is appropriate to use 2.26 fish per facility (Table 9).

Because EPA did not provide estimates of Atlantic sturgeon take by DPS, we will calculate the 

likely proportion of the total take that will affect each DPS. Because this is a national 

programmatic and sturgeon from a particular DPS are generally concentrated more around their 

natal rivers, and furthermore, most CWIS are located upstream in freshwater portions of rivers, 

it’s likely that the DPSs most exposed to impingement and entrainment are the largest DPSs. 

Because there are no population estimates, we must estimate the likely proportions. Furthermore, 

even if we knew exact ratios of each DPS along the coast, due to changes in movement patterns 

and just by chance, there will be variability around those proportions, making it necessary to 

identify maximum ranges of each DPS that could be killed to ensure the identified level of take 

is not exceeded. 

The BE estimated the number of CWIS that overlap with some species’ ranges but did not for 

other species. For instance, the BE estimates the number of CWIS in shortnose sturgeon and 

Gulf sturgeon habitat, but not for Atlantic sturgeon or green sturgeon. Because of this, NMFS 

had to map the location of all CWIS and overlay species range data where it was available. In 

our assessment, we determined 481, 484, 41, and 31 facilities overlapped with shortnose,

Atlantic, Gulf, and green sturgeon habitat (Table 9). While none of these numbers are the same 

as were provided in the BE, NMFS is confident these facilities overlap with listed sturgeon 

habitat.

Table 9. Estimated annual impingement and entrainment mortality of sturgeon by facility and for 

all facilities affecting each species and/or DPS.

Species Overlapping facilities Annual mortality/facility Total annual mortality 

Shortnose 481 2.49 1,198

Atlantic* 484 2.26 1,094

 Gulf of Maine DPS 329

 NYB DPS 493

 Chesapeake Bay DPS 383

 Carolina DPS 274

 South Atlantic DPS 438

Gulf 41 2.26 93

Green, Southern DPS 31 2.49 78

* Total numbers of Atlantic sturgeon captured or killed will not exceed the identified totals, however the DPS make-up of that total 

take may fluctuate seasonally and annually.
49

6.3 Response

CWIS are likely to cause impingement or entrainment, thermal discharges, chemical discharges,

and the indirect effect of prey and habitat reduction.

6.3.1 Impingement and Entrainment

Impingement occurs when organisms are trapped against cooling water intake screens, racks, or 

removal equipment by the force of moving water. Generally, fish are impinged when their 

swimming speed is overtaken by the intake velocity. Such speeds are determined by the 

individual’s size and age, body condition, level of fatigue, ability to remain a head-first 

orientation into current, and surrounding environmental conditions, such as water temperature 

(Mayfield and Cech 2004, Cech Jr. and Doroshov 2005, Kynard et al. 2005, Allen et al. 2006a, 

Deslauriers and Kieffer 2012, Poletto et al. 2014). Kynard et al. (2005) found that yearling or 

older shortnose sturgeon (≥ 28 cm) are likely to avoid impingement, when intake velocities are 1 

ft/sec or less in laboratory conditions (e.g., fish are healthy and free of heat stress, pollution, 

and/or disease). This study did not account for fatigue, which results in impingement of juvenile 

shortnose sturgeon at swimming speeds of 0.7 ft/sec or 22.3 cm/sec (Deslauriers and Kieffer 

2012).

Entrainment is when fish, larvae, or eggs are sucked into the CWIS when eggs are small enough 

to pass by the screen or there is no screen in place. Sturgeon eggs are demersal; they sink and 

adhere to the bottom of the river. They are unlikely to be entrained by CWIS. Upon hatching, the 

larvae in yolk-sac and post-yolk-sac stages remain on the bottom of the river. Sturgeon larvae are 

intolerant of salinity (Dovel and Berggren 1983, Kahnle et al. 1998, Bain et al. 2000, Allen et al. 

2009), . They occur only in freshwater, in the deepest waters (Taubert and Dadswell 1980, Bath 

et al. 1981, Kieffer and Kynard 1993, Allen et al. 2009)(Sweka et al. 2007, Randall and Sulak 

2012). Larvae grow rapidly and by the time they begin down-stream migrations, they are too 

large to be entrained by CWIS (Sulak and Clugston 1999, Kynard and Parker 2004, Allen et al. 

2006b). While there have been studies of impingement at 13 CWIS, there have only been 

entrainment studies at two Indian Point CWIS on the Hudson River out of 577 CWIS in sturgeon 

occupied waters. In addition to only monitoring 0.35 percent of the CWIS in shortnose, Atlantic, 

Gulf, and green sturgeon habitat, the lone study was conducted between 1981 and 1987, starting 

over 30 years ago. In that study, no sturgeon larvae were collected during intense entrainment 

monitoring (i.e., nearly 24 hours per day, four to seven days per week, during the spawning 

season, in the spring; Woodland and Secor 2007). This was during a period of likely recovery for 

shortnose sturgeon, as the population estimates increased during this time through 2000. 

However, this was during a series of recruitment failures for Atlantic sturgeon and therefore it is 

likely there were fewer Atlantic sturgeon eggs available to be collected. Therefore, we conclude 

that the entrainment of sturgeon eggs or larvae is unlikely. 

Currently facilities are not required to install trash bars, travelling screens, or fish removal 

systems; however, if installed, the following expectations apply. We expect large fish to either 

swim away or become impinged on trash bars (if present); we expect small fish to pass through 
50

trash bars (if present) and possibly become impinged on the screens, if present (NMFS 2000b). 

The velocity in front of travelling screens, including the Ristroph screens installed at the Indian 

Point facility, averages 1.0 ft/sec or less (Fletcher 1990). Kynard et al. (2005) suggests that 

shortnose sturgeon older than one year (≥ 28 cm) should be able to avoid impingement by the 

travelling screen; however, all fish impinged at Indian Point ranged in size from 32 to 71 cm

(i.e., large enough to theoretically avoid impingement). Poletto et al. (2014), Allen et al. (2006), 

and Amaral et al. (2002) also identify top speeds to avoid being impinged of at least 20 cm/sec 

and up to 55 cm/sec. It is possible that the young sturgeon naturally drift with the current to 

move downstream, so when confronted with intake velocities, they don’t attempt to swim off 

until it’s too late (Dadswell et al. 1984, Gilbert 1989, NMFS 1998a, Kynard and Horgan 2002) . 

In addition, larger fish may become fatigued, stressed, or disoriented while trying to avoid the 

screens or trash bars. Even if through-rack velocity is not high enough to preclude fish from 

exiting the area, they may have difficulty finding a way out, especially if there is debris in front 

of the trash bars. Fletcher (1990) found that striped bass spent an average of 9.73 hours between 

the trash racks and screens prior to removal. Therefore, it is likely that entrapped fish first 

become stressed, tired or disoriented, and then become impinged on the screens or captured in 

the traveling buckets.

Impingement may kill organisms immediately or result in latent mortality as a result of 

exhaustion, suffocation, injury, or exposure to air when screens are rotated for cleaning. At 

Indian Point, previous data indicated mortality rates of 78 percent for shortnose sturgeon and 59 

percent for Atlantic sturgeon. However, the installation of modified Ristroph screens may reduce 

fish impingement mortality to rates of 9 to 62 percent (Fletcher 1990). NMFS generally assumes 

100 percent mortality for the following reasons: 

 The above studies do not use sturgeon;

 Species considered in the monitoring and testing studies are not morphologically similar 

to sturgeon and are considerably smaller than sturgeon;

 No studies compare the impingement mortality or likelihood of injury of sturgeon versus 

other species;

 Post-impingement survival has never been studied; and

 Sturgeon impinged on the trash bars are likely to die because there is no opportunity for 

fish removal.

6.3.2 Thermal Discharges

Thermal discharges have the potential to cause lethal or sublethal effects, positive effects, to 

create barriers, and indirect effects by affecting food resources. To evaluate the effects of thermal 

discharges as a result of CWIS, a thermal plume study was conducted at the Indian Point facility.

The extent and shape of the thermal plume varies greatly, primarily in response to tidal currents 

(Swanson et al. 2011b). Generally, the warmest water remains close to the surface, and plume 
51

temperatures tend to decrease with depth; however, occasionally the thermal plume extends 

deeply rather than across the surface. The maximum observed temperature of thermal discharges 

is approximately 46°C (Hester and Doyle 2011). Waters deeper than 5 m are not likely to exceed 

32°C. Shortnose, Atlantic, Gulf, and green sturgeon occupy the mainstems of large rivers and 

avoid shallow off-channel habitat. We do not expect temperature-related mortality because 

sturgeon can avoid the surface waters, and occasional deep hot spots, that may exceed tolerable 

temperatures.

Niklitschek (2001), Mayfield and Cech (2004), Chapman and Carr (1995), and (Niklitschek and 

Secor 2005) (2005) have identified temperature ranges that allow for optimal growth of 

shortnose, Atlantic, Gulf, and green sturgeon. Shortnose sturgeon will utilize water as warm as 

26 to 30°C (Dadswell et al. 1984, Kynard 1997, Niklitschek 2001) . Atlantic sturgeon will use 

waters up to approximately 32°C (annual permit reports to NMFS Office of Protected 

Resources). While there is limited information on lethal limits of Gulf sturgeon temperature 

tolerance, as a sub-species of Atlantic sturgeon, adapted to the warmer waters of the Gulf of 

Mexico, it is likely they can tolerate temperatures very similar to Atlantic sturgeon or maybe 

slightly higher. Green sturgeon though are more sensitive to high temperatures, sometimes 

encountering lethal temperatures as low as 25°C (Mayfield and Cech 2004) (Cech Jr. et al. 2000, 

Allen et al. 2006a). The 48 hour 50 percent mortality rate for shortnose sturgeon was between 28 

and 30°C, with instantaneous lethal thermal maxima for young-of-the-year shortnose sturgeon 

between 34.8 and 36.1°C (Ziegeweid et al. 2008). At 5 to 6°C prior to the lethal endpoint, fish 

frantically swim around the tank, presumably looking for an escape route (Ziegeweid et al. 

2008). 

Dissolved oxygen likely plays a key role in temperature tolerance (Niklitschek 2001). Water 

temperature and dissolved oxygen levels are related, with warmer water generally holding less 

dissolved oxygen. In summer, the coupling of low dissolved oxygen at depth and water 

temperatures greater than 20°C above the thermocline limits non-stressful habitat due to a 

temperature-oxygen habitat squeeze (Coutant 1987). Sturgeon are more sensitive to low level 

dissolved oxygen conditions than other fishes and become stressed in hypoxic conditions 

(generally under 5 mg/L), which may limit growth, metabolism, activity, and swimming (Cech et 

al. 1984, Secor and Gunderson 1998, Secor and Niklitschek 2001, Cech and Crocker 2002, Secor 

and Niklitschek 2002, Campbell and Goodman 2004) . 

Thermal plumes during portions of the year can create areas that are uninhabitable for shortnose, 

Atlantic, Gulf, and green sturgeon. However, because sturgeon inhabit large mainstem rivers 

along the Atlantic, Gulf, and Pacific Coasts, thermal plumes are expected to displace sturgeon 

during portions of the year and potentially provide areas of optimal bioenergetic environments 

when the rest of the river is less than optimal. Thermal plumes may have a short term adverse 

effect on shortnose, Atlantic, Gulf, and green sturgeon, but should not result in long-term or sublethal impacts. Furthermore, in situations where the thermal plume is stressful, all sturgeon 

species will be able to move up or downstream or even laterally and avoid them. 
52

6.3.3 Chemical Discharges

Chemical discharges from CWIS may include radionuclides, including: tritium, strontium, 

nickel, and cesium. Chlorine, lithium hydroxide, boron, and total suspended solids may also be 

discharged from CWIS. At CWIS facilities, total residual chlorine is often limited to a daily 

average of 0.2mg/L, as measured at the point of discharge, prior to dilution in the water body. 

Therefore, sturgeon would be exposed to chlorine discharge. However, chlorine quickly dilutes 

in water, particularly in the large rivers sturgeon inhabit and more importantly, chlorine is highly 

reactive and evaporates from water very quickly, so chlorine levels in the river are not expected 

to be at toxic levels or to adversely affect shortnose, Atlantic, Gulf, or green sturgeon. 

6.3.4 Indirect Effects

Sturgeon food resources, benthic invertebrates, have limited mobility. Benthic invertebrates are 

small and not likely to be impinged. However, benthic invertebrates could be entrained at CWIS, 

potentially reducing the number of invertebrates in the area. Similarly, benthic invertebrates may 

be affected by thermal or chemical plumes, but the effect is unlikely to reduce the abundance of 

benthic invertebrates and rather would be expected to alter the community dynamics, giving a 

competitive advantage to benthic invertebrates that are more tolerant or chemicals or 

temperatures. Because shortnose, Atlantic, Gulf, and green sturgeon are generalist feeders (Haley 

1998, Miller 2004, Collins et al. 2008, Dumbauld et al. 2008), a change in the composition of the 

benthic invertebrate community will most likely have no effect on individual sturgeon. The loss 

of some benthic invertebrates due to entrainment may limit food resources locally, and therefore 

slightly reduce the total carrying capacity of sturgeon in the river.

Despite the fact that EPA, in their BE, was unable to calculate the number of CWIS that 

overlapped with each listed species, NMFS provided estimates of the likely lethal take of 

shortnose, Atlantic, Gulf, and green sturgeon. Based on the best available scientific information, 

NMFS analysis to date, with limited site specific information anticipates 1,198 shortnose 

sturgeon, 329 Gulf of Maine DPS Atlantic sturgeon, 493 New York Bight DPS Atlantic 

sturgeon, 383 Chesapeake Bay DPS Atlantic sturgeon, 274 Carolina DPS Atlantic sturgeon, 438 

South Atlantic DPS Atlantic sturgeon, 93 Gulf sturgeon, and 78 southern DPS green sturgeon 

could be killed every year by impingement at CWIS. However, this information is based on 

monitoring impingement at only 13 of 577 CWIS (2.25 percent) in shortnose, Atlantic, Gulf, or 

green sturgeon habitat since 1972. And as poor as impingement monitoring has been, 

entrainment has been monitored at only 2 of 577 CWIS (0.35 percent) in that time.

6.4 Shortnose Sturgeon

Many shortnose sturgeon population estimates have been increasing over the past 30 years;

however there are no known recolonized populations in this time. This could be an indication of 

an upward population trend, or of increased research and more refined sampling procedures. 

While the Hudson River has a shortnose sturgeon population possibly four times larger than the 

next largest shortnose sturgeon spawning population (Delaware or Kennebec Rivers), most rivers 

along the East Coast have total populations with fewer than 1,000 adults, sub-adults, and 
53

juveniles. Those populations are at greater risk of being extirpated by a combination of 

anthropogenic threats and natural, stochastic events.

Currently, shortnose sturgeon appear to have been extirpated from Florida, the southern half of 

Georgia (below the Altamaha River), all of north Carolina above the Cape Fear River, all of 

Virginia, and likely all of Maryland (Rogers and Weber 1995, Kynard 1997, Kahnle et al. 1998, 

NMFS 1998b, Collins et al. 2000, Skjeveland et al. 2000, Welsh et al. 2002, Oakley 2003).

These large, in some cases, statewide extirpations of shortnose sturgeon represent critical 

fragmentation within their range. Furthermore, shortnose sturgeon are typically not found in 

waters with a salinity of 31 ppt or higher (Gilbert 1989) and therefore are unlikely to stray long 

distances along the coast to colonize another river if that population is extirpated.

The Rule will allow for the operation of 481 CWIS within the range of shortnose sturgeon. Our 

analysis based on available information at this time, with limited site specific data, suggests that 

the operation of CWIS could result in the lethal impingement of 1,198 shortnose sturgeon every 

year. While incalculable, these 481 CWIS could reduce the available food resources within the 

immediate vicinity of the intakes via entrainment, limiting the potential carrying capacity of each 

river slightly. Rivers with multiple CWIS would experience greater limitations in recovery 

potential. The largest river systems along the coast also support the largest shortnose sturgeon 

populations. This is likely because there is more habitat available and a higher carrying capacity. 

Therefore, the populations most at risk as a result of this rule are the small populations found in 

smaller river systems that have shown only stable or in some cases, downward trends, despite 

increased research.

The life stage of sturgeon impinged is another important consideration as to whether extirpation 

is likely or the anticipated lethal take associated with CWIS can be withstood. While most of the 

impinged shortnose sturgeon may be juveniles, the minimal monitoring data that exists suggests 

at least some of the impingement will affect sub-adult and adult shortnose sturgeon. The loss of 

1,198 shortnose sturgeon of all life stages each year would have significant and sustained 

adverse impacts to each of the shortnose sturgeon spawning populations along the Atlantic 

Coast. 

In summary, shortnose sturgeon will be directly and indirectly affected by CWIS.

6.5 Atlantic Sturgeon

There are only two published Atlantic sturgeon spawning population estimates and both of those 

are at least a decade old. Many managers believe that since the commercial fishery was closed in 

1998 (ASMFC 1998), populations in many rivers have been growing. However, while 

researchers are able to capture and tag fish, analyses of effective population sizes from genetic 

fin clips from the juveniles of these “recovering” populations suggest very small effective 

population sizes along the coast (O’Leary et al. 2014). As far as spawning population sizes, it is 

likely that few rivers have over 1,000 adults that return to spawn every one to five years, with 

annual spawning runs likely in the range of 300 to 400 individuals (ASSRT 2007, Kahnle et al. 
54

2007, Peterson et al. 2008). Most Atlantic sturgeon spawning populations are thought to be very 

small (ASSRT 2007)

Historically, spawning occurred in approximately 36 rivers along the Atlantic Coast, but 

currently is only known to occur in 21 (ASSRT 2007). Currently, Atlantic sturgeon appear to 

have been extirpated from Florida, all of north Carolina between the Cape Fear River and 

Roanoke River and those two rivers support very small populations, the Rappahanock River in 

Virginia, likely all of Maryland except the Nanticoke River, the entire New York Bight DPS 

except for the Delaware and Hudson Rivers, and possibly most rivers in Maine except for the 

Kennebec and Penobscot (ASSRT 2007). These large, in some cases, statewide extirpations of 

Atlantic sturgeon represent critical fragmentation within their range. However, a primary 

difference between shortnose and Atlantic sturgeon is that Atlantic sturgeon are much more 

migratory. While Atlantic sturgeon will travel long distances and spend time in various locations, 

both north and south of their natal rivers, they are extremely accurate in returning to their natal 

rivers to spawn. At the riverine level, Atlantic sturgeon return at an approximately 85 percent 

rate to their natal river. This number, while high, is well over 90 percent in rivers from the 

Roanoke River/Albemarle Sound and north, but there is substantial straying in the rivers of 

southern South Carolina and Georgia (T. King, unpublished data, 2014). However, some 

individuals from every generation appear to stray to nearby rivers, but at very low rates (less than 

one individual from its natal river per generation) (Grunwald et al. 2008).

The Rule, will allow for the operation of 484 CWIS within the range of Atlantic sturgeon. The 

operation of these CWIS could result in the lethal impingement of 329 Gulf of Maine DPS, 493 

New York Bight DPS, 383 Chesapeake Bay DPS, 274 Carolina DPS, and 438 South Atlantic 

DPS Atlantic sturgeon every year. While incalculable, these 484 CWIS could reduce the 

available food resources within the immediate vicinity of the intakes via entrainment, limiting 

the potential carrying capacity of each river slightly. Atlantic sturgeon only use freshwater 

portions of rivers for juvenile rearing, so the loss of this habitat would equate to a reduction in 

juvenile carrying capacity. Rivers with multiple CWIS would experience greater limitations in 

recovery potential. Therefore, the populations most at risk as a result of this rule are the small 

populations north of Albemarle Sound, where straying is rare and the loss of a spawning 

population would take longer to recovery, assuming it ever would (currently there are still 15 

spawning populations that have been extirpated and not recovered despite many states closing 

their commercial fisheries in the 1970s and it closing throughout the U.S. in 1998). The species 

was listed in 2012 with little information on its status because of the numerous threats facing its 

populations and DPSs. 

The life stage of sturgeon impinged is another important consideration as to whether extirpation 

is likely or the anticipated lethal take associated with CWIS can be withstood. Most of the 

impinged Atlantic sturgeon will be juveniles and sub-adults based on the minimal monitoring 

data that exists, which suggests impingement will generally affect individuals less than 700 mm 

in length. The loss of 329 Gulf of Maine DPS, 493 New York Bight DPS, 383 Chesapeake Bay 
55

DPS, 274 Carolina DPS, and 438 South Atlantic DPS Atlantic sturgeon (Table 9) every year 

would have direct effects to each of the Atlantic sturgeon spawning populations along the 

Atlantic Coast. Some DPSs, such as Carolina, Chesapeake Bay, and Gulf of Maine DPSs would 

be expected to experience extirpations more quickly than the New York Bight and South Atlantic 

DPS because of the size of the extant populations remaining in those DPSs and the straying rate 

between extant systems. 

In summary, all of the DPSs of Atlantic sturgeon will be directly and indirectly affected by 

CWIS.

6.6 Gulf Sturgeon

Gulf sturgeon continue to spawn in seven basins along the U.S. Gulf Coast. Gulf sturgeon 

populations in the Suwannee River have increased in the past 40 years (Pine et al. 2001), but the 

populations in the other spawning rivers have remained stable or decreased slightly in response 

to large-scale adverse events, such as hurricanes and chemical spills (USFWS and NMFS 2009). 

This, despite increased research and more refined sampling procedures. Now the Suwannee 

River has a Gulf sturgeon population considerably larger than the other Gulf sturgeon spawning 

populations. The other Gulf Coast rivers have total populations of only several hundred adults 

(Morrow Jr. et al. 1998, Zehfuss et al. 1999). Those populations are at greater risk of being 

extirpated by a combination of anthropogenic threats and natural, stochastic events.

The Rule, as proposed, will allow for the continued operation of 41 CWIS within the range of 

Gulf sturgeon. The operation of these CWIS is likely to result in the lethal impingement of 93 

Gulf sturgeon every year. While in other systems, these 41 CWIS will reduce the available food 

resources and therefore limit the potential carrying capacity of each river slightly, Gulf sturgeon 

do not feed when they enter freshwater portions of the river and therefore should not be affected 

by any changes to benthic invertebrate resources (Sulak et al. 2012) . The populations most at 

risk as a result of this rule are the six small populations found to the west of the Suwannee River 

that have shown only stable or in some cases, downward trends, despite increased research and 

23 years of protection under the ESA.

The life stage of sturgeon impinged is another important consideration as to whether extirpation 

is likely or the anticipated lethal take associated with CWIS can be withstood. While most of the 

impinged Gulf sturgeon may be juveniles, the minimal monitoring data that exists suggests at 

least some of the impingement will affect sub-adult Gulf sturgeon. The loss of 93 juvenile and 

sub-adult Gulf sturgeon each year from the Suwannee River would have different effects than the 

loss of 93 Gulf sturgeon from the Pearl, Pascagoula, Escambia, Yellow, Choctawhatchee, or 

Apalachicola Rivers. The continued annual loss of Gulf sturgeon populations would have 

adverse impacts to each of those spawning populations along the Gulf Coast. 

In summary, Gulf sturgeon will be directly and indirectly affected by CWIS.
56

6.7 Green Sturgeon

Southern DPS green sturgeon reproduce in the Sacramento and Feather River, a tributary to the 

Sacramento River. The population has been steady since it was listed as threatened in 2007. The 

primary threats to the southern DPS of green sturgeon are its isolation at the southern extent of 

their range and the threat of extinction from a number of causes affecting the Sacramento River 

and Bay Delta system. 

The Rule will allow for the operation of 31 CWIS within the range of southern DPS green 

sturgeon. The operation of these CWIS could result in the lethal impingement of 78 green 

sturgeon every year. While incalculable, these 31 CWIS could reduce the available food 

resources within the immediate vicinity of the intakes via entrainment, resulting in a slight 

reduction in the potential carrying capacity of the river. There is only one spawning population in 

the Sacramento River system and any impingement mortalities will affect that population.

The life stage of sturgeon impinged is another important consideration as to whether extirpation 

is likely or the anticipated lethal take associated with CWIS can be withstood. While most of the 

impinged green sturgeon may be juveniles, the minimal monitoring data that exists suggests at 

least some of the impingement will affect sub-adult green sturgeon. The loss of shortnose 

sturgeon of any life stages each year would have adverse impacts to the southern DPS green 

sturgeon spawning population. Furthermore, green sturgeon appear to be more susceptible to 

impingement (Poletto et al. 2014) than other sturgeon, but there has been no monitoring of any of 

the 31 CWIS in green sturgeon habitat, so EPA and NMFS does not know whether the Rule will 

have an even greater effect than is being estimated using the best available information in this 

Opinion.

In summary, green sturgeon will be directly and indirectly affected by CWIS.

6.8 Critical Habitat

Critical habitat has been designated for Gulf sturgeon and green sturgeon (Southern DPS), but is 

not designated for Atlantic or shortnose sturgeon. In the BE, EPA estimates that 12 facilities are 

likely to overlap with Gulf sturgeon designated critical habitat and we concur with that finding. 

We have determined that the effects of 31 CWIS are likely to overlap with green sturgeon critical 

habitat. Designated gulf sturgeon critical habitat includes 14 geographic areas among the Gulf of 

Mexico rivers and tributaries. These areas include river, estuarine and marine habitat (68 FR 

13370). The primary constituent elements essential for the conservation of Gulf sturgeon are 

those habitat components that support feeding, resting, and sheltering, reproduction, migration, 

and physical features necessary for maintaining the natural processes that support these habitat 

components. The primary constituent elements include: 

 abundant prey items within riverine habitats for larval and juvenile life stages, and within 

estuarine and marine habitats and substrates for juvenile, subadult, and adult life stages;

 riverine spawning sites with substrates suitable for egg deposition and development, 

such as limestone outcrops and cut limestone banks, bedrock, large gravel or cobble beds, 

marl, soapstone or hard clay; 
57

 riverine aggregation areas, also referred to as resting, holding, and staging areas, used by 

adult, subadult, and/or juveniles, generally, but not always, located in holes below normal 

riverbed depths, believed necessary for minimizing energy expenditures during fresh 

water residency and possibly for osmoregulatory functions; 

 a flow regime (i.e., the magnitude, frequency, duration, seasonality, and rate-of-change of 

fresh water discharge over time) necessary for normal behavior, growth, and survival of 

all life stages in the riverine environment, including migration, breeding site selection, 

courtship, egg fertilization, resting, and staging; 

 and necessary for maintaining spawning sites in suitable condition for egg attachment, 

eggs sheltering, resting, and larvae staging; 

 water quality, including temperature, salinity, pH, hardness, turbidity, oxygen content, 

and other chemical characteristics, necessary for normal behavior, growth, and viability 

of all life stages; and

 sediment quality, including texture and other chemical characteristics, necessary for 

normal behavior, growth, and viability of all life stages; and safe and unobstructed 

migratory pathways necessary for passage within and between riverine, estuarine, and 

marine habitats (e.g. a river unobstructed by any permanent structure, or a dammed river 

that still allows for passage). 

Green sturgeon (Southern DPS) critical habitat includes the following areas: coastal U.S. marine 

waters within 60 fathoms depth from Monterey Bay, California (including Monterey Bay), north 

to Cape Flattery, Washington, including the Strait of Juan de Fuca, Washington, to its U.S. 

boundary; the Sacramento River, lower Feather River, and lower Yuba River in California; the 

Sacramento-San Joaquin Delta and Suisun, San Pablo, and San Francisco bays in California; the 

lower Columbia River estuary; and certain coastal bays and estuaries in California (Humboldt 

Bay), Oregon (Coos Bay, Winchester Bay, Yaquina Bay, and Nehalem Bay), and Washington 

(Willapa Bay and Grays Harbor). It also includes freshwater river, estuarine, and marine habitats 

in California (74 FR 52300). In freshwater riverine and estuarine systems, the physical and 

biological features essential to the species include: 

 food resources (abundant prey items for larval, juvenile, subadult, and adult life stages);

 substrate type or size (i.e., structural features of substrates) suitable for egg deposition 

and development, larval development, and spawning adults;

 water flow necessary for normal behavior, growth, and survival of all life stages;

 water quality including temperature, salinity, oxygen content, and other chemical 

characteristics, necessary for normal behavior, growth, and viability of all life stages; and

 a migratory pathway necessary for the safe and timely passage of fish within riverine 

habitats and between riverine and estuarine habitats.

As discussed above, CWIS are likely to entrain some of the many benthic invertebrates around 

the intake pipe and thermal discharge may cause a change in the invertebrate community. These 

alterations caused by the Rule will affect designated critical habitat of both Gulf and green 
58

sturgeon by changing food resources in the immediate vicinity of the CWIS, affecting water 

quality in the immediate vicinity of the CWIS, and possibly affecting migratory pathways in the 

immediate vicinity of the CWIS. 

Gulf sturgeon are wide ranging, reproducing in seven rivers along the Gulf Coast, with only 12 

CWIS affecting their critical habitat, which covers all of those rivers as well as some shoreline 

areas. However, Gulf sturgeon generally do not feed while in freshwater portions of their range 

(Mason Jr. and Clugston 1993, Randall and Sulak 2012) , so a reduction in food resources in 

freshwater will not affect Gulf sturgeon critical habitat. Gulf sturgeon rely on cool water refuges 

while in freshwater portions of rivers and the thermal discharges could force them to use other 

areas of the river. However, because Gulf sturgeon are highly mobile, the limitations of water 

quality in the immediate vicinity of 12 CWIS within their habitat range will have a negligible 

impact on their designated critical habitat. 

The most important aspect of Gulf sturgeon’s time spent in fresh water is their upstream 

migration to spawning areas, followed by a downstream migration back to the Gulf of Mexico. 

Thermal plumes have the potential to impede upstream migration by making water too warm to 

migrate through, thus blocking their migratory pathway. However, there is no evidence of this 

occurring as all researchers in the seven Gulf sturgeon spawning rivers report Gulf sturgeon 

continue to spawn at upstream sites (Foster and Clugston 1997, Fox et al. 2000, Heise et al. 

2004, Rogillio et al. 2007). Therefore the rivers must be large enough that while the thermal 

plume makes portions of the river uninhabitable, Gulf sturgeon are able to migrate by using the 

rest of the river. Therefore, the presence of CWIS is not likely to destroy or adversely modify 

Gulf sturgeon critical habitat.

Southern DPS green sturgeon only reproduce in one river system, though the Sacramento River 

is large and they also reproduce in a tributary to the Sacramento, the Feather River. There are 31 

CWIS in southern DPS green sturgeon critical habitat. The CWIS are likely to remove benthic 

invertebrates from the Sacramento River system via entrainment, thus slightly reducing the 

amount of food available to juvenile green sturgeon. The presence of 31 CWIS in critical habitat 

means there will be a diminished food supply throughout their downstream migratory corridor. 

However, green sturgeon are generalists (Miller 2004, Dumbauld et al. 2008) and will be able to 

feed in other areas. The limitation is the removal of food resources from 31 locations within their 

designated critical habitat may limit the carrying capacity of the southern DPS green sturgeon 

populations. Thermal plumes may change the benthic macroinvertebrate community, but being 

generalists this will have no impact to green sturgeon. Furthermore, because the Sacramento 

River is maintained in an artificially cool state through the summer to provide rearing habitat for 

Sacramento River winter-run Chinook salmon, which no longer exists in the river, these areas of 

warmer water should actually increase juvenile green sturgeon bioenergetic responses and 

growth. Also, because of the size of the Sacramento River, for the same reasons migratory 

habitat is not likely affected for Gulf sturgeon, it is also unaffected for green sturgeon.
59

7 Sawfish

In the BE, EPA does not estimate the number of facilities likely to overlap with the range of 

ESA-listed sawfish species. Using ArcGIS to map EPA’s list of facilities likely to be regulated 

under the Rule, we identified seven facilities that overlap with smalltooth sawfish, U.S. DPS.

7.1 Exposure

In the BE, EPA determines that impingement, entrainment, thermal and chemical discharges, and 

flow alterations are likely to adversely affect sawfish; however, they do not provide in depth 

details on these effects. We found two examples of smalltooth sawfish in thermal plumes of 

CWIS. In January 2001, a sawfish was reported in the warm water outflow (approximately 28°C) 

of the Apollo Bay power plant. A smalltooth sawfish was later caught adjacent to the outfall in 

an area with elevated water temperatures (22.9 °C plume compared to 17.7 °C in surrounding 

areas). Based on their size and other characteristics, there were at least two sawfish within the 

thermal plume. 

There has been one example of a sawfish being impinged at a CWIS at the St. Lucie Nuclear 

Power Plant in Port St. Lucie, FL. This incident was the only impingement of sawfish at the 

facility since 1976 (30 years), resulting in a probability of 0.03 (standard deviation = 0.18) 

sawfish impingements annually at each CWIS. Therefore, we were able to calculate the probable 

annual impingement using the empirical impingement rate of 0.033 multiplied by the number of 

CWIS (Table 10). Because juvenile sawfish inhabit mangrove estuaries, and CWIS are not likely 

to be located in mangrove estuaries, we expect sub-adult and adult sawfish of either sex to be 

impinged. 

Table 10. Total smalltooth sawfish impingement at all facilities in smalltooth sawfish habitat.

Species Overlapping facilities Annual mortality range 

Smalltooth sawfish 7

0.23 (approximately 1 every 4 

years)

7.2 Response

In the BE, EPA determines that impingement, entrainment, thermal and chemical discharges, and 

flow alterations are likely to adversely affect sawfish.

7.2.1 Impingement

Impingement of sawfish is likely to occur as a result of entanglement of the rostrum or “saw” in 

screens or nets. The lone example of a smalltooth sawfish being impinged came from the St. 

Lucie Nuclear Power Plant in Port St. Lucie, FL (FPL 2005):

“On May 16, 2005, during the course of normal sea turtle netting activities at the St. 

Lucie Nuclear Power Plant intake canal, a smalltooth sawfish (Pristis pectinata) became 

entangled in the north capture net at approximately 5:20 PM. The biologist on duty

determined that the animal was too large to handle himself and called for assistance at 
60

approximately 5:30 PM. A crew of four biologists assembled at the intake canal at 6:00 

PM and discussed a plan to remove the sawfish from the net and release it back to the 

ocean safely. The 100-foot net was released from the west end anchor point and was 

pulled into the boat up to the location of the sawfish. The net was then released from the 

east end anchor point and the remaining net was pulled into the boat leaving the 

entangled sawfish in the water alongside the boat. The rostrum, or saw, was the only part 

of the animal that was entangled in the net, which left the rest of its body unencumbered.

The animal was pulled into the boat ramp area, where the remaining net was offloaded. 

The animal remained in the shallow water of the boat ramp until preparations were made 

for its removal. A stretcher was laid out on the boat ramp and a winch was attached to the 

remaining net in order to pull the sawfish onto the stretcher. At approximately 6:30 PM, 

the animal was pulled from the water up the boat ramp and onto the stretcher. It was then 

moved into the back of a trailer normally used for transporting large sea turtles. At this 

point the sawfish was disentangled from the net and measurements were taken. The 

sawfish measured 415 cm (13.62 feet) from tail to end of rostrum and the rostrum itself 

measured 86 cm (2.82 feet) from base to tip. The animal was then transported via an allterrain vehicle across the dune and to the ocean, a distance of about 100 meters. Two 

biologists walked behind the trailer holding up the tail end of the stretcher to ensure the 

animal would not slide out. The trailer was then filled with ocean water by backing it into 

the nearshore trough, and the animal was able to float out of the trailer and swim away 

freely at approximately 6:45 PM. The area where the sawfish was released was then 

monitored for another 25 minutes to make sure that it had acclimated and did not wash 

ashore (FPL 2005).”

As a result of the monitoring protocols and removal efforts at the St. Lucie facility, the sawfish 

survived impingement. At the time of the incident, St. Lucie had the following control measures 

in place: velocity cap; 5 inch mesh barrier nets; tangle nets deployed in daylight hours, seven 

days a week; hourly monitoring of barrier and tangle nets; quarterly inspection and repair of 

holes in nets; sea turtle response program; and exempted incidental take for sea turtles. These 

control measures were designed to minimize the adverse effects to sea turtles, but because of 

these controls, the impinged sawfish was released alive. 

7.2.2 Thermal Discharges

The recovery plan for the smalltooth sawfish identifies warm water discharges from power 

stations to be a low-severity threat, leading to the compromised health of sawfish (NMFS 2009) .

Two smalltooth sawfish (U.S. DPS) have been identified in the thermal discharges of a CWIS 

(Simpfendorfer 2001). Sawfish may utilize these plumes as thermal refuges during colder 

months to enhance their survival, or they may become trapped by surrounding cold water from 

which they would normally migrate (Simpfendorfer and Wiley 2004). The impact of thermal 

discharges on the fitness of sawfish is unknown; however, there was an unconfirmed report of 
61

two sawfish being killed in the Hillsborough River during a cold-snap in January 2001 

(Simpfendorfer 2001). Simpfendorfer (2001) concluded that significant use of thermal 

discharges may disrupt the normal migratory patterns of smalltooth sawfish. 

7.2.3 Indirect Effects

Sawfish prey upon schooling fish and bottom-dwelling invertebrates. Their prey are likely to be 

impinged as adults (e.g., fish) or entrained as eggs or larvae (e.g., fish and invertebrates). 

Reduced prey availability is not considered to be a major threat to the survival or recovery of 

sawfish species. We do not expect the indirect effects of CWIS to reduce the fitness of any 

individuals. 

Smalltooth sawfish appear to be recovering at a rate of 2 to5 percent per year and there is also 

evidence that their range is expanding. While EPA was unable to estimate the number of CWIS

in smalltooth sawfish habitat, NMFS was able to determine there are seven facilities that overlap 

with their range. However, due to the low probability of impingement (0.033), NMFS anticipates 

one smalltooth sawfish will be impinged and killed once every four years at one of the seven 

CWIS in smalltooth sawfish habitat. There is the potential that with the range expansion will 

come increased interactions with CWIS. At this time, there is no solid evidence of which 

additional facilities, if any, would pose a threat to smalltooth sawfish and as such, no additional 

facilities are considered.

Thermal plumes may also affect sawfish but in an undetermined way. There is the possibility that 

they provide refuge during cold snaps, providing optimal and life-saving habitat, which is a 

beneficial effect. However, as is noted by Simpfendorfer (2001), the thermal plumes could also 

result in the disruption of natural migrations, with unknown, but likely negative effects (limited 

growth, exposure to poor water quality, exposure to fishing (commercial and recreational) 

bycatch, etc.). The lethal take of one smalltooth sawfish every four years is not expected to have 

a population or DPS level effect on smalltooth sawfish.

In summary, smalltooth sawfish will be directly and indirectly affected by CWIS.

7.3 Critical Habitat

Designated critical habitat for the U.S. DPS of smalltooth sawfish consists of two units: the 

Charlotte Harbor Estuary Unit, which comprises approximately 221,459 acres of coastal habitat; 

and the Ten Thousand Islands/Everglades Unit, which comprises approximately 619,013 acres of 

coastal habitat (74 FR 45353). The two units are located along the southwestern coast of Florida 

between Charlotte Harbor and Florida Bay. These specific areas contain the following physical 

and biological features that are essential to the conservation of this species and that may require 

special management considerations or protection: red mangroves and shallow euryhaline habitats 

characterized by water depths between the mean high water line and 3 ft (0.9 m) measured at 

mean lower low water. There is only one CWIS in smalltooth sawfish critical habitat. The 

potential effects to critical habitat from this CWIS are a change in depth and available habitat 

because of water intake. However, it is unlikely that the CWIS will remove so much water that 

the depth will be altered to such an extent as to make the habitat unusable for smalltooth sawfish. 
62

Therefore, NMFS does not believe smalltooth sawfish critical habitat will likely be destroyed or 

adversely modified as a result of this Rule.

8 Rockfish

Several studies have been conducted on the impingement and entrainment of rockfish. These 

studies were conducted to evaluate population abundance and trends, rather than the effects of 

CWIS on rockfish; still they provide the best available information on such effects. We describe 

these studies in the impingement and entrainment response sections. We assume that the 

facilities used in these studies represent the typical facility regulated under the Rule because they 

did not incorporate protective measures for rockfish, as a result of ESA Section 7(a)(2) 

consultations or permit requirements (unlike our “best case” scenarios, described for other 

species). 

8.1 Stressors

Rockfish are likely to be adversely affected by impingement and entrainment in CWIS; thermal, 

chemical, flow alteration, and indirect effects (such as prey reduction) are also likely to adversely 

affect rockfish. 

8.2 Exposure

Applying the best available information to the three ESA-listed species, we expect larval and 

juvenile rockfish of 0 to 2 years to be impinged in CWIS because older rockfish are demersal 

and less likely to be impinged. We expect larval rockfish of up to 16 days of age to be entrained 

in CWIS. Impinged and entrained fish may be male or female. EPA does not identify the number 

of facilities that overlap with each species’ range. To estimate exposure, we mapped the facilities 

listed in the BE against species ranges in ArcGIS. We found that one facility overlaps with each 

species (Table 11). Using the best available information on rockfish impingement and 

entrainment, we calculated the expected annual impingement and entrainment mortality rates. In 

addition, individuals are likely to be exposed to thermal and chemical discharges, flow alteration, 

and indirect effects. 

Table 11. Expected annual rockfish impingement and entrainment mortality at CWIS based on 

current information.

Puget Sound DPS Overlapping facilities Impingement Entrainment

Bocaccio 1 406 – 1,360 23 – 1,120

Canary rockfish 1 406 – 1,360 23 – 1,120

Yelloweye rockfish 1 406 – 1,360 23 – 1,120

8.3 Response

Stressors that may affect ESA-listed pinniped species are entrapment and thermal discharges; 

indirect effects to prey species may also affect ESA-listed pinnipeds. General responses to these 

stressors are discussed below followed by subsequent species specific discussions.
63

8.3.1 Impingement

A study of fish impingement rates was conducted at four power-generating facilities: Ormond 

Beach in Oxnard, CA, Redondo Beach plant in Redondo Beach, CA, Huntington Beach plant in 

Huntington Beach, CA, and San Onofre in San Diego Count, CA. Samples were collected at 

least monthly for 17 years (1977 – 1993). A total of 27,546 impinged rockfish were counted 

during the study, with bocaccio and five other rockfish species accounting for 99 percent of this 

total (Love et al. 1998). These rockfish exhibit a range of habitat preferences and behaviors, 

indicating that they are representative of rockfish likely to be impinged by CWIS. In this study, 

impinged rockfish were between 0 and 2 years of age. Over the course of the study, overall 

impingement rates declined by at least two orders of magnitude, signifying severe declines in 

rockfish populations. By the end of the study period, bocaccio were no longer observed in the 

sample. 

A similar study was conducted at the Moss Landing Power Plant in Moss Landing, CA, from 

1979 to 1980 (Tenera 2007b). Data from the surveys was used to calculate the estimated 

concentration and estimated number of fish impinged per day. For bocaccio at all units, these 

estimates are 0.11/km3fish/intake volume and 194 fish/day. For other rockfishes (mainly five 

other species, not including bocaccio) at all units, these estimates are 0.0017/km3fish/intake 

volume and 3 fish/day. Bocaccio and rockfish were impinged throughout the year. Nearly all 

impinged bocaccio were young of the year; nearly all other impinged rockfish were juveniles 

(Tenera 2007b). 

A similar study was conducted at the Morro Bay Power Plant in San Luis Obispo County, CA 

from 1977-1978. The number of impinged bocaccio was 1,104 individuals, which comprised 

seven percent of the total fish impingement. The number of impinged rockfish (not bocaccio) 

was 256 individuals, which comprised 1.6 percent of the total fish impingement. For all 

rockfishes, the estimated annual biomass was 187.62 grams per million cubic meter flow. 

Comparing these datasets, annual impingement estimates are: 1,621 rockfish/year at the four 

power generators (406 rockfish/year/facility); 1,360 rockfish/year at Morro Bay; and 71,905 

rockfish/year at Moss Landing plant in Moss Landing, CA. The last average is based on 

estimates, rather than total counts and is likely an overestimate. To simplify calculations, we 

estimate that an average CWIS facility is likely to impinge 1,000 rockfish annually. We assume 

that the rockfish will be 0 to 2 years in age (because older rockfish are demersal and less likely to 

be impinged). Finally, we assume that impinged rockfish are likely to be killed.

8.3.2 Entrainment

Table 12 shows the estimated annual entrainment rates of rockfishes (i.e., kelp, gopher, and 

black-and-yellow rockfishes) at Morro Power Plant in 2000 and at Diablo Canyon Power Plant in 

1996 – 1997 (1996) and 1997 – 1998 (1997) (Tenera 2007a). They used the weekly sample data 

to calculate losses using the fecundity hindcast model, the adult equivalent loss model, and the 

empirical transport model (Table 12). The fecundity hindcast model describes the loss of 
64

reproductive output of adult females, and the empirical transport model describes the 

proportional mortality (Tenera 2007a). 

Table 12. Annual estimated larvae entrainment rates and calculated loss of rockfish based on 

available information.

Facility No. 

larvae

Annual 

entrained 

larvae

Age 

(mean/ 

max)

Fecundity 

hindsight 

(adult 

females)

Adult 

equivalent 

(adults)

Empirical transport 

(proportion 

mortality)

Morro 2000 360 6,407,000 5.5/11.3 13 23 0.027

Diablo 1996 17,576 275,000,000 6.4/16.4 617 1,120 0.039

Diablo 1997 222,000,000 6.4/16.4 497 905 0.048

Newborn larval rockfish (0 to 16 days) are likely to be entrained in CWIS. The number of 

estimated annual entrained larvae varies widely from 6 to 275 million larvae. This range likely 

reflects the location and characteristics of the CWIS, as well as natural variation in rockfish 

spawning. Entrained larvae are unlikely to survive. 

8.3.3 Thermal Discharges

We were unable to find specific information on the effects of thermal discharges on rockfish. 

Elevated temperatures are linked to low levels of dissolved oxygen. Lethal low levels of 

dissolved oxygen are one of the most serious threats to the listed rockfish DPSs. Low dissolved 

oxygen has been found to result in the death of adult rockfish in Hood Canal (Palsson et al. 

2009).

8.3.4 Chemical Discharges

While we were unable to find specific information on the effects of chemical discharges on 

rockfish, anoxic conditions and chemical contamination are also considered threats to rockfish 

recovery (NMFS 2008b). 

8.3.5 Flow Alteration

Juveniles settle in nearshore habitats with sand, rock and/or cobble substrates, which provide 

adequate prey and protection from predators. To survive, rockfish need a specific type of 

substrate structure and rugosity to support feeding opportunities and predator avoidance. 

Changes in flow velocity and turbidity may alter the substrate.

8.3.6 Indirect Effects

Juvenile rockfish require a sufficient quantity and quality of prey items to survive. Such prey 

items include zooplankton (including crustaceans, polychaetes, and euphasiid eggs and larvae) 

and fishes (including rockfishes, hake, anchovies, etc.). These prey are likely to be impinged or 

entrained in CWIS. 
65

8.4 Population and Species Level Effects

We do not have sufficient site specific information to complete the species level effects. Based 

on the limited information available we conclude that bocaccio, yelloweye rockfish, and canary 

rockfish will be directly and indirectly affected by CWIS.

8.5 Critical Habitat

Critical habitat designations have been proposed for the Puget Sound DPSs of bocaccio, canary 

rockfish, and yelloweye rockfish, but these do not overlap with CWIS.

9 Abalone

In the BE, EPA did not identify impingement and entrainment impacts to abalone; however, 

extensive adverse effects of CWIS on black abalone are documented in peer-reviewed scientific 

literature (Martin et al. 1977, Steinbeck et al. 1992, Neuman et al. 2010). The discharges from 

Diablo Canyon Power Plant have been linked to the mortality of black abalone (Martin et al. 

1977, Steinbeck et al. 1992). Though NMFS issued a biological opinion in 2006 on NRC’s 

approval of the continued operation of the Diablo Canyon Power Plant, this opinion did not 

describe effects on abalone, which were not listed under the ESA until 2009. 

The Diablo Canyon Power Plant is a two-unit, nuclear-powered, steam-turbine power plant. It 

has one intake cove, housing a common intake structure, which provides cooling water to both 

units for the cooling of the main condensers and other machinery necessary for operation of the 

plant. The intake is a shoreline structure that houses bar racks, vertical traveling screens, 

auxiliary cooling water structures, and main circulating water pumps. On the ocean side of the 

intake structure, a concrete curtain wall extends approximately 2.4 m below mean sea level to 

prevent floating debris from entering the intake structure. As seawater enters the intake structure, 

it passes through one of 16 sets of bar racks designed to exclude large debris from the forebays. 

The bar racks consist of vertical, inclined rows of steel bars spaced about 8 centimeters (cm) 

apart. The underwater portion of the bar rack is approximately 10 m high depending on the tide. 

The overall intake opening is approximately 10 m high by 52.6 m wide.

The flow velocity of seawater is 0.3 m/sec. Sets of traveling screens with 0.95 cm stainless steel 

mesh screens are located behind the bar racks to remove smaller debris. The Diablo Canyon 

Power Plant normally operates at full power unless shut down for scheduled maintenance or 

refueling or for an unscheduled forced outage. During maintenance outages the circulating water 

pumps may be turned off for periods up to one month; however, usually one unit remains 

operational during these maintenance periods. During normal operations, four circulating water 

pumps (two for each unit) provide an average of 1,613 m3/min, for a total of 6,450 m3/min of 

ocean cooling water. The cooling water is returned to the ocean via stair-step weir structure that 

opens on the eastern end of Diablo Cove. At the discharge the water is usually 10 to 11°C 

warmer than the intake water. The maximum temperature rise allowed under the NPDES permit 

is 12°C. To help control biofouling of the CWIS, a combination of sodium hypochlorite and 

sodium bromide is injected into the water downstream of the traveling screens via a chlorine 
66

injection system. The chemicals are injected six times daily for 20 minutes per injection. The 

total residual oxidant concentration in the discharge stream is usually between 20 and 60 parts 

per billion (ppb), which is below the permitted level of 200 ppb allowed under the NPDES 

permit. 

Copper discharged from the cooling system of Diablo Canyon Nuclear Power Plant resulted in 

heavy mortality to the adjacent red and black abalone populations (Martin et al. 1977). In 1988, 

mass mortality of black abalone occurred in association with warm water discharged from the 

facility (Steinbeck et al. 1992).

9.1 Stressors

Black and white abalone are likely to be adversely effected by several stressors caused by CWIS. 

These include: entrainment of gametes and larvae; thermal and chemical discharges; and 

degradations to the water quality of designated critical habitat.

9.2 Exposure

Black abalone occur from Point Arena, CA, to Bahia Tortugas and Isla Guadalupe, Baja 

California, Mexico. Black abalone are likely to be adversely affected by CWIS whose area of 

influence of the intake and/or discharge includes intertidal and shallow subtidal rocky habitat 

with crevices and cracks. We have determined that four facilities overlap with the range of black 

abalone. 

White abalone occur from Point Conception, CA, to Punta Abreojos, Baja California, Mexico. 

White abalone are likely to be adversely affected by CWIS whose area of influence includes 

open low and high relief subtidal rock or boulder habitat interspersed with sand channels (NMFS 

2008a). We have determined that 29 facilities overlap with the range of white abalone. 

The adverse effects of entrainment, thermal discharge, and chemical discharges are likely to 

affect gametes, juveniles, and adults. These stressors are likely to affect a large proportion of the 

species or their annual recruitment, if the CWIS is located near abalone populations. 

9.3 Response

Stressors that may affect ESA-listed pinniped species are entrapment and thermal discharges; 

indirect effects to prey species may also affect ESA-listed pinnipeds. General responses to these 

stressors are discussed below followed by subsequent species specific discussions.

9.3.1 Entrainment

Abalone gametes and fertilized eggs (prior to settlement) are likely to be entrained by CWIS. 

Black abalone may also be entrained at the larval stage, which lasts for approximately 1 to 2 

weeks. Neuman et al. (2010) report that juveniles (settled and 10 to45-mm shell length) may also 

be entrained by power-generating facilities. Entrainment is likely to result in mortality (Neuman 

et al. 2010). 

Abalone are broadcast spawners, releasing their gametes to the environment in synchrony. 

Fertilization is reliant upon dense adult aggregations and high gamete density. Below an adult 

threshold density, gametes released by males and females into the water column do not meet 
67

successfully because of limited gamete dispersal distances, exacerbated by the highly turbulent 

character of shallow ocean waters, and fertilization does not take place (Neuman et al. 2010). 

Depending on the environmental conditions in a given year, a facility withdrawing > 2 mgd of 

cooling water has the potential to entrain a high proportion of released gametes, leading to 

recruitment failure for that year. Though we are not aware of any such scenarios, it is unlikely 

that such a scenario would be detected without targeted monitoring. White et al. (2010) evaluated 

the consequences of larval entrainment in CWIS on benthic populations, using transport and 

spatial metapopulation models. They found that entrainment threatens the persistence of 

populations with reduced densities (i.e., endangered or threatened species). In scenarios 

involving extremely low settlement rates or reduced density adult populations (both apply to 

ESA-listed abalone species), entrainment led to population collapse (White et al. 2010). In the 

case of black abalone, accumulating evidence suggests that low reproductive success of widely 

dispersed adult populations coupled with short larval dispersal distances limits the recovery of 

severely reduced populations (Gruenthal and Burton 2008). 

9.3.2 Thermal Discharges

In 1988, thermal discharges from the Diablo Canyon Power Plant increased water temperatures 

11°C above ambient, resulting in an isolated outbreak of withering syndrome and a massive dieoff of black abalone (Steinbeck et al. 1992). The heated water increases the incidence of the fatal 

disease, which has been identified as the primary threat to the species and continues to result in 

population decline (Raimondi et al. 2002). From first appearance of the signs of withering 

syndrome usually leads to rapid and dramatic declines in population size, most often in excess of 

90 percent (Neuman et al. 2010). Temperature was indicated to be the single most important 

factor influencing population recovery (Tissot 1995). Thermal discharges are likely to increase 

the incidence and accelerate the spread of the disease (Raimondi et al. 2002), especially at 

temperatures over 18°C (Neuman et al. 2010). For black abalone, increased water temperatures 

are correlated with increased manifestation of the withering syndrome and accelerated mortality 

(Raimondi et al. 2002). Though white abalone are susceptible to withering syndrome in captive 

settings, no manifestations have been recorded in the wild. 

Neuman et al. (2010) reported that power plant effluent is likely to result in the mortality or 

reduced growth of adults, juveniles, and larvae abalone; even moderate temperature increases are 

likely to be detrimental. Lab studies conducted at Diablo Canyon indicate that black abalone 

sperm become non-motile when released into waters above 27°C (Corporation et al. 1982). 

Black abalone optimum temperatures for early development (egg-to-larvae) range from 10 to 

22°C (Tera Corporation 1982). In laboratory studies with white abalone the optimum 

temperature range for larval development and survival is 14 to18°C (Leighton 1972). 

Temperatures above these optimal ranges are likely to slow or terminate development. With 

acclimation, black abalone may survive temperatures of 29°C, and white abalone may survive 

temperatures 29°C; however, we consider their thermal tolerance to be 26.1 to 28°C and < 19°C, 

respectively (Tera Corporation 1982; Leighton 1972; unpublished data by Lafferty, cited in 

Hobday and Tegner 2000). 
68

9.3.3 Chemical Discharges

Chemical discharges also adversely affect abalone. Toxic levels of copper discharged from the 

CWIS of Diablo Canyon Nuclear Power Plant were associated with red abalone and black 

abalone mortalities in a nearshore cove that received significant effluent flows (Martin et al. 

1977). The median threshold lethal dose for adult red and black abalone were 65 ppb and 50 ppb 

Copper, respectively. The median threshold lethal dose for larval red abalone was 114 ppb 

Copper concentration. Histopathological abnormalities in gill tissues occur at concentrations 

above 32 ppb. A single toxic discharge, depending on where it occurs, could irreparably damage 

the few remaining viable populations of black abalone (Neuman et al. 2010). 

9.3.4 Indirect Effects

CWIS are likely to entrain abalone food. In several locations, starvation, due to the reduced 

availability of drift algae, has also been documented (Lafferty and Kuris 1993). The reduced 

availability of food may increase susceptibility to withering disease (Raimondi et al. 2002). 

9.4 Population and Species Level Effects

Based on the information above, entrainment and thermal discharges could contribute to 

recruitment failure. Neuman et al. (2010) explain that reduction in local densities below the 

threshold necessary for successful fertilization (0.34/m2) has been a widespread and pervasive 

consequence of population reductions by withering syndrome and other factors. For example, at 

Diablo Canyon, the site of the mass mortalities due to CWIS, the density of newly recruited 

abalone declined to zero at an adult density of 0.32/m2in 1997 (Neuman et al. 2010).

Throughout most of the species’ range, local densities are less than the critical threshold density 

required for successful spawning and recruitment (Neuman et al. 2010). Long-term and largescale datasets demonstrate an almost complete failure of recruitment to black abalone 

populations following mass mortalities due to withering syndrome (Miner et al. 2006). A lack of 

local larval production and dispersal limitation due to extremely localized dispersal of black 

abalone larvae may be the most plausible explanation for the lack of abalone recruitment to sites 

impacted by withering syndrome. Miner et al. (2006) conclude that the prospect of recovery of 

extirpated populations is poor due to a combination of documented recruitment failure and shifts 

in community composition away from habitat suitable for abalone.

Distant black abalone populations are not likely to seed those devastated by withering syndrome 

(Miner et al. 2006). Given the continued decline of most populations and the continued 

northward expansion of withering syndrome with warming events (Raimondi et al. 2002), we 

expect the trends of recruitment failure and population decline to continue. The black abalone is 

currently in danger of becoming extinct in the United States within the next 30 years, due to 

stressors that drive adult densities below values required for successful spawning and recruitment 

(Neuman et al. 2010). The most important of these stressors is the accelerated spread of and 

mortality caused by withering syndrome resulting from elevated water temperatures, which in at 

least one case was caused by thermal discharges from CWIS (Raimondi et al. 2002). According 

to Neuman et al. (2010), maximum levels of protection from other sources of mortality will be 
69

essential to maintain any prospect for recovery of black abalone while population-scale disease 

countermeasures are considered, developed, and implemented. Management actions that have the 

highest likelihood of helping to conserve and recover the species are those that reduce 

interactions between black abalone and anthropogenic sources of elevated sea surface 

temperatures, including CWIS, such that rates of withering syndrome transmission and diseaseinduced mortality may slow (Neuman et al. 2010). 

Adverse impacts from CWIS have already resulted in mortalities of black abalone, reducing the 

viability of populations. White abalone are likely to be adversely affected in a similar manner, 

but without the catastrophic effects of withering syndrome. The black abalone has declined by 

more than 95 percent as a result of withering syndrome. Both species have experienced extreme 

declines, as a result of overexploitation. The resilience of both species to additional perturbations 

is low as a result of reduced population size and reduced recruitment. 

In summary, both black and white abalone will be directly and indirectly affected by CWIS.

9.5 Critical Habitat

Black abalone critical habitat designation includes approximately 360 km2of rocky intertidal and 

subtidal habitat within five segments of the California coast between the Del Mar Landing 

Ecological Reserve to the Palos Verdes Peninsula, as well as on the Farallon Islands, Año Nuevo 

Island, San Miguel Island, Santa Rosa Island, Santa Cruz Island, Anacapa Island, Santa Barbara 

Island, and Santa Catalina Island. This designation includes rocky intertidal and subtidal habitats 

from the mean higher high water line to a depth of 6 m (relative to the mean lower low water 

line), as well as the coastal marine waters encompassed by these areas (76 FR 66806). The 

designated areas include the following physical feature that is essential to the conservation of the 

species: suitable water quality, including temperature, salinity, pH, and other chemical 

characteristics necessary for normal settlement, growth, behavior, and viability of black abalone. 

Black abalone critical habitat overlaps with at least one CWIS facility. As described above and in 

the designation (76 FR 66806), CWIS thermal discharges may raise water temperatures and 

introduce contaminants into the water. Elevated water temperatures have been linked to 

increased virulence of withering syndrome.

10 Corals

In the BE, EPA explains that they were unable to find data with which to evaluate whether coral 

species have been affected by existing CWIS and associated discharges. We performed a 

literature search to find any available information with which to evaluate the effects of CWIS on 

corals. We found information on the effects of CWIS on coral survival at the Tanguisson Power 

Plant in Guam (Birkeland et al. 1979) and at the Kahe Point Power Plant in Hawaii (Jokiel and 

Coles 1974, Coles 1984, Jokiel and Coles 1990, Richmond 1993). We also found extensive 

literature on the effects of elevated temperatures on corals. We found one relevant study on the 

entrainment of coral eggs and larvae. The study investigated the environmental impact of the 

CWIS at the Tanguisson Power Plant in Guam (Smith et al. 2005). 
70

The Tanguisson Power Plant in Guam was not included in EPA’s list of facilities that overlaps 

with species ranges or critical habitat because the BE did not include any facilities listed outside 

of the United States, though facilities in Territories are regulated under the Rule (with EPA as 

the permitting authority). The CWIS of the facility is located adjacent to the shore line northwest 

of the facility and draws water from the Philippine Sea (Smith et al. 2005). Its low intake 

velocity is 0.93 ft/sec in the channel and 1.55 ft/sec in the intake pipes. The cooling water is 

drawn through an intake channel cut through the reef margin and reef flat. The intake channel is 

14 m wide and 2 m below the mean tide level. A retaining wall on either side of the channel 

flanks a portion of the intake, thus separating it from sections of the reef flat. We are not aware 

of ESA Section 7 consultations on the facility, nor has the facility received a Section 10 permit 

for incidental take. The facility has been working on an administratively extended permit from 

EPA since 2001. On September 30, 2010, EPA sent the facility a letter, identifying violations of 

the NPDES permit that included: failure to continuously monitor effluent flow, report toxicity, 

monitor temperature, or perform sampling and analysis. The facility appears to be typical of 

CWIS facilities, likely to be regulated under the Rule. 

The Kahe Point Power Plant in Hawaii is an oil-fired steam electric generating station (Jokiel 

and Coles 1974). Cooling water for the plant is withdrawn from the ocean at the intake basin and 

is returned to the sea at an outfall located on a small beach. In 1971, three 90-megawatt 

generating units were in operation, drawing a total of approximately 14 m3/sec (230,000 gallons 

per minute) of seawater for cooling purposes and discharging this water. A fourth unit of the 

same capacity was added in 1972, increasing the waste heat discharge rate by over 30 percent 

(Jokiel and Coles 1974). We are not aware of ESA section 7 consultations on the facility, nor has 

the facility received a section 10 permit for incidental take. The facility appears to be typical of 

CWIS facilities, likely to be regulated under the Rule. 

10.1 Stressors

The following stressors are likely to adversely affect ESA-listed corals: entrainment of gametes 

and larvae, thermal discharges, and chemical discharges.

10.2 Exposure

In the BE, EPA estimates that staghorn and elkhorn coral are likely to be directly or indirectly 

affected by the CWIS of 16 facilities regulated under the Rule (EPA 2013). We determined that 

28 facilities overlap with the ranges of staghorn and elkhorn coral. These facilities also overlap 

with many proposed coral species, including: pillar, boulder star, mountainous star, star, rough

cactus, Lamarck’s sheet, and elliptical star corals. Five facilities overlap with blue rice coral and 

sandpaper rice coral in Hawaii. 

The BE did not include any facilities listed outside of the United States, though facilities in 

Territories are regulated under the Rule (with EPA as the permitting authority). For the purposes 

of this Opinion, we will assume that all proposed coral species overlap with at least one facility. 

Because we have no information on these facilities, we will assume that effects on proposed 

corals are likely to be similar to effects on listed corals. 
71

10.3 Response

Stressors that may affect ESA-listed pinniped species are entrapment and thermal discharges; 

indirect effects to prey species may also affect ESA-listed pinnipeds. General responses to these 

stressors are discussed below followed by subsequent species specific discussions.

10.3.1 Entrainment

During sexual reproduction, corals release gametes during annual spawning events, which last 

for one or a few nights. Upon fertilization, planktonic planulae larvae form. Gametes or planulae 

larvae are likely to be entrained in CWIS. Smith et al. (2005) estimated entrainment rates by 

placing surface and bottom nets near the entrance of a CWIS. The collection did not occur during 

the large annual reproductive event that is characteristic of approximately 85 percent of the reefbuilding corals in Guam. Still, an estimated total of 13,144 eggs (of unknown origin) and 80 

possible coral larvae were collected in a 24-hour period. Coral larvae were collected in both the 

surface and bottom nets. Though Smith et al. (2005) caution against using these values for 

statistical projections regarding the magnitude of entrainment, we provide some qualitative 

observations. First, coral eggs and larvae are likely to be entrained in CWIS in the vicinity of 

spawning corals. Second, the volume of water withdrawals from a single facility during a single 

24-hour period is large: 127,363.16 m3of water passed through the surface net and 89,393.76 

m3 passed through the bottom net. Finally, during the annual reproductive spawning event, we 

would expect egg and larval entrainment to be orders of magnitude higher than the observed 

values (e.g., hundreds of thousands or millions). We were unable to find information on the 

viability of entrained coral gametes; however, at least some coral larvae are likely to survive 

entrainment. Entrainment is proposed to be the principal mechanism promoting high coral 

recruitment near the offshore thermal outfall at the Hawaii facility (Coles 1984). 

White et al. (2010) evaluated the consequences of larval entrainment in CWIS on benthic 

populations, using transport and spatial metapopulation models. They found that entrainment 

threatens the persistence of populations with reduced densities (i.e., endangered or threatened 

species). In scenarios involving extremely low settlement rates or reduced density adult 

populations, entrainment led to population collapse (White et al. 2010). Staghorn and elkhorn 

corals have experienced extreme density reductions (i.e., greater than 97 percent) and 

recruitment failures. Therefore, the entrainment of gametes or larvae of these and other proposed 

endangered species may result in population reductions. Coral species that are proposed for 

listing due to concerns for future effects of climate change are less likely have reduced densities 

or low settlement rates; therefore, we do not expect reductions in species viability as a result. 

10.3.2 Indirect Effects

Indirect effects to corals could occur from thermal discharges and chemical discharges.

Thermal Discharges

Nearly all corals transplanted to the thermal effluent area at the Tanguisson Power Plant died (3 

percent survival) and those surviving were in poor health (Birkeland et al. 1979); this was true 

even though transplanted species had relatively high thermal tolerances. The colonies lost their 
72

zooxanthellae and died within a few weeks, apparently due to the thermal effects (Birkeland et 

al. 1979).

Corals rely on symbiotic, photosynthesizing zooxanthellae for energy. When water temperatures 

exceed 29°C, the zooxanthellae begin to lose chlorophyll; at extreme temperatures, there is a 

mass expulsion of the zooxanthellae. This process is known as coral bleaching. Coral mortality 

rates, as a result of bleaching, depend on the species, temperature increase, and exposure time. 

Temperature increases of 4 to 5°C for 1 to 2 days result in extreme bleaching and 90 to 95 

percent mortality rates. Temperature increases of 2 to3°C for 1 to 2 days result in less extensive 

bleaching and 0 to 10 percent mortality rates (Jokiel and Coles 1990). 

The first quantitative measurements of photosynthetic pigmentation reduction (i.e., bleaching) 

were performed on corals that had been exposed to thermal effluent from a power station in 

Hawaii (Jokiel and Coles 1974). The abstract is as follows: 

“The effect of thermal enrichment on hermatypic corals was investigated at Kahe 

Point, Oahu, Hawaii. The reef off the Kahe Power Plant was surveyed before and 

after an increase in thermal discharge that accompanied plant expansion. 

Abundances of dead and damaged corals correlated strongly with proximity to 

plant discharge and with levels of thermal enrichment. Nearly all corals in water 

4° to 5° C above ambient were dead. ]n areas characterized by temperature 

increases from 2° to 4° C, the corals lost zooxanthellar pigment and suffered high 

mortality rates. Damage to the corals was most severe in late summer, and 

coincided with annual ambient temperature maxima. During the winter months 

the surviving corals slowly regained zooxanthellar pigment, but there was high 

mortality of corals during the recovery period. When generating capacity of the 

plant was increased from 270 to 360 megawatts, the area of dead and damaged 

corals increased from 0.38 hectare (0.94 acre) to 0.71 hectare (1.76 acre).”

The thermal effluent resulted in extensive coral mortality (Jokiel and Coles 1974). For Hawaiian 

coral species, 31 to 32°C is lethal, and prolonged exposure to 30°C will eventually pale, bleach, 

and kill most coral species. The percent abundance of dead, bleached, and pale corals is 

correlated with outfall discharge and increased discharge resulted in increased damage. Exposure 

to increased levels of thermal loading did not appear to kill the corals outright but gradually 

weakened and eliminated them over a period of time. Such sublethal effects bring into question 

the practice of using short-term tolerance limits to predict environmental damage (Jokiel and 

Coles 1974). 

Coral reefs often recover from naturally occurring temperature disturbances, such as El Nino, but 

recovery of the coral community did not occur at the Hawaii site until the power plant outfall 

was redesigned and rebuilt (Richmond 1993; Coles 1984). After the construction of an offshore 

thermal outfall, recruitment rates increased ten-fold above surrounding areas (Coles 1984). This 

elevated recruitment was temporary at some sites, where recruitment declined to zero after 

several years (Coles and Brown 2007). 
73

In Taiwan, the operation of a power facility led to two mass coral bleachings, one which 

bleached over 90 percent of the corals on the fringing reef due to thermal effluent of more than 

4°C (31.9 to over 34 °C) and the other which bleached 30 percent of the corals living between 3 

to 5 m depth (Hung et al. 1998). 

Transplantation is not an effective method of establishing corals in a thermal effluent (Birkeland 

et al. 1979). While transplantation may be a mechanism for securing the survival of endangered 

coral population, transplantation to reestablish a large area of reef is exceedingly expensive and 

economically unfeasible (Birkeland et al. 1979). 

Chemical Discharges

Chlorine is often found in the chemical discharges of CWIS. Chlorine bleach has a negative 

effect on coral reefs (Richmond 1993). Chlorine may contribute to the death of corals, either 

adults or larvae (DaVis 1971). 

10.4 Population and Species Level Effects

There appear to be variable effects of CWIS. Offshore discharges without excessive thermal 

discharges aide in recruitment (Coles 1984); however, all other studies indicate that CWIS result 

in coral death (Jokiel and Coles 1974, Birkeland et al. 1979, Jokiel and Coles 1990, Smith et al. 

2005). 

Staghorn and elkhorn corals have experienced extreme declines in abundance, greater than 97 

percent. These species are therefore susceptible to recruitment failure. The impingement of large 

numbers of gametes or larvae is likely to reduce annual recruitment and result in population 

collapse for endangered species. Thermal discharges from CWIS are likely to result in bleaching 

events, one of the primary and continuing causes of species decline. For all species, adult corals 

within the range of the thermal plume of facilities are also likely to be exposed to elevated water 

temperatures and resultant bleaching. Because population density is already low and recruitment 

is already reduced, these species are not resilient to additional perturbations. 

In summary, staghorn and elkhorn corals will be directly and indirectly affected by CWIS.

10.5 Critical Habitat

Critical habitat has been designated for elkhorn and staghorn coral in the following four areas: 

Florida, Puerto Rico, St. John/St. Thomas, and St. Croix. These areas include the following 

feature, which is essential to the conservation of corals: substrate of suitable quality and 

availability to support successful larval settlement and recruitment, and reattachment and 

recruitment of fragments. For purposes of this definition, ‘‘substrate of suitable quality and 

availability’’ means natural consolidated hard substrate or dead coral skeleton that is free from 

fleshy or turf macroalgae cover and sediment cover. Though critical habitat overlaps with five 

CWIS facilities (within 1 km of the facility), their discharges are not likely to adversely affect 

hard substrate or dead coral skeleton. Therefore, the promulgation of the Rule under 316(b) of

the Clean Water Act is not likely to result in destruction or adverse modification of critical 

habitat.
74

11 Johnson’s Seagrass

In the BE, EPA identifies Johnson’s seagrass as a species potentially affected by the proposed 

action. We are not aware of any biological opinions or permits that have evaluated the effect of 

CWIS on Johnson’s seagrass; however, the effects of CWIS discharges on seagrasses are well 

documented in peer-reviewed scientific literature. As described in more detail below, the thermal 

discharges from CWIS have resulted in seagrass denuding and population decline in Florida 

(Roessler 1971, Thorhaug et al. 1978, Thorhaug 1979) and other areas (Robinson 2010). 

11.1 Stressors

In the BE, EPA identifies the following stressors associated with the proposed action: thermal 

discharge, chemical discharge, flow alteration, and indirect effects. We agree that these stressors 

are likely to adversely affect Johnson’s seagrass.

11.2 Exposure

Three CWIS facilities overlap with the range of Johnson’s seagrass. 

11.3 Response

Stressors that may affect Johnson’s seagrass are thermal discharge, chemical discharge, flow 

alteration, and indirect effects.. General responses to these stressors are discussed below 

followed by subsequent species specific discussions.

11.3.1 Thermal discharge

Though we could not find information on the effect of CWIS on Johnson’s seagrass, we found 

information on the adverse effects of CWIS on other seagrass species. Johnson’s seagrass is 

likely to be similarly affected. Seagrass declines in Florida have been directly attributed to 

temperature increases, as a result of thermal discharges from CWIS (Roessler 1971, Thorhaug et 

al. 1978, Thorhaug 1979). Sustained temperatures increases of 5°C denude seagrass communities 

and increases of 4°C cause severe damage (Thorhaug et al. 1978). Roessler (1971) explains that 

thermal discharges from a power plant in Biscayne Bay caused seagrasses to be replaced by algal 

mats. Such damage is likely to increase over time. Roessler and Zieman (1969) report that 

although thermal discharge from the Turkey Point Power Plant in Biscayne Bay remained 

constant during the period from September 1968 to September 1969, damage to the shallow 

water Thalassia (turtle grass) community increased. In September 1968, an area of 12 to 14 

hectares (30 to 35 acres) off the outfall was devoid of all vegetation except bluegreen algae. 

Surrounding this was an area of approximately 20 to 24 hectares (50 to 60 acres) where all 

macroalgae had been eliminated and the Thalassia heavily damaged. By September 1969 the 

barren area had increased to about 20 hectares (50 acres) and the surrounding damaged areas to 

38 to 39 hectares (70 to 75 acres) (Roessler and Zieman 1969).

Thorhaug (1979) demonstrates that seagrass beds denuded by the thermal effects of CWIS are 

not likely to reseed themselves, but instead, require restoration. In other areas, CWIS lead to a 

total loss of seagrass, including the extirpation of species (Robinson 2010). CWIS reduce the 

species diversity, abundance, and density of seagrasses; such losses are likely due to increases in 
75

turbidity and temperature (Robinson 2010). Therefore, thermal discharges as a result of CWIS, 

are likely to reduce the abundance and distribution of Johnson’s seagrass. 

11.3.2 Chemical Discharge

CWIS often use chlorine to clean their systems and reduce unwanted biological growth. Chlorine 

bleach (sodium hypochlorite) kills seaweed and seagrasses, and is often used to eradicate these 

species (Williams and Schroeder 2004). Copper, which is also released in CWIS discharges, 

adversely affects several seagrass species. Copper toxicity in seagrasses inhibits metabolic 

activity, interferes with vital pathways including photosynthesis, and reduces growth and 

development (Prange and Dennison 2000). 

11.3.3 Flow Alteration

Flow alteration may effect seagrass as a result of increased turbidity (Robinson 2010). Increased 

turbidity reduces light levels in the environment and limits photosynthesis. For example, the San 

Onofre Nuclear Generating Station creates a turbid plume that moves over a kelp bed, reducing 

light and increasing the flow of particles near the substrate, which adversely affects early stages 

(Ambrose 1994). Unlike kelp, seagrasses store minerals in rhizomes; however, sustained periods 

of light deprivation are likely to result in large losses. Therefore, flow alteration as a result of 

CWIS is likely to reduce the fitness of Johnson’s seagrass. 

11.3.4 Indirect Effects

CWIS lead to extreme modifications in community structure, including an increase in the 

numbers of grazing gastropods, likely as a result of increased water temperatures and current 

flow (Robinson 2010). These grazing gastropods contribute to the loss in density and occurrence 

of seagrasses. 

11.4 Population and Species Level Effects

The distribution of Johnson’s seagrass is characterized as patchy, disjunct, and temporally 

fluctuating; its ability to repopulate an area after anthropogenic or natural disturbances is limited 

(69 FR 49035). The major threats to its survival and recovery include altered water quality and 

siltation. Given its limited distribution and inability to quickly repopulate, the species’ is 

expected to have little resilience to further perturbations. As described above, the thermal 

discharges from one facility have resulted in the denuding of seagrass beds; therefore, the 

thermal discharges from three facilities are likely to result in the denuding of three areas of 

Johnson’s seagrass, and the overall decline of the species. Chemical discharges of three facilities 

are likely to reduce the viability of local seabeds. Flow alterations of three facilities are likely to 

increase turbidity and reduce photosynthesis, resulting in fitness losses throughout the species. 

While additional individual impacts may continue to occur, over the last decade the species has 

not demonstrated any declining trends. The proposed action will not reduce or destabilize the 

present range of Johnson's seagrass.

In summary, Johnson’s seagrass will be directly affected by CWIS.
76

11.4.1 Critical Habitat

Designated critical habitat does not overlap with any CWIS facility likely to be regulated under 

the Rule. All CWIS facilities are located at least 8 km from designated Johnson’s seagrass 

critical habitat. Therefore, the promulgation of the Rule under 316(b) of the Clean Water Act is 

not likely to result in destruction or adverse modification of critical habitat.
77

12 Literature Cited

Abt Associates. 2014. Environmental Protection Agency memorandum: Estimates of the number 

of facilities regulated by the 316(b) rule.

Abookire, A. A., and J. F. Piatt. 2005. Oceanographic conditions structure forage fishes into 

lipid-rich and lipid-poor communities in lower Cook Inlet, Alaska, USA. Marine Ecology 

Progress Series 287:229-240.

Allen, P. J., J. A. Hobbs, J. J. Cech, J. P. Van Eenennaam, and S. I. Doroshov. 2009. Using trace 

elements in pectoral fin rays to assess life history movements in sturgeon: Estimating age 

at initial seawater entry in Klamath River green sturgeon. Transactions of the American 

Fisheries Society 138:240-250.

Allen, P. J., B. Hodge, I. Werner, and J. J. Cech. 2006a. Effects of ontogeny, season, and 

temperature on the swimming performance of juvenile green sturgeon (Acipenser 

medirostris). Canadian Journal of Fisheries and Aquatic Sciences 63:1360-1369.

Allen, P. J., B. Hodge, I. Werner, and J. J. Cech Jr. 2006b. Effects of ontogeny, season, and 

temperature on the swimming performance of juvenile green sturgeon (Acipenser 

medirostris). Canadian Journal of Fisheries and Aquatic Sciences 63:1360-1369.

Amaral, S. V., J. L. Black, B. J. McMahon, and D. A. Dixon. 2002. Evaluation of angled bar 

racks and louvers for guiding lake and shortnose sturgeon. American Fisheries Society 

Symposium 28:197-210.

Ambrose, R. F. 1994. Mitigating the effects of a coastal power plant on a kelp forest community:

rationale and requirements for an artificial reef. Bulletin of Marine Science 55:2-3.

ASMFC. 1998. American shad and Atlantic sturgeon stock assessment peer review: Terms of 

reference and advisory report. Atlantic States Marine Fisheries Commission, Washington, 

D. C.

ASSRT. 2007. Status review of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus). National 

Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast 

Regional Office, Atlantic Sturgeon Status Review Team.

Ayres, K. L., R. K. Booth, J. A. Hempelmann, K. L. Koski, C. K. Emmons, R. W. Baird, K. 

Balcomb-Bartok, M. B. Hanson, M. J. Ford, and S. K. Wasser. 2012. Distinguishing the 

impacts of inadequate prey and vessel traffic on an endangered killer whale (Orcinus 

orca) population. PLoS One 7:e36842.

Bain, M., N. Haley, D. Peterson, J. R. Waldman, and K. Arend. 2000. Harvest and habitats of 

Atlantic sturgeon Acipenser oxyrinchus Mitchill, 1815 in the Hudson River Estuary: 

lessons for sturgeon conservation. Boletín Instituto Español de Oceanografía 16:43-53.

Baker, J. D., A. L. Harting, T. A. Wurth, and T. C. Johanos. 2011. Dramatic shifts in Hawaiian 

monk seal distribution predicted from divergent regional trends. Marine Mammal Science 

27:78-93.

Baker, J. D., and T. C. Johanos. 2004. Abundance of the Hawaiian monk seal in the main 

Hawaiian Islands. Biological Conservation 116:103-110.

Bamber, R. N., and R. M. Seaby. 2004. The effects of power station entrainment passage on 

three species of marine planktonic crustacean, Acartia tonsa (Copepoda), Crangon 

crangon (Decapoda) and Homarus gammarus (Decapoda). Mar Environ Res 57:281-294.

Barlett, L. 2012. Eulachon. Alaska Department of Fish and Game.

Barraclough, W. E. 1964. Contribution to the marine life history of the eulachon Thaleichthys 

pacificus. Journal of the Fisheries Research Board of Canada 21:1333-1337.
78

Bath, D. W., J. M. O'Connor, J. B. Alber, and L. G. Arvidson. 1981. Development and 

identification of larval atlantic sturgeon (Acipenser oxyrhynchus) and shortnose sturgeon 

(A. brevirostrum) from the Hudson River Estuary, New York. Copeia 1981:711-717.

Baumgartner, M., C. Mayo, and R. Kenney. 2007. Enormous carnivores, microscopic food, and a 

restaurant that's hard to find. Pages pp. 138 -171 in S. Kraus and R. Rolland, editors. The 

Urban Whale: North Atlantic Right Whales at the Crossroads. Kraus, SD

Rolland, RM, Cambridge, MA.

Baumgartner, M. F., T. V. Cole, R. G. Campbell, G. J. Teegarden, and E. G. Durbin. 2003. 

Associations between North Atlantic right whales and their prey, Calanus finmarchicus, 

over diel and tidal time scales. Marine Ecology Progress Series 264:66.

Baumgartner, M. F., N. S. Lysiak, C. Schuman, J. Urban-Rich, and F. W. Wenzel. 2011. Diel 

vertical migration behavior of Calanus finmarchicus and its influence on right and sei 

whale occurrence. Marine Ecology Progress Series 423:167-184.

Baumgartner, M. F., and B. R. Mate. 2003. Summertime foraging ecology of North Atlantic right 

whales.

Bell, M. C. 1974. Fish passage through turbines, conduits, and spillway gates. Pages 251-261 in

Proceedings of the Second Workshop on Entrainment and Intake Screening. Johns 

Hopkins University, Balitmore, Maryland.

Benson, S. R., T. Eguchi, D. G. Foley, K. A. Forney, H. Bailey, C. Hitipeuw, B. P. Samber, R. F. 

Tapilatu, V. Rei, P. Ramohia, J. Pita, and P. H. Dutton. 2011. Large-scale movements 

and high-use areas of western Pacific leatherback turtles, Dermochelys coriacea. 

Ecosphere 2:27.

Benson, S. R., K. M. Kisokau, L. Ambio, V. Rei, P. H. Dutton, and D. Parker. 2007. Beach use, 

internesting movement, and migration of leatherback turtles, Dermochelys coriacea, 

nesting on the north coast of Papua New Guinea. Chelonian Conservation and Biology 

6:7-14.

Birkeland, C., R. H. Randall, and G. Grimm. 1979. Three methods of coral transplantation for 

the purpose of reestablishing a coral community in the thermal effluent area at the 

Tanguisson power plant. University of Guam, Marine Laboratory.

Blahm, T. H., and R. J. McConnell. 1971. Mortality of adult eulachon (Thaleichthys pacificus) 

subjected to sudden increases in water temperature. Northwest Science 45:178-182.

Bridges, W., and R. Anderson. 1984. A brief summary of Pilgrim Nuclear Power Plant effect 

upon the marine aquatic environment. Pages P. 263-271. in J. Davis and D. Merriman, 

editors. Observations on the ecology and biology ofwestern Cape Cod Bay, 

Massachusetts. .

Brodie, P. F. 1975. Cetacean energetics, an overview of intraspecific size variation. Ecology 

56:152-161.

Brungs, W. A. 1973. Effects of residual chlorine on aquatic life. Journal Water Pollution Control 

Federation 45:2180-2193.

Burns, J. J., and G. A. Seaman. 1986. Investigations of beluga whales in coastal waters of 

western and northern Alaska. II Biology and ecology.

Calkins, D. G. 1989. Status of beluga whales in Cook Inlet. Gulf of Alaska, Cook Inlet, and 

North Aleutian Basin Information Update:109-112.

Campbell, J. G., and L. R. Goodman. 2004. Acute sensitivity of juvenile shortnose sturgeon to 

low dissolved oxygen concentrations. Transactions of the American Fisheries Society 

133:772-776.
79

Carpenter, E. J., B. B. Peck, and S. J. Anderson. 1974. Survival of copepods passing through a 

nuclear power station on northeastern Long Island Sound, USA. Marine Biology 24:49-

55.

Carretta, J. V., E. Oleson, D. W. Weller, A. R. Lang, K. A. Forney, J. Baker, B. Hanson, K. 

Martien, M. M. Muto, M. S. Lowry, J. Barlow, D. Lynch, L. Carswell, R. L. Brownell Jr., 

D. K. Mattila, and M. C. Hill. 2013. U.S. Pacific marine mammal stock assessments: 

2012. National Oceanic and Atmospheric Administration, National Marine Fisheries 

Service, Southwest Fisheries Science Center.

Cech, J. J., and C. E. Crocker. 2002. Physiology of sturgeon: effects of hypoxia and hypercapnia. 

Journal of Applied Ichthyology 18:320-324.

Cech, J. J., S. J. Mitchell, and T. E. Wragg. 1984. Comparative growth of juvenile white 

sturgeon and striped bass: effects of temperature and hypoxia. Estuaries 7:12-18.

Cech Jr., J. J., and S. I. Doroshov. 2005. Environmental requirements, preferences, and tolerance 

limits of North American sturgeons. Pages 73-86 in G. T. O. LeBreton, F. W. H. 

Beamish, and R. S. McKinley, editors. Sturgeons and paddlefish of North America. 

Kluwer Academic Publishers, Dordrecht, The Netherlands.

Cech Jr., J. J., S. I. Doroshov, G. P. Moberg, B. P. May, R. G. Schaffter, and D. M. Kohlhorst. 

2000. Biological assessment of green sturgeon in the Sacramento-San Joaquin watershed 

(phase 1). CALFED Bay-Delta Program.

Chapman, F. A., and S. H. Carr. 1995. Implications of early life stages in the natural history of 

the Gulf of Mexico sturgeon, Acipenser oxyrinchus de sotoi. Environmental Biology of 

Fishes 43:407-413.

Clapham, P. J., and C. A. Mayo. 1987. Reproduction and recruitment of individually identified 

humpback whales, Megaptera novaeangliae, observed in Massachusetts Bay, 1979-1985. 

Canadian Journal of Zoology 65:2853-2863.

Coles, S., and E. Brown. 2007. Twenty-five years of change in coral coverage on a hurricane 

impacted reef in Hawai ‘i: the importance of recruitment. Coral Reefs 26:705-717.

Coles, S. L. 1984. Colonization of Hawaiian reef corals on new and denuded substrata in the 

vicinity of a Hawaiian power station. Coral Reefs 3:123-130.

Collins, M. R., C. Norwood, and A. Rourk. 2008. Shortnose and Atlantic sturgeon age-growth, 

status, diet, and genetics. Final Report to National Fish and Wildlife Foundation, 

Charleston, South Carolina.

Collins, M. R., S. G. Rogers, T. I. J. Smith, and M. L. Moser. 2000. Primary factors affecting 

sturgeon populations in the southeastern United States: Fishing mortality and degradation 

of essential habitats. Bulletin of Marine Science 66:917-928.

Corporation, T., P. Gas, and E. Company. 1982. Diablo Canyon Power Plant. Tera Corporation.

Coutant, C. C. 1973. Effects of thermal shock on the vulnerability of juvenile salmonids to 

predation. Journal of the Fisheries Research Board of Canada 31:351-354.

Coutant, C. C. 1987. Thermal preference: when does an asset become a liability? Environmental 

Biology of Fishes 18:161-172.

Craddock, D. R. 1976. Impact of cooling waters on the aquatic resources of the Pacific 

Northwest. Marine Fisheries Review:27-33.

Dadswell, M. J., B. D. Taubert, T. S. Squiers, D. Marchette, and J. Buckley. 1984. Synopsis of 

biological data on short nose sturgeon, Acipenser brevirostrum LeSueur 1818. NOAA 

Technical Report NMFS 14, FAO Fisheries Synopsis No. 140, NMFS, NOAA, U.S. 

Department of Commerce.
80

Dai, L., D. Vorselen, K. S. Korolev, and J. Gore. 2012. Generic indicators for loss of resilience 

before a tipping point leading to population collapse. Science 336:1175-1177.

DaVis, K. K. 1971. Levels of Residual Chlorine in Kaneohe Bay, Oahu, Hawaii, and the Effects 

of Residual Chlorine on Coral Planulae. University of Hawaii, Honolulu.

Deslauriers, D., and J. D. Kieffer. 2012. The effects of temperature on swimming performance of 

juvenile shortnose sturgeon (Acipenser brevirostrum). Journal of Applied Ichthyology 

28:176-181.

Dodd, C. K. 1988. Synopsis of the biological data on the loggerhead sea turtle: Caretta caretta 

(Linnaeus, 1758). Fish and Wildlife Service, U.S. Dept. of the Interior, Washington, D.C.

Dolphin, W. 1987. Prey densities and foraging of humpback whales, Megaptera novaeangliae. 

Experientia 43:468-471.

Dovel, W. L., and T. J. Berggren. 1983. Atlantic sturgeon of the Hudson Estuary, New York. 

New York Fish and Game Journal 30:140-172.

Drake, A., and L. Wilson. 1991. Eulachon, a fish to cure humanity. UBC Museum of 

Anthropology, Museum Note 32.

Dumbauld, B. R., D. L. Holden, and O. P. Langness. 2008. Do sturgeon limit burrowing shrimp 

populations in Pacific Northwest Estuaries? Environmental Biology of Fishes 83:283-

296.

Dunham, J. B., G. L. Vinyard, and B. E. Rieman. 1997. Habitat fragmentation and extinction risk 

of Lahontan cutthroat trout. North American Journal of Fisheries Management 17:1126-

1133.

ECONorthwest. 2011. Draft economic analysis of critical habitat designation for the Hawaiian 

monk seal. ECONorthwest, Eugene, Oregon.

ENSR. 2000. Demonstration Report for Pilgrim Nuclear Power Station, Prepared for Entergy 

Nuclear Generation Company.

ENSR Corporation. 2000. 316 demonstration report - Pilgrim Nuclear Power Station: redacted 

version.

EPA. 2011. Environmental and economic benefits analysis for proposed Section 316(b) existing 

facilities rule. U.S. Environmental Protection Agency.

EPA. 2013. ESA biological evaluation for CWA Section 316(b) rulemaking. Engineering and 

Analysis Division, Office of Water, U.S. Environmental Protection Agency, Washington, 

D.C.

Evans, M. S., G. J. Warren, and D. I. Page. 1986. The effects of power plant passage on 

zooplankton mortalities: Eight years of study at the Donald C. Cook Nuclear Plant. Water 

Research 20:725-734.

Fahrig, L. 2002. Effect of habitat fragmentation on the extinction threshold: a synthesis. 

Ecological Applications 12:346-353.

Fischer, J., and D. B. Lindenmayer. 2007. Landscape modification and habitat fragmentation: a 

synthesis. Global Ecology and Biogeography 16:265-280.

Fletcher, R. I. 1990. Flow dynamics and fish recovery experiments: water intake systems. 

Transactions of the American Fisheries Society 119:393-415.

Ford, J. K., and G. M. Ellis. 2006. Selective foraging by fish-eating killer whales Orcinus orca in 

British Columbia. Marine Ecology Progress Series 316:185-199.

Ford, J. K., G. M. Ellis, P. F. Olesiuk, and K. C. Balcomb. 2010. Linking killer whale survival 

and prey abundance: food limitation in the oceans' apex predator? Biology Letters 6:139-

142.
81

Ford, M. J., M. B. Hanson, J. A. Hempelmann, K. L. Ayres, C. K. Emmons, G. S. Schorr, R. W. 

Baird, K. C. Balcomb, S. K. Wasser, K. M. Parsons, and K. Balcomb-Bartok. 2011. 

Inferred Paternity and Male Reproductive Success in a Killer Whale (Orcinus orca) 

Population. J Hered 102:537-553.

Foster, A. M., and J. P. Clugston. 1997. Seasonal migration of Gulf sturgeon in the Suwannee 

River, Florida. Transactions of the American Fisheries Society 126.

Fox, D. A., J. E. Hightower, and F. M. Parauka. 2000. Gulf sturgeon spawning migration and 

habitat in the Choctawhatchee River system, Alabama-Florida. Transactions of the 

American Fisheries Society 129:811-826.

Gilbert, C. R. 1989. Species profiles: Life histories and environmental requirements of coastal 

fishes and invertebrates (Mid-Atlantic Bight)--Atlantic and shortnose sturgeons. U.S. 

Fish and Wildlife Service Biol. Rep. 82(11). U.S. Army Corps of Engineers TR EL-82-4,

Report prepared for National Wetlands Research Center, Research and Development, 

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

Experiment Station, Coastal Ecology Group , U.S. Army Corps of Engineers.

Gilpin, M. E., and M. E. Soule. 1986. Minimum viable populations: processes of species 

extinction.

Goetz, K. T., D. J. Rugh, A. J. Read, and R. C. Hobbs. 2007. Habitat use in a marine ecosystem: 

beluga whales Delphinapterus leucas in Cook Inlet, Alaska. Marine Ecology Progress 

Series 330:247-256.

Gregory, L. F., T. S. Gross, A. B. Bolten, K. Bjorndal, and L. J. Guillette. 1996. Plasma 

corticosterone concentrations associated with acute captivity stress in wild loggerhead sea 

turtles (Caretta caretta). General and Comparative Endocrinology 104:312-320.

Gruenthal, K. M., and R. S. Burton. 2008. Genetic structure of natural populations of the 

California black abalone (Haliotis cracherodii Leach, 1814), a candidate for endangered 

species status. Journal of Experimental Marine Biology and Ecology 355:47-58.

Grunwald, C., L. Maceda, J. Waldman, J. Stabile, and I. Wirgin. 2008. Conservation of Atlantic 

sturgeon Acipenser oxyrinchus oxyrinchus: delineation of stock structure and distinct 

population segments. Conservation Genetics 9:1111-1124.

Guenette, S., S. J. J. Heymans, V. Christensen, and A. W. Trites. 2006. Ecosystem models show 

combined effects of fishing, predation, competition, and ocean productivity on Steller sea 

lions (Eumetopias jubatus) in Alaska. Canadian Journal of Fisheries and Aquatic 

Sciences 63:2495-2517.

Haines, H., and W. C. Kleese. 1977. Effect of water temperature on a herpesvirus infection of 

sea turtles. Infection and Immunity 15:756-759.

Haley, N. 1998. A gastric lavage technique for characterizing diets of sturgeons. North American 

Journal of Fisheries Management 18:978 - 981.

Hanson, C. H., J. R. White, and H. W. Li. 1977. Entrapment and impingement of fish by power 

plant cooling-water intakes: an overview. Marine Fisheries Review 39:7-17.

Hanson, M. B., R. W. Baird, J. K. B. Ford, J. Hempelmann-Halos, D. M. Van Doornik, J. R. 

Candy, C. K. Emmons, G. S. Schorr, B. Gisborne, K. L. Ayres, S. K. Wasser, K. C. 

Balcomb, K. Balcomb-Bartok, J. G. Sneva, and M. J. Ford. 2010. Species and stock 

identification of prey consumed by endangered southern resident killer whales in their 

summer range. Endangered Species Research 11:69-82.
82

Harrison, J. T. 1987. The 40 MWe OTEC Plant at Kahe Point, Oahu, Hawaii: A case study of 

potential biological impacts. National Oceanic and Atmospheric Administration, National 

Marine Fisheries Service, Southwest Fisheries Center.

Hay, D. E., and P. B. McCarter. 2000. Status of the eulachon Thaleichthys pacificus in Canada. 

Department of Fisheries and Oceans Canada. Canadian Stock Assessment Secretariat, 

Ottawa, Ontario.

Hays, G. C. 2000. The implications of variable remigration intervals for the assessment of 

population size in marine turtles. J Theor Biol 206:221-227.

Heise, R. J., W. T. Slack, S. T. Ross, and M. A. Dugo. 2004. Spawning and associated 

movement patterns of Gulf sturgeon in the Pascagoula River drainage, Mississippi. 

Transactions of the American Fisheries Society 133:221-230.

Henwood, T. A., and W. E. Stuntz. 1987. Analysis of sea turtle captures and mortalities during 

commercial shrimp trawling. Fishery Bulletin 85:813-817.

Hilborn, R., S. P. Cox, F. M. D. Gulland, D. G. Hankin, N. T. Hobbs, D. E. Schindler, and A. W. 

Trites. 2012. The effects of salmon fisheries on Southern Resident killer whales: final 

report of the Independent Science Panel. Report prepared by the Independent Science 

Panel with assistance of D. R. Marmorek and A. W. Hall, ESSA Technologies Ltd., 

Vancouver, British Columbia, Canada for NMFS, NOAA, U.S. Department of 

Commerce, Seattle, Washington, and Fisheries and Oceans Canada, Vancouver, British 

Columbia, Canada, Independent Science Panel of the Bilateral Scientific Workshop 

Process to Evaluate the Effects of Salmon Fisheries.

Hobbs, R. C., K. E. W. Shelden, D. J. Rugh, and S. A. Norman. 2008. 2008 status review and 

extinction risk assessment of Cook Inlet belugas (Delphinapterus leucas). National 

Oceanic and Atmospheric Administration, National Marine Fisheries Service, Alaska 

Fisheries Science Center.

Hobday, A. J., and M. J. Tegner. 2000. Status review of white abalone (Haliotis sorenseni) 

throughout its range in California and Mexico. NOAA Technical Memorandum NOAATM-NMFS-SWR-035, Southwest Region Office, NMFS, NOAA, U.S. Department of 

Commerce, Long Beach, California.

Hung, T.-C., C.-C. Huang, and K.-T. Shao. 1998. Ecological Survey of Coastal I Water Adjacent 

to Nuclear Power I Plants in Taiwan. Chemistry and Ecology 15:129-142.

Huntington, H. 2000. Traditional knowledge of the ecology of belugas, Delphinapterus leucas, 

in Cook Inlet, Alaska. Marine Fisheries Review 62:134-140.

Janzen, D. H. 1974. The deflowering of Central America. Natural History 83:48-53.

Jessop, T. S., C. J. Limpus, and J. M. Whittier. 2002. Nocturnal activity in the green sea turtle 

alters daily profiles of melatonin and corticosterone. Hormones and behavior 41:357-365.

Jokiel, P., and S. Coles. 1990. Response of Hawaiian and other Indo-Pacific reef corals to 

elevated temperature. Coral Reefs 8:155-162.

Jokiel, P. L., and S. L. Coles. 1974. Effects of heated effluent on hermatypic corals at Kahe 

Point, Oahu.

Kahnle, A. W., K. A. Hattala, and K. A. McKown. 2007. Status of Atlantic sturgeon of the 

Hudson River Estuary, New York, USA. American Fisheries Society Symposium 

56:347-363.

Kahnle, A. W., K. A. Hattala, K. A. McKown, C. A. Shirey, M. R. Collins, J. T. S. Squiers, and 

T. Savoy. 1998. Stock status of Atlantic sturgeon of Atlantic coast estuaries. Draft III. 

Atlantic States Marine Fisheries Commission.
83

Kenney, R. 2007. Right Whales and Climate Change: Facing the Prospect of a Greenhouse 

Future. Pages Pp. 436-459 in S. Kraus and R. Rolland, editors. The Urban Whale: North 

Atlantic Right Whales at the Crossroads. Harvard University Press, Cambridge, MA.

Kenney, R. D., M. A. M. Hyman, R. E. Owen, G. P. Scott, and H. E. Winn. 1986. Estimation of 

prey densities required by western North Atlantic right whales. Marine Mammal Science 

2:1-13.

Kenney, R. D., G. P. Scott, T. J. Thompson, and H. E. Winn. 1997. Estimates of prey 

consumption and trophic impacts of cetaceans in the USA northeast continental shelf 

ecosystem. Journal of Northwest Atlantic Fishery Science 22:155-171.

Kieffer, M. C., and B. Kynard. 1993. Annual movements of shortnose and Atlantic sturgeons in 

the Merrimack River, Massachusetts. Transactions of the American Fisheries Society 

122:1088-1103.

Krahn, M. M., M. J. Ford, W. F. Perrin, P. R. Wade, R. P. Angliss, M. B. Hanson, B. L. Taylor, 

G. M. Ylitalo, M. Dahlheim, J. E. Stein, and R. S. Waples. 2004. 2004 status review of 

southern resident killer whales (Orcinus orca) under the Endangered Species Act. 

National Oceanic and Atmospheric Administration, National Marine Fisheries Service, 

Northwest Fisheries Science Center.

Kynard, B. 1997. Life history, latitudinal patterns, and status of the shortnose sturgeon, 

Acipenser brevirostrum. Environmental Biology of Fishes 48:319-334.

Kynard, B., and M. Horgan. 2002. Ontogenetic behavior and migration of Atlantic sturgeon, 

Acipenser oxyrinchus oxyrinchus, and shortnose sturgeon, A. brevirostrum, with notes on 

social behavior. Environmental Biology of Fishes 63:137-150.

Kynard, B., and E. Parker. 2004. Ontogenetic behavior and migration of Gulf of Mexico 

sturgeon, Acipenser oxyrinchus desotoi, with notes on body color and development. 

Environmental Biology of Fishes 70:43-55.

Kynard, B., E. Parker, and T. Parker. 2005. Behavior of early life intervals of Klamath River 

green sturgeon, Acipenser medirostris, with a note on body color. Environmental Biology 

of Fishes 72:85-97.

Lafferty, K. D., and A. M. Kuris. 1993. Mass mortality of abalone Haliotis cracherodii on the 

California Channel Islands: tests of epidemiological hypotheses. Marine EcologyProgress Series 96:239-239.

Leighton, D. L. 1972. Laboratory observations on the early growth of the abalone, Haliotis 

sorenseni, and the effect of temperature on larval development and settling success. 

Fishery Bulletin 70:373-381.

Litzow, M. A., K. M. Bailey, F. G. Prahl, and R. Heintz. 2006. Climate regime shifts and 

reorganization of fish communities: The essential fatty acid limitation hypothesis. Marine 

Ecology Progress Series 315:1-11.

Love, M. S., J. E. Caselle, and K. Herbinson. 1998. Declines in nearshore rockfish recruitment 

and populations in the southern California Bight as measured by impingement rates in

coastal electrical power generating stations. Fishery Bulletin 96:492-501.

Magnuson, J., K. Bjorndal, W. DuPaul, G. Graham, D. Owens, C. Peterson, P. Pritchard, J. 

Richardson, G. Saul, and C. West. 1990. Decline of the sea turtle; causes and prevention. 

Committee on Sea turtle Conservation, National Research Council (US). National 

Academy Press, Washington, DC.

Mahoney, B. A., and K. E. W. Shelden. 2000. Harvest history of belugas, Delphinapterus leucas, 

in Cook Inlet, Alaska. Marine Fisheries Review 62:124-133.
84

Martin, M., M. Stephenson, and J. Martin. 1977. Copper toxicity experiments in relation to 

abalone deaths observed in a power plant's cooling waters. Calif. Fish Game 63:95-100.

Masilamoni , J. G., K. S. Jesudoss, K. Nandakumar, K. K. Satpathy, K. V. K. Nair, and J. 

Azariah. 2000. Jellyfish ingress: a threat to the smooth operation of coastal power plants 

Current Science 79:567-569.

Mason Jr., W. T., and J. P. Clugston. 1993. Foods of the gulf sturgeon in the Suwannee River, 

Florida. Transactions of the American Fisheries Society 122:378-385.

Mayfield, R. B., and J. J. Cech. 2004. Temperature Effects on Green Sturgeon Bioenergetics. 

Transactions of the American Fisheries Society 133:961-970.

MBC Applied Environmental Sciences. 2001. Marine Mammal Protection Act Application for 

Small Take Permit. Costa Mesa, CA.

McLaren, J. B., and L. R. Tuttle Jr. 2000. Fish survival on fine mesh traveling screens. 

Environmental Science and Policy 3:S369-S376.

Melbourne, B. A., and A. Hastings. 2008. Extinction risk depends strongly on factors 

contributing to stochasticity. Nature 454:100-103.

Meylan, A., and S. Sadove. 1986. Cold stunning in Long Island Sound, New York. Marine 

Turtle Newsletter:7-8.

Meylan, A. M., B. Schroeder, and A. Mosier. 1994. Marine Turtle Nesting Activity in the State 

of Florida, 1979-1992. Page 83 in Proceedings of the Fourteenth Annual Symposium on 

Sea Turtle Biology and Conservation. NOAA Technical Memorandum NMFS-SEFSC351. National Malrine Fisheries Service, Southeast Fisheries Science Center, Hilton 

Head, SC.

Miara, A., C. J. Vörösmarty, R. J. Stewart, W. M. Wollheim, and B. Rosenzweig. 2013. Riverine 

ecosystem services and the thermoelectric sector: strategic issues facing the Northeastern 

United States. Environmental Research Letters 8.

Miller, M. 2004. The ecology and functional morphology of feeding of North American sturgeon 

and paddlefish. Pages 87-102 in G. T. O. LeBreton, F. W. H. Beamish, and R. S. 

McKinley, editors. Sturgeon and Paddlefish of North America.

Milton, S. L., and P. L. Lutz. 2003. Natural and human impacts on turtles. Pages 27-34 in G. 

Shigenaka, editor. Oil and Sea Turtles: Biology, Planning, and Response. National 

Oceanic and Atmospheric Administration, National Ocean Service, Office of Response 

and Restoration, Seattle.

Miner, C., J. M. Altstatt, P. T. Raimondi, and T. E. Minchinton. 2006. Recruitment failure and 

shifts in community structure following mass mortality limit recovery prospects of black 

abalone. MARINE ECOLOGY-PROGRESS SERIES- 327:107.

Morrow Jr., J. V., J. P. Kirk, K. J. Killgore, H. Rogillio, and C. Knight. 1998. Status and 

recovery potential of Gulf sturgeon in the Pearl River System, Louisiana–Mississippi. 

North American Journal of Fisheries Management 18:798-808.

Moulton, L. L. 1997. Early marine residence, growth, and feeding by juvenile salmon in northern 

Cook Inlet, Alaska. Alaska Fishery Research Bulletin 4.

National Research Council. 1990. Decline of the Sea Turtles: Causes and Prevention. 

.in N. A. Press, editor., Washington, D.C.

Neuman, M., B. Tissot, and G. Vanblaricom. 2010. Overall Status and Threats Assessment of 

Black Abalone (Haliotis Cracherodii Leach, 1814) Populations in California. Journal of 

Shellfish Research 29:577-586.
85

Niklitschek, E. J. 2001. Bioenergetics modeling and assessment of suitable habitat for juvenile 

Atlantic and shortnose sturgeons (Acipenser oxyrinchus and A. brevirostrum) in the 

Chesapeake Bay. Doctoral dissertation. University of Maryland at College Park, 

Solomons, Maryland.

Niklitschek, E. J., and D. H. Secor. 2005. Modeling spatial and temporal variation of suitable 

nursery habitats for Atlantic sturgeon in the Chesapeake Bay. Estuarine Coastal and Shelf 

Science 64:135-148.

NMFS. 1991. Final recovery plan for the humpback whale (Megaptera novaeangliae). National 

Marine Fisheries Service, Office of Protected Resources, Silver Spring, Maryland.

NMFS. 1992. Endangered Species Act - section 7 consultation biological opinion reinitiation on 

U.S. Nuclear Regulatory Commission's continued operation of the Salem and Hope 

Creek Nuclear Generating Stations on the eastern shore of the Delaware River in New 

Jersey. Northeast Region, NMFS, NOAA, U.S. Department of Commerce, Silver Spring, 

Maryland.

NMFS. 1998a. Final recovery plan for the shortnose sturgeon Acipenser brevirostrum. National 

Oceanic and Atmospheric Administration, National Marine Fisheries Service, Silver 

Spring, Maryland.

NMFS. 1998b. Status review of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus). National 

Oceanic and Atmospheric Administration, National Marine Fisheries Service.

NMFS. 2000a. Endangered Species Act - section 7 consultation biological opinion on U.S. 

Nuclear Regulatory Commission's operation of the cooling water intake system at the 

Brunswick Steam Electric Plant, Carolina Power and Light Company. Southeast Region, 

NMFS, NOAA, U.S. Department of Commerce, Silver Spring, Maryland.

NMFS. 2000b. Endangered Species Act section 7 consultation biological opinion on the 

incidental take permit for Roseton and Danskammer Point Generating Stations. 

Consultation #F/FPR/2000/01023, Northeast Regional Office, NMFS, NOAA, U.S. 

Department of Commerce.

NMFS. 2001. Endangered Species Act - section 7 consultation biological opinion on U.S. 

Nuclear Regulatory Commission's continued operation of the St. Lucie Nuclear Power 

Plant's circulating seawater cooling system, Jensen Beach, Hutchinson Island, Florida. 

F/SER/2000/01394, Southeast Region, NMFS, NOAA, U.S. Department of Commerce, 

St. Petersburg, Florida.

NMFS. 2002. Endangered Species Act - section 7 consultation biological opinion on U.S. 

Nuclear Regulatory Commission's operation of the cooling water intake system at the 

Crystal River Energy Complex. F/SER/2001/01080, Southeast Region, NMFS, NOAA, 

U.S. Department of Commerce, St. Petersburg, Florida.

NMFS. 2006a. Biological Opinion on Formal Consultation on the Continued Operation of the 

Diablo Canyon

Nuclear Power Plant and San Onofre Nuclear Generating Station.

NMFS. 2006b. Endangered Species Act - section 7 consultation biological opinion and incidental 

take statement on U.S. Nuclear Regulatory Commission's continued operation of the 

Diablo Canyon Nuclear Power Plant and San Onofre Nuclear Generating Station. 

Southwest Region, NMFS, NOAA, U.S. Department of Commerce, Long Beach, 

California.

NMFS. 2008a. Final white abalone recovery plan (Haliotis sorenseni). NMFS, NOAA, U.S. 

Department of Commerce, Long Beach, California.
86

NMFS. 2008b. Preliminary scientific conclusions of the review of the status of 5 species of 

rockfish: bocaccio (Sebastes paucispinis), canary rockfish (Sebastes pinniger), yelloweye 

rockfish (Sebastes ruberrimus), greenstriped rockfish (Sebastes elongatus) and redstripe 

rockfish (Sebastes proriger) in Puget Sound, Washington. NMFS, NWFSC, Seattle, 

Washignton.

NMFS. 2009. Smalltooth sawfish recovery plan (Pristis pectinata). Report prepared by the 

Smalltooth Sawfish Recovery Team for NMFS, NOAA, U.S. Department of Commerce, 

Silver Spring, Maryland.

NMFS. 2011. Endangered Species Act - section 7 consultation biological opinion reinitiation on 

the continued operation of Oyster Creek Nuclear Generating Station pursuant to a 

License issued by the NRC in April 2009. F/NER/2010/01855, Northeast Region, NMFS, 

NOAA, U.S. Department of Commerce.

NMFS. 2012. Letter to U.S. Nuclear Regulatory Commission re: Pilgrim Nuclear Power Station. 

Northeast Region, NMFS, NOAA, U.S. Department of Commerce, Gloucester, 

Massachusetts.

NMFS. 2013a. Endangered Species Act - section 7 consultation biological opinion on the relicensing of the Yadkin-Pee Dee Hydroelectric project (FERC Project No. 2206-030). 

F/SER/2009/05521, Southeast Regional Office, NMFS, NOAA, U.S. Department of 

Commerce, St. Petersburg, Florida.

NMFS. 2013b. Endangered Species Act - section 7 consultation biological opinion reinitiation on 

U.S. EPA's greenhouse gas permit to Florida Power & Light (FPL) for proposed 

improvements at the Port Everglades Next Generation Clean Energy Center. SER-2012-

657, Southeast Region, NMFS, NOAA, U.S. Department of Commerce, St. Petersburg, 

Florida.

NMFS. 2013c. Endangered Species Act section 7 consultation biological opinion on the 

continued operations of the Indian Point Nuclear Generating Station, Units 2 and 3, 

pursuant to existing and proposed renewed Nuclear Regulatory Commission operating 

licenses. NER-2012-2252, Northeast Regional Office, NMFS, NOAA, U.S. Department 

of Commerce.

NMFS USFWS. 2013. Leatherback sea turtle (Dermochelys coriacea) 5-year review: Summary 

and evaluation. NOAA, National Marine Fisheries Service, Office of Protected Resources 

and U.S. Fish and Wildlife Service, Southeast Region, Jacksonville Ecological Services 

Office.

Norem, A. 2005. Injury assessment of sea turtles utilizing the neritic zone of the southeastern 

United States. University of Florida.

Normandeau Associates, I. 2011. Impingement of organisms on the intake screens at Pilgrim 

Nuclear Power Station, January - December 2010 Normandeau Associates, Inc.,

Falmouth, Massachusetts.

NRC. 1979. Docket Numbers 50-272, 50-311, 50-354, 50-355 to Mr. Julio Morales-Sanchez, 

Director Enforcement Division Environmental Protection Agency. October 31, 1979.

O’Leary, S. J., K. J. Dunton, T. L. King, M. G. Frisk, and D. D. Chapman. 2014. Genetic 

diversity and effective size of Atlantic sturgeon, Acipenser oxyrhinchus oxyrhinchus river 

spawning populations estimated from the microsatellite genotypes of marine-captured 

juveniles. Conservation Genetics:1-9.

Oakley, N. C. 2003. Status of shortnose sturgeon, Acipenser brevirostrum, in the Neuse River, 

North Carolina. North Carolina State University, Raleigh, North Carolina.
87

Oleson, E., C. Boggs, K. Forney, M. Hanson, D. Kobayashi, B. Taylor, P. Wade, and G. Ylitalo. 

2010. Status review of Hawaiian insular false killer whales (Pseudorca

crassidens) under the Endangered Species Act. Page 140 in U. S. D. o. Commerce, editor. 

NOAA Technical Memo.

Ordal, E. J., and R. E. Pacha. 1963. The effects of temperature on disease in fish. Pages 39-56 

Water temperature: influence, effects and control. Proceedings of the Twelfth Pacific 

Northwest Symposium on Water Pollution Research, Portland, Oregon.

Pace, R. I., and R. Merrick. 2008. Northwest Atlantic Ocean Habitats Important to the 

Conservation ofNorth Atlantic Right Whales (Eubalaena glacialis). NEFSC Ref. Doc. 08-

07.

Palsson, W. A., T.-S. Tsou, G. G. Bargmann, R. M. Buckley, J. E. West, M. L. Mills, Y. W. 

Cheng, and R. E. Pacunski. 2009. The biology and assessment of rockfishes in Puget 

Sound. FPT 09-04, Fish Management Division, Fish Program, Washington Department 

of Fish and Wildlife.

Payne, S. A., B. A. Johnson, and R. S. Otto. 1999. Proximate composition of some north-eastern 

Pacific forage fish species. Fisheries Oceanography 8:159-177.

Pearse, D., and J. Avise. 2001. Turtle mating systems: behavior, sperm storage, and genetic 

paternity. Journal of Heredity 92:206-211.

Peterson, D. L., P. Schueller, R. DeVries, J. Fleming, C. Grunwald, and I. Wirgin. 2008. Annual 

run size and genetic characteristics of Atlantic sturgeon in the Altamaha River, Georgia. 

Transactions of the American Fisheries Society 137:393-401.

Piatt, J. F., and D. A. Methven. 1992. Threshold foraging behavior of baleen whales. Marine 

Ecology Progress Series 84:205-210.

Picton, H. D. 1979. The application of insular biogeographic theory to the conservation of large 

mammals in the northern Rocky Mountains. Biological Conservation 15:73-79.

Pine, W. E., M. S. Allen, and V. J. Dreitz. 2001. Population viability of the Gulf of Mexico 

sturgeon: Inferences from capture–recapture and age-structured models. Transactions of 

the American Fisheries Society 130:1164-1174.

Plotkin, P. T. 1995. National Marine Fisheries Service and U. S. Fish and Wildlife Service Status

Reviews for Sea Turtles Listed under the Endangered Species Act of 1973.in N. Department of 

Commerce, editor. National Marine

Fisheries Service. Silver Spring, Silver Spring, MD.

Poletto, J. B., D. E. Cocherell, N. Ho, J. J. Cech, A. P. Klimley, and N. A. Fangue. 2014. 

Juvenile green sturgeon (Acipenser medirostris) and white sturgeon (Acipenser 

transmontanus) behavior near water-diversion fish screens: experiments in a laboratory 

swimming flume. Canadian Journal of Fisheries and Aquatic Sciences:1-9.

Prange, J., and W. Dennison. 2000. Physiological responses of five seagrass species to trace 

metals. Mar Pollut Bull 41:327-336.

Prentice, E. F., and F. J. Ossiander. 1974. Fish diversion systems and biological investigation of 

horizontal traveling screen Model VIII. Pages 205-214 in Proceedings of the Second 

Workshop on Entrainment and Intake Screening. Johns Hopkins University, Balitmore, 

Maryland.

Price, E. R., B. P. Wallace, R. D. Reina, J. R. Spotila, F. V. Paladino, R. Piedra, and E. Velez. 

2004. Size, growth, and reproductive output of adult female leatherback turtles 

Dermochelys coriacea. Endangered Species Research 5:1-8.
88

Pritchard, P. C. H. 1982. Nesting of the leatherback turtle, Dermochelys coriacea in Pacific 

Mexico, with a new estimate of the world population status. Copeia 4:741-747.

Raimondi, P. T., M. C. Wilson, R. F. Ambrose, J. M. Engle, and T. E. Minchinton. 2002. 

Continued declines of black abalone along the coast of California: are mass mortalities 

related to El Niño events? Marine Ecology-Progress Series 242:143-152.

Randall, M. T., and K. J. Sulak. 2012. Evidence of autumn spawning in Suwannee River gulf 

sturgeon, Acipenser oxyrinchus desotoi (Vladykov, 1955). Journal of Applied 

Ichthyology 28:489-495.

Reina, R. D., P. A. Mayor, J. R. Spotila, R. Piedra, and F. V. Paladino. 2002. Nesting ecology of 

the leatherback turtle, Dermochelys coriacea, at Parque Nacional Marino Las Baulas, 

Costa Rica: 1988-1989 to 1999-2000. Copeia 2002:653-664.

Richmond, R. H. 1993. Coral reefs: present problems and future concerns resulting from 

anthropogenic disturbance. American Zoologist 33:524-536.

Robinson, K. 2010. Effects of thermal power station effluent on the seagrass benthic 

communities of Lake Macquarie, a New South Wales coastal lagoon. Wetlands 

(Australia) 7:1-12.

Roessler, M. 1971. Environmental changes associated with a Florida power plant. Mar Pollut 

Bull 2:87-90.

Roessler, M. A., and J. Zieman. 1969. The effects of thermal additions on the biota of southern 

Biscayne Bay, Florida. Proc. Gulf Caribb. Fish Inst. 22nd Annu Ser:136-145.

Rogers, S. G., and W. Weber. 1995. Status and restoration of Atlantic and shortnose sturgeons in 

Georgia., National Oceanic and Atmospheric Administration, National Marine Fisheries 

Service, Southeast Regional Office, St. Petersburg, Florida.

Rogillio, H. E., R. T. Ruth, E. H. Behrens, C. N. Doolittle, W. J. Granger, and J. P. Kirk. 2007. 

Gulf Sturgeon Movements in the Pearl River Drainage and the Mississippi Sound. North 

American Journal of Fisheries Management 27:89-95.

Scheffer, M., S. R. Carpenter, T. M. Lenton, J. Bascompte, W. Brock, V. Dakos, J. van de 

Koppel, I. A. van de Leemput, S. A. Levin, E. H. van Nes, M. Pascual, and J. 

Vandermeer. 2012. Anticipating critical transitions. Science 338:344-348.

Secor, D. H., and T. E. Gunderson. 1998. Effects of hypoxia and temperature on survival, 

growth, and respiration of juvenile Atlantic sturgeon, Acipenser oxyrinchus. Fishery 

Bulletin 96:603-613.

Secor, D. H., and E. J. Niklitschek. 2001. Hypoxia and sturgeons: report to the Chesapeake Bay 

Program Dissolved Oxygen Criteria Team. Chesapeake Biological Laboratory, 

University of Maryland Center for Environmental Science, Solomons, Maryland.

Secor, D. H., and E. J. Niklitschek. 2002. Sensitivity of sturgeons to environmental hypoxia: A 

review of physiological and ecological evidence. Pages 61-78 in R. V. Thurston, editor. 

Fish Physiology, Toxicology, and Water Quality. U.S. Environmental Protection Agency, 

Office of Research and Development, Ecosystems Research Division, Athens, Georgia.

Shelden, K. E., S. E. Moore, J. M. Waite, P. R. Wade, and D. J. Rugh. 2005. Historic and current 

habitat use by North Pacific right whales Eubalaena japonica in the Bering Sea and Gulf 

of Alaska. Mammal review 35:129-155.

Shields, P., and A. Dupuis. 2013. Upper Cook Inlet commercial fisheries annual managem.

Sigler, M. F., D. J. Tollit, J. J. Vollenweider, J. F. Thedinga, D. J. Csepp, J. N. Womble, M. A. 

Wong, M. J. Rehberg, and A. W. Trites. 2009. Steller sea lion foraging response to 

seasonal changes in prey availability. Marine Ecology Progress Series 388:243-261.
89

Sigler, M. F., J. N. Womble, and J. J. Vollenweider. 2004. Availability to Steller sea lions 

(Eumetopias jubatus) of a seasonal prey resource: A prespawning aggregation of 

eulachon (Thaleichthys pacificus). Canadian Journal of Fisheries and Aquatic Sciences 

61:1475-1484.

Simpfendorfer, C. 2001. Essential habitat of smalltooth sawfish (Pristis peetinata) Mote Marine 

Laboratory Technical Report 786, Center for Shark Research, Mote Marine Laboratory.

Simpfendorfer, C. A., and T. R. Wiley. 2004. Determination of the distribution of Florida’s 

remnant sawfish population, and identification of areas critical to their conservation. 

Mote Marine Laboratory, Sarasota, Florida.

Sinclair, E., and T. Zeppelin. 2002. Seasonal and spatial differences in diet in the western stock 

of Steller sea lion (Eumetopias jubatus). Journal of Mammalogy 83:973-990.

Skjeveland, J. E., S. A. Welsh, M. F. Mangold, S. M. Eyler, and S. Nachbar. 2000. A report of 

investigations and research on Atlantic and shortnose sturgeon in Maryland waters of 

Chesapeake Bay (1996-2000). U.S. Fish and Wildlife Service, Annapolis, Maryland.

Smith, B. D., S. d. C. Wilkins, and T. J. Donaldson. 2005. Environmental impact of the cooling 

water intake structure, Tanguisson Power Plant Section 316b study, Phase I: a screening 

analysis. Technical Report No. 111 submitted to Environmental Engineering and Pruvient 

Energy, Inc., Guam, Marine Laboratory, University of Guam.

Smith, W. E., and R. W. Saalfeld. 1955. Studies on Columbia River smelt Thaleichthys pacificus

(Richardson). Washington Department of Fisheries, Fisheries Research Paper 1:3-26.

Soulé, M. E., and B. A. Wilcox, editors. 1980. Conservation biology: an evolutionary-ecological 

perspective. Sinauer, Sunderland, Massachusetts.

Spotila, J. R., A. E. Dunham, A. J. Leslie, A. C. Steyermark, P. T. Plotkin, and F. V. Paladino. 

1996. Worldwide population decline of Dermochelys coriacea: Are leatherback turtles 

going extinct? Chelonian Conservation and Biology 2:209-222.

Spotila, J. R., M. P. O'Connor, and F. V. Paladino. 1997. Thermal biology. Pages 297-314 in P. 

L. Lutz and J. A. Musick, editors. The Biology of Sea Turtles. CRC Press, Boca Raton, 

Florida.

Sprague, R., C. Littnan, and J. Walters. 2013. Estimation of Hawaiian monk seal consumption in 

relation to ecosystem biomass and overlap with fisheries in the main Hawaiian Islands.in

P. I. F. S. Center, editor.

Stabenau, E., and K. Vietti. 1999. Physiological effects of short-term submergence of loggerhead 

sea turtles, Caretta caretta, in TED-equipped commercial fishing nets. .

Stamieszkin, K., L. Ganley, Charles A. Mayo, Ruth H. Leeney, and Marilyn K. Marx. 2010. 

Surveillance, monitoring and management of North Atlantic right whales in Cape Cod 

Bay and adjacent waters – 2010: final report. Provincetown Center for Coastal Studies, 

Provincetown, Massachusetts.

Steinbeck, J., J. Groff, C. Friedman, T. McDowell, and R. Hedrick. 1992. Investigations into 

mortality among populations of the California black abalone, Haliotis cracherodii, on the 

central coast of California, USA. Abalone of the world: biology, fisheries and culture. 

Fishing News Books, Blackwell Scientific, Cambridge, UK:203-213.

Stinson, M. L. 1984. Biology of sea turtles in San Diego Bay, California, and in the northeastern 

Pacific. San Diego State University.

Sturdevant, M. V., T. M. Willette, S. Jewett, and E. Deberec. 1999. Diet composition, diet 

overlap, and size of 14 species of forage fish collected monthly in PWS, Alaska, 1994-

1995.
90

Sulak, K. J., J. J. Berg, and M. Randall. 2012. Feeding habitats of the Gulf sturgeon, Acipenser 

oxyrinchus desotoi, in the Suwannee and Yellow rivers, Florida, as identified by multiple 

stable isotope analyses. Environmental Biology of Fishes 95:237-258.

Sulak, K. J., and J. P. Clugston. 1999. Recent advances in life history of Gulf of Mexico 

sturgeon, Acipenser oxyrinchus desotoi, in the Suwannee river, Florida, USA: a synopsis. 

Journal of Applied Ichthyology 15:116-128.

Sustainable Fisheries Partnership. 2014. Alaska wild salmon. Sustainable Fisheries Partnership, 

http://www.sustainablefish.org/fisheries-improvement/supply-chainroundtables/salmon/alaska-salmon.

Sweka, J. A., J. Mohler, M. J. Millard, T. Kehler, A. Kahnle, K. Hattala, G. Kenney, and A. 

Higgs. 2007. Juvenile Atlantic sturgeon habitat use in Newburgh and Haverstraw Bays of 

the Hudson River: implications for population monitoring. North American Journal of 

Fisheries Management 27.

Sylvester, J. R. 1972. Effect of thermal stress on predator avoidance in sockeye salmon. Journal 

of the Fisheries Research Board of Canada 29:601-603.

Taubert, B. D., and M. J. Dadswell. 1980. Description of some larval shortnose sturgeon 

(Acipenser brevirostrum) from the Holyoke Pool, Connecticut River, Massachusetts, 

U.S.A., and the Saint John River, New Brunswick, Canada. Canadian Journal of Zoology 

58:1125-1128.

Tenera. 2007a. Assessing Power Plant Cooling Water Intake System Entrainment Impacts.

Tenera. 2007b. Moss Landing Power Plant Units 1&2 and Units 6&7 Impingement Study Data 

Report 

Thorhaug, A. 1979. The flowering and fruiting of restored< i> Thalassia</i> beds: A preliminary 

note. Aquatic Botany 6:189-192.

Thorhaug, A., N. Blake, and P. Schroeder. 1978. The effect of heated effluents from power 

plants on seagrass (< i> Thalassia</i>) communities quantitatively comparing estuaries in 

the subtropics to the tropics. Mar Pollut Bull 9:181-187.

Tissot, B. N. 1995. Recruitment, growth, and survivorship of black abalone on Santa Cruz Island 

following mass mortality. Bulletin of the Southern California Academy of Sciences 

94:179-189.

Trites, A., and C. Donnelly. 2003. The decline of Steller sea lions Eumetopias jubatus in Alaska: 

a review of the nutritional stress hypothesis. Mammal review 33:3-28.

Trites, A. W., A. J. Miller, H. D. G. Maschner, M. A. Alexander, S. J. Bograd, J. A. Calder, A. 

Capotondi, K. O. Coyle, E. D. Lorenzo, B. P. Finney, E. J. Gregr, C. E. Grosch, S. R. 

Hare, G. L. Hunt, J. Jahncke, N. B. Kachel, H.-J. Kim, C. Ladd, N. J. Mantua, C. 

Marzban, W. Maslowski, R. O. Y. Mendelssohn, D. J. Neilson, S. R. Okkonen, J. E. 

Overland, K. L. Reedy-Maschner, T. C. Royer, F. B. Schwing, J. X. L. Wang, and A. J. 

Winship. 2007. Bottom-up forcing and the decline of Steller sea lions (Eumetopias 

jubatus) in Alaska: assessing the ocean climate hypothesis. Fisheries Oceanography 

16:46-67.

USFWS, and NMFS. 2009. Gulf sturgeon (Acipenser oxyrinchus desotoi), 5-year review: 

summary and evaluation. Panama City Ecological Services Field Office, U.S. Fish and 

Wildlife Service, U.S. Department of the Interior and Southeast Region, NMFS, NOAA, 

U.S. Department of Commerce.

Vos, D. J., and K. E. W. Shelden. 2005. Unusual mortality in the depleted Cook Inlet beluga 

(Delphinapterus leucas) population. Northwestern Naturalist 86:59-65.
91

Vos, D. J., K. E. W. Shelden, and J. Orr. 2005. Unusual mortality in the depleted Cook Inlet 

beluga (Delphinapterus leucas) population. Northwestern Naturalist 86:59-65.

Wallace, B. P., and T. T. Jones. 2008. What makes marine turtles go: A review of metabolic 

rates and their consequences. Journal of Experimental Marine Biology and Ecology 

356:8-24.

Wallace, B. P., S. S. Kilham, F. V. Paladino, and J. R. Spotila. 2006. Energy budget calculations 

indicate resource limitation in Eastern Pacific leatherback turtles. Marine Ecology 

Progress Series 318:263-270.

Wallace, B. P., P. R. Sotherland, P. S. Tomillo, R. D. Reina, J. R. Spotila, and F. V. Paladino. 

2007. Maternal investment in reproduction and its consequences in leatherback turtles. 

Oecologia 152:37-47.

Ward, E. J., M. J. Ford, R. G. Kope, J. K. B. Ford, L. A. Velez-Espino, C. K. Parken, L. W. 

Lavoy, M. B. Hanson, and K. C. Balcomb. 2013. Estimating the impacts of chinook 

salmon abundance and prey removal by ocean fishing on Southern Resident killer whale 

population dynamics. NOAA, National Marine Fisheries Service, Northwest Fisheries 

Science Center.

Ward, E. J., E. E. Holmes, and K. C. Balcomb. 2009. Quantifying the effects of prey abundance 

on killer whale reproduction. Journal of Applied Ecology 46:632-640.

WDFW, and ODFW. 2001. Washington and Oregon eulachon management plan. Washington 

Department of Fish and Wildlife and Oregon Department of Fish and Wildlife.

Weinrich, M. 1998. Early experience in habitat choice by humpback whales (Megaptera 

novaeangliae). Journal of Mammalogy 79:163-170.

Weishampel, J. F., D. A. Bagley, L. M. Ehrhart, and B. L. Rodenbeck. 2003. Spatiotemporal 

patterns of annual sea turtle nesting behaviors along an East Central Florida beach. 

Biological Conservation 110:295-303.

Welsh, S. A., M. F. Mangold, J. E. Skjeveland, and A. J. Spells. 2002. Distribution and 

movement of shortnose sturgeon (Acipenser brevirostrum) in Chesapeake Bay. Estuaries 

25:101-104.

Werme, C., A. C. Rex, M. P. Hall, K. E. Keay, W. S. Leo, M. J. Mickelson, and C. D. Hunt. 

2011. 2010 outfall monitoring overview. Environmental Quality Department, 

Massachusetts Water Resources Authority.

Whitcomb, R. F., C. S. Robbins, J. F. Lynch, B. L. Whitcomb, M. K. Klimkiewicz, and D. 

Bystrak. 1981. Effects of forest fragmentation on avifauna of the eastern deciduous 

forest. Pages 126-205 in R. L. Burgess and D. M. Sharpe, editors. Forest island dynamics 

in man-dominated landscapes. Springer-Verlag, New York, New York.

White, J. W., K. J. Nickols, L. Clarke, and J. L. Largier. 2010. Larval entrainment in cooling 

water intakes: spatially explicit models reveal effects on benthic metapopulations and 

shortcomings of traditional assessments. Canadian Journal of Fisheries and Aquatic 

Sciences 67:2014-2031.

Wilcox, B. A., and D. D. Murphy. 1985. Conservation strategy: the effects of fragmentation on 

extinction. The American Naturalist 125:879-887.

Willette, T. M. 2010. Eulachon and Pacific salmon abundances and run timing in Upper Cook 

Inlet, Alaska. Cook Inlet Beluga Whale Recovery Plan Joint Science Panel and 

Stakeholder Panel Meeting. Alaska Department of Fish and Game, Anchorage, Alaska.

Williams, S. L., and S. L. Schroeder. 2004. Eradication of the invasive seaweed Caulerpa 

taxifolia by chlorine bleach. Marine Ecology Progress Series 272:69-76.
92

Winship, A. J., A. W. Trites, and D. A. S. Rosen. 2002. A bioenergetic model for estimating the 

food requirements of Steller sea lions Eumetopias jubatus in Alaska, USA. Marine 

Ecology Progress Series 229:291-312.

Witherington, B. E., and L. M. Ehrhart. 1989. Hypothermic stunning and mortality of marine 

turtles in the Indian River Lagoon System, Florida. Copeia 1989:696-703.

Woodland, R. J., and D. H. Secor. 2007. Year-class strength and recovery of endangered 

shortnose sturgeon in the Hudson River, New York. Transactions of the American 

Fisheries Society 136:72-81.

Zehfuss, K. P., J. E. Hightower, and K. H. Pollock. 1999. Abundance of Gulf Sturgeon in the 

Apalachicola River, Florida. Transactions of the American Fisheries Society 128:130-

143.

Ziegeweid, J. R., C. A. Jennings, and D. L. Peterson. 2008. Thermal maxima for juvenile 

shortnose sturgeon acclimated to different temperatures. Environmental Biology of 

Fishes 82:299-307.
Appendix D

Example of Species Specific 

Control Measures, Monitoring, and Reporting.
Example Species Specific Control Measures Control Measures

1.0 Cetaceans

If Southern Resident killer whales or Cook Inlet beluga whales may occur within the 

area(s) directly or indirectly affected by your cooling water intake structure(s), you must:

1.1) Implement the requirements as described for salmonids (see 7.0)

2.0 Pinnipeds 

If ESA-listed seals, sea lions, or fur seals or their designated critical habitat may occur 

within the area(s) directly or indirectly affected by your cooling water intake structure(s), 

you must:

2.1) You must contact the NMFS Regional Office to determine whether you need 

to apply for a Marine Mammal Protection Act permit.

2.2) Install large organism exclusion devices, having a distance between 

exclusion bars of no greater than nine inches; and

2.3) Monitor the intake structure(s) at least every 4 hours (unless otherwise 

determined by the NMFS Regional Office) for the presence of pinnipeds. In the 

event a pinniped is found in the intake structure, you must: 

 Observe the animal to determine if it has any injuries or appears stressed 

or unhealthy.

 Immediately contact the NMFS Regional marine mammal stranding 

coordinator and follow their instructions

 Gather and record information on the animal, including the species, size, 

condition (dead, injured, or healthy/released). Also record any tags or 

markings and include photos of the animal in the intake structure. Enter 

this information on a Marine Mammal Stranding Report Form, which 

must be submitted to the NMFS Regional marine mammal stranding 

coordinator within 48 hours of discovery. Also enter this information in

your annual incidental take report, which must be submitted to the NMFS 

Regional Office, NMFS Office of Protected Resources, and Director.

 For healthy, sick, or injured pinnipeds, follow the procedure in 2.4.

 For dead pinnipeds, follow the procedure in 2.5.

2.4) If a live pinniped is impinged, entrapped, or entrained, you must contact and 

follow the instructions of the NMFS Regional marine mammal stranding 

coordinator. You must take all measures necessary to enable the pinniped to swim 

out of the intake structure on its own (e.g., reduce flow, turn off pumps, or close 

cover to intake wells so that sunlight enters only through the intake entrance). 

You must continue to monitor the pinniped every 15 minutes until it leaves or is 

released. Do not attempt to capture or handle the pinniped unless you are 

instructed to do so by the Regional marine mammal stranding coordinator. If you 

are instructed to capture or handle the pinniped, you must follow the instructions

provided by the NMFS Regional marine mammal stranding coordinator.
2.5) If you observe a dead pinniped in the area(s) directly or indirectly affected 

by your cooling water intake structure(s), you must contact and follow the 

instructions of NMFS Regional marine mammal stranding coordinator. You must 

follow the NMFS Regional marine mammal stranding coordinator’s protocols for 

collecting, storing, and transporting the carcass for necropsy. If instructed to do 

so, you must follow the NMFS Regional marine mammal stranding coordinator’s 

protocol for sampling and disposing of the carcass.

3.0 Sea Turtles

If Federally-listed sea turtles or their designated critical habitat (e.g., prey) may occur

within the area(s) directly or indirectly affected by your cooling water intake structure(s), 

you must:

3.1) Install large organism exclusion devices, having a distance between 

exclusion bars of no greater than nine inches; and

3.2) Monitor the intake structure(s) at least every 4 hours (unless otherwise 

determined by the NMFS Regional Office) for the presence of sea turtles. In the 

event a sea turtle is found in the intake structure, you must: 

 Observe the turtle to determine if it has any injuries or appears stressed or 

unhealthy.

 Immediately contact the NMFS Regional sea turtle stranding coordinator 

and regional stranding network center and follow their instructions

 Gather and record information on the turtle, including the species, size, 

condition (dead, injured, or healthy/released). Also record any tags or 

markings on the turtle and include photos of the turtle in the intake 

structure. Enter this information on a Sea Turtle Stranding Report Form 

and submit to the sea turtle stranding coordinator and NMFS Regional 

Office within 48 hours. Also enter this information in your annual 

incidental take report, which must be submitted to the NMFS Regional 

Office, NMFS Office of Protected Resources, and Director.

 For healthy turtles, follow the procedure in 3.3.

 For sick or injured turtles, follow the procedure in 3.3, and 3.4, if 

instructed to do so.

 For dead turtles, follow the procedure in 3.5.

 For hatchlings, you must contact the NMFS Regional Office for additional 

requirements and instructions.

3.3) If a live sea turtle is impinged, entrained, or otherwise adversely affected, 

you must contact and follow the instructions of the NMFS Regional sea turtle 

stranding coordinator and regional stranding network center. You must take all 

measures necessary to enable the sea turtle to swim out of the intake structure on 

its own (e.g., reduce flow, turn off pumps, or close cover to intake wells so that 

sunlight enters only through the intake entrance). You must continue to monitor 

the turtle every 15 minutes until it leaves or is released. Do not attempt to capture 

or handle the sea turtle unless you are instructed to do so by the NMFS Regional 

sea turtle stranding coordinator and regional stranding network center. If you are 
instructed to capture or handle the sea turtle, you must follow the following 

guidelines or other instructions provided by the NMFS Regional sea turtle 

stranding coordinator or the regional stranding network center: 

3.3.1. All sea turtles should be handled with care.

3.3.2. Pick up sea turtles by the front and back of the top of the carapace 

or by the flippers. Do not pick up sea turtles by the head or tail.

3.3.3. Dip nets, cargo nets, and other equipment should be used to lift and 

move turtles whenever possible.

3.3.4. If a sea turtle is actively moving, it should be released (only if 

healthy) or picked up by the NMFS Regional stranding coordinator or

regional sea turtle stranding network center.

3.4) To resuscitate a comatose (non responsive) turtle, follow the following 

guidelines (50 CFR 223.206(d)(1): 

3.4.1. Place the animal on its bottom shell (plastron) so that the turtle is 

right side up.

3.4.2 Elevate the hindquarters at least 6 inches for a period no less than 4 

hours and no more than 24 hours.

3.4.3. A reflex test, performed by gently touching the eye and pinching 

the tail, must be administered at least every 3 hours to 

determine if the sea turtle is responsive.

3.4.4. Keep the turtle in a safe, contained place, shaded and moist (e.g., 

with a watersoaked towel over the eyes, carapace, and flippers). Observe 

the turtle for up to 24 hours.

3.4.5 If the turtle begins actively moving, do not release the turtle until 

the stranding coordinator or rehabilitation center can evaluate it.

3.4.6. If the turtle fails to move within 24 hours, it should be transported 

to the NMFS stranding coordinator or rehabilitation center for necropsy.

3.5) If you observe a dead sea turtle the area(a) directly or indirectly affected by 

your cooling water intake structure(s), you must contact and follow the 

instructions of the NMFS Regional sea turtle stranding coordinator, which may 

include contacting a sea turtle rehabilitation center. You must follow the NMFS 

stranding coordinator or rehabilitation center’s protocols for collecting, storing, 

and transporting the carcass for necropsy. If instructed to do so, you must follow 

the rehabilitation center’s protocol for sampling and disposing of the carcass.

If leatherback sea turtle designated critical habitat may occur within the area(s) directly 

or indirectly affected by your cooling water intake structure(s), you must:

3.8) Conduct monitoring studies to determine if jellyfish (e.g., larvae, polyps, 

medusa) are being entrained or impinged by your cooling water intake structure 

and provide this information to the appropriate NMFS Regional Office on an 

annual basis. Monitoring should:

 Be conducted between May 1st and November 30th or otherwise based on 

the timing and mode of local jellyfish blooms within designated critical 

habitat.
 Identify planula, polyps, and medusa to the lowest taxonomic level 

possible.

 Annual reports should include descriptions of weekly, monthly, and 

annual estimates of jellyfish entrainment across life stages.

 Annual reports should include a complete description of the methodology 

used to estimate jellyfish entrainment.

4.0 Sawfish

If Federally-listed sawfish may occur within the area(s) directly or indirectly affected by 

your cooling water intake structure(s), you must:

4.1) Install large organism exclusion devices, having a distance between 

exclusion bars of no greater than nine inches; and

4.2) Monitor the intake structure(s) at least every 4 hours (unless otherwise 

determined by the NMFS Regional Office) for the presence of sawfish. In the 

event a sawfish is found in the intake structure, you must: 

 Observe the sawfish to determine if it has any injuries or appears stressed 

or unhealthy.

 Immediately contact the NMFS Regional Office and follow their 

instructions

 Gather and record information on the sawfish, including the species, size, 

condition (dead, injured, or healthy/released). Also record any tags or 

markings and include photos of the sawfish in the intake structure. Record

this information in your annual incidental take report, which must be 

submitted to the NMFS Regional Office, NMFS Office of Protected 

Resources, and Director.

 For live sawfish, follow the procedure in 4.3.

 For dead sawfish, follow the procedure in 4.4.

4.3) If a live sawfish is impinged, entrapped, or entrained, you must contact and 

follow the instructions of the NMFS Regional Office. You must take all measures 

necessary to enable the sawfish to swim out of the intake structure on its own 

(e.g., reduce flow, turn off pumps, or close cover to intake wells so that sunlight 

enters only through the intake entrance). You must continue to monitor the 

sawfish every 15 minutes until it leaves or is released. Do not attempt to capture 

or handle the sawfish unless you are instructed to do so by NMFS. If you are 

instructed to capture or handle the sawfish, you must follow the following 

guidelines or other instructions provided by NMFS: 

4.3.1. All sawfish should be handled with care.

4.3.2. Pick up sawfish at the center of the body. Do not pick up sawfish

by the head or tail.

4.3.3. Dip nets, cargo nets, and other equipment should be used to lift and 

move sawfish whenever possible.

4.3.4. If a sawfish is actively moving, it should be released 

4.4) If you observe a dead sawfish the area(a) directly or indirectly affected by 

your cooling water intake structure(s), you must contact and follow the 

instructions of NMFS. You must follow NMFS’ protocols for collecting, storing, 
and transporting the carcass for necropsy. If instructed to do so, you must follow 

NMFS’ protocol for sampling and disposing of the carcass.

4.5) For juvenile sawfish, you must also:

4.5.1 Use diversion structures near the intake canal to block sawfish

from entering the cooling water intake structure.

4.5.2 Use mechanisms to reduce approach-flow velocity (i.e., the Vshaped screen) that will allow sawfish to avoid impingement on their own 

power should they make it into the canal.

4.5.2 Monitor diversion structure on a daily basis.

5.0 Abalone

5.0 Abalone

If Federally-listed abalone, their designated critical habitat, or habitats suitable for 

abalone (e.g., rocky intertidal or subtidal habitats within the depth range of the species) 

occur within the intake or discharge structure’s area of impact (including within XX

meters of the area of impact), you must:

5.1) Conduct a benthic and/or intertidal habitat characterization study within the 

area affected by your cooling water intake structure and discharge, and submit 

this information along with your NPDES permit application. This benthic habitat 

characterization study should include the following information:

5.1.1. A map of the study area, indicating the area of impact for the intake 

and/or discharge structure(s). 

5.1.2. Substrate type and extent and distance from intake/discharge

5.1.3. Water depth (for subtidal studies)

5.1.4. Water temperature

5.1.5. Current patterns 

5.1.6. Observation of abalone individuals in the study area, including but 

not limited to: 

5.1.6.1. Identification of abalone species and their location

5.1.6.2. Enumeration of the number of individuals by species and 

the estimated shell length, habitat type (e.g., in a crevice, on open 

vertical or horizontal surface), and nearest neighbor distance (e.g., 

distance to the nearest other abalone) for each individual.

5.1.6.3. Identification of abalone aggregations (i.e., two or more 

individuals with nearest neighbor distances measuring two meters 

or less), including the number of individuals in the aggregation and 

the location of the aggregation. 

5.2) Conduct an entrainment risk modeling study to determine the risk of 

federally-listed abalone (e.g., larvae) being entrained by your cooling water intake 

structure, and submit this information along with your NPDES permit application.

5.3) Monitor entrainment of federally-listed abalone (e.g., larvae) and provide 

reports to the appropriate NMFS Regional Office according to the schedule 

specified below. Monitoring should be based on the timing and mode of abalone 
spawning appropriate to the listed species present in the area affected by the 

intake and/or discharge structure(s). 

5.3.1. Monitoring schedule: Monitoring for entrainment of abalone (e.g., 

larvae) is to be conducted at least twice a week during the months of 

March and August (peak spawning months for black abalone and white 

abalone, respectively) and at least once a week during the months of 

February, April, July, and September (white abalone spawning: February –

April; black abalone spawning: July – September. Monitoring methods 

must be appropriate to ensure adequate and representative sampling of the 

intake water and entrainment of abalone. 

5.3.2. Reporting schedule: During the entrainment monitoring period 

(February – April and July – September), weekly reports must be 

submitted to the appropriate NMFS Regional Office (electronic 

submissions are acceptable). An annual report must be submitted to the 

appropriate NMFS Regional Office by December 31 of each calendar 

year. Weekly reports should describe monitoring and analysis methods, 

abalone entrainment results (see 5.3.3. and 5.3.4. below), and relevant 

information regarding the facility’s operations for the monitoring period. 

Annual reports should include a summary of the monitoring and analysis 

methods, abalone entrainment results, and relevant information regarding 

the facility’s operations throughout the entrainment monitoring period for 

that year (e.g., water temperature data, spatial analysis of the water masses 

affected by intake and discharge, and data on other species entrained, 

particularly other invertebrate larvae).

5.3.3. Monitoring and estimation of abalone entrainment: As technologies 

allow, monitoring should include:

5.3.3.1. Identification of larvae to the lowest taxonomic level 

possible. It is recognized that currently taxonomic identification is 

limited, but advances in genetic studies, marker development, or 

other techniques may allow identification in the near future. 

5.3.3.2. Enumeration of abalone larvae, and estimation of the 

number of abalone larvae entrained over the monitoring period 

(e.g., weekly, annually). 

5.3.4. If identification and/or enumeration of abalone larvae is not feasible 

given currently available technologies or methods, then entrainment of 

abalone larvae may be estimated by:

5.3.4.1. Conducting a survey of the invertebrate community in the 

area of impact to determine the proportion of abalone compared to 

other invertebrates that overlap in spawning seasons. 

5.3.4.2. Monitoring entrainment to enumerate invertebrate larvae 

and estimate the number of invertebrate larvae entrained over the 

monitoring period (e.g., weekly, annually).
5.3.4.3. Estimating the number of abalone larvae entrained (by 

species) over the monitoring period, based on the proportion of 

abalone in the invertebrate community within the area of impact.

5.4) If the average estimated weekly entrainment of abalone larvae (by species) 

exceeds 99.9% of the veliger potential (see 5.4.1. below) for the adult abalone 

population in the area of impact, your facility must reduce intake volumes to 

reduce the estimated average weekly entrainment of abalone larvae to be less than 

this level. You also must contact the appropriate NMFS Regional Office within 

one day of exceeding 99.9% of the veliger potential. 

5.4.1. Veliger potential: The estimated number of veligers produced from 

a spawning event involving all adult abalone (by species) within the area, 

assuming (a) the ratio of females to males in the population is 1:1; (b) each 

individual spawns once per year; (c) each female can release 4 million 

eggs per spawning event; and (d) natural mortality from the egg to veliger 

stage is 99.9%. 

5.5) Monitor the effects of the discharge on the abalone community and 

recruitment as follows and submit annual reports to the appropriate NMFS 

Regional Office. 

5.6) Ensure that discharges do not increase water temperatures where any 

Federally-listed abalone may be found, including available suitable habitat in the 

area of impact, above the maximum thermal threshold identified under 5.6.1. and 

5.6.2 below. Quarterly monitoring reports must be submitted to the appropriate 

NMFS Regional Office that describe the temperature monitoring methods, results, 

and relevant information on the facility’s operations for the monitoring period. 

5.6.1. Ensure discharges do not increase water temperatures by more than 

2°C above ambient water temperatures where any Federally-listed abalone 

may be found, including available suitable habitat within the facilities’ 

area of impact. 

5.6.2. Ensure discharges do not increase water temperatures above a 

maximum of 23°C for facilities south of Point Conception, CA, or 20°C 

for facilities north of Point Conception, CA where any Federally-listed 

abalone may be found, including available suitable habitat within the 

facilities’ area of impact 

5.7) Establish replicate monitoring sites (e.g., transects, quadrats), using noninvasive, scientifically acceptable methods to monitor abalone demographics and 

recruitment. Experimental design should include sites within the area of influence 

of the discharge and an equal number of replicate sites in comparable habitat (e.g., 

substrate type, currents, depth, abalone presence) outside of the area of influence 

of the discharge. Sites should be monitored every 4 to 6 months. 
5.7.1. Annual reports must include a description of the monitoring 

methods; a map and description of the monitoring area and sites; the 

number and estimated size of individual abalone (by species); the location, 

habitat (e.g., crevice or open vertical/horizontal surface), depth (for 

subtidal species), and nearest neighbor distance for each individual 

abalone; identification of abalone aggregations; and an evaluation of the 

health of each individual abalone via visual assessment (e.g., note signs of 

withering syndrome disease, such as a withered and discolored foot 

muscle or an inability to hold on to the substrate) and/or collection and 

analysis of fecal samples. Facilities must contact the appropriate NMFS 

Regional Office and follow the guidelines or instructions regarding 

protocols for sample collection. 

5.7.2. Dead or obviously dying abalone must be collected and placed in a 

plastic bag (one individual per bag) labeled with the date and location of 

collection and immediately frozen or preserved as instructed by 

pathologists. Discovery of the dead or obviously dying abalone must be 

reported to the appropriate NMFS Regional Office as soon as possible and 

provide the location(s) and potential cause(s) of the mortality or 

mortalities. Facilities must follow the guidelines or instructions from the 

appropriate NMFS Regional Office regarding collection, preservation, and 

transport protocols.

If Federally-listed juvenile and/or adult abalone are found to be impinged, entrained or 

otherwise adversely affected, you must: 

5.8) Immediately contact the appropriate NMFS Regional Office immediately, and follow 

the guidelines or instructions provided. 

6.0 Corals

If Federally-listed corals or their designated critical habitat may occur within the area(s) 

directly or indirectly affected by your cooling water intake structure(s), you must use 

scientifically acceptable (e.g., published in scientific journals) methods to:

6.1) Conduct a benthic habitat characterization study of the immediate area 

extending 50 x 50 meters from your cooling water intake structure. This benthic 

habitat characterization study should include the following information:

6.1.1. Substrate type and extent

6.1.2. Water depth

6.1.3. Water temperature

6.1.4. Current patterns

6.1.5. Identification of coral species and coral coverage in the study area

6.1.6. Coral demographics (size-class structure) in the study area

6.2) Conduct plankton collection studies, using either towed or stationary nets, of 

the immediate area within 20 m from cooling water intake structure. Studies 

should be based on timing and mode of coral spawning appropriate to the listed 

species present.
6.2.1. Identify eggs (gametes) and larvae to the lowest taxonomic level 

possible (It is recognized that currently taxonomic identification is limited 

but advances are expected in genetic bar-coding studies, marker 

development, or other techniques that should allow identification in the 

near future.)

6.2.2. Enumerate coral eggs and larvae, as technologies allow.

6.3) Contact and coordinate with the appropriate NMFS Regional Office. 

If NMFS determines your facility has a high risk for entrainment of federally listed coral 

species, you must:

6.4) Conduct on-going studies to determine the effect of cooling water intake on 

coral community and recruitment.

6.4.1. Monitor effects on coral populations.

6.4.1.1. Establish replicate benthic quadrats (i.e., 10 m radius) 

using scientifically acceptable methods to monitor coral 

demographics and recruitment. Experimental design should 

include at least three replicates within 25 m of intake and an equal 

number of replicates in comparable habitat (e.g., currents, depth, 

coral composition/cover) at a distance greater than 100 m. 

Quadrats should be monitored every 4-6 months.

6.4.1.2. Variation in coral size structure or recruitment 

rates/success between control and impacted quadrats in excess of 

25% should be reported to the appropriate NMFS Regional Office.

6.4.2. Conduct an entrainment study to determine if federally listed corals 

(i.e., coral fragments, gametes, or larvae) are being entrained by your 

cooling water intake structure (Technological considerations mentioned in

6.2.1, above, apply.)

If Federally-listed coral species are found to be entrained or otherwise adversely affected, 

you must: 

6.5) Contact the appropriate NMFS Regional Office immediately. 

7.0 Larval fishes (bocaccio, eulachon, rockfish, larval sturgeon)

If Federally-listed bocaccio, eulachon, rockfish, or sturgeon larval-stage fishes or their 

designated critical habitat may occur within the area(s) directly or indirectly affected by 

your cooling water intake structure(s), you must implement the attached screen 

guidelines, as described in the July 2011 Fish Facilities Technical Team Bay Delta 

Conservation Plan.

7.1. Use the most biologically protective fish screen concepts as the foundation of the

proposed designs, as determined by the NMFS Regional Office.

7.2. Operate at an approach velocity of 0.2 ft/s.

7.3. Required sweeping velocities should be measured adjacent (within twelve inches) to 
the screen face and should be equal to or greater than the approach velocity criterion (i.e., 

0.2 ft/s or greater).

7.4. Target the height of fish screen panels to fifteen feet of submerged screen height to

operate at 0.33 ft/s approach velocity at low river stage; taller screens may be appropriate

at specific sites for purposes of reducing the length of the diversion structure. If the

screens are constructed 40% taller (additional 6 feet), when the river stage exceeds the

design minimum, the extra water depth will allow increased diversion capacity while

meeting a 0.2 ft/s approach velocity (during critical times when fish are present).

Further refinement of the relationship between screen height and river stage should be

addressed during an optimization process associated with final design.

7.5. Bottoms of screen panels should be elevated three to five feet off the existing river

bottom to minimize sediment and bed load impacts, and to limit exposure to benthicoriented fish species. In the Atlantic, where sturgeon are present but salmon are not, 

locate the screens in shallow waters. In the Atlantic, where salmon are present but 

sturgeon are not, locate the screens in deep waters. Where both species are present, 

contact the NMFS regional Office regarding screen location.

7.6. An approximate distance of 100 feet for spacing between refugia is suggested 

however, final refugia spacing should be further evaluated prior to final design. In order 

to optimize design, construction, operations and maintenance, the refugia should be 

modular systems that may be installed in any fish screen slot.

7.7. Flow control baffles should allow diverted flow to be distributed vertically as well as

horizontally along the screen face to distribute flow evenly over all operating screen area.

Dynamic baffling should be considered to automatically regulate flow through discrete

portions of the screen. Selective withdrawal to allow water to be diverted from selected

areas of screen (vertically or horizontally) should also be considered.

8.0 Anadromous salmonids and adult sturgeon

If Federally-listed anadromous salmonids or sturgeon, or their designated critical habitat 

may occur within the area(s) directly or indirectly affected by your cooling water intake 

structure(s), you must implement the design criteria identified in the latest Anadromous 

Salmonid Passage Facility Design guidelines and coordinate with the appropriate NMFS 

Regional Office. 

In addition, for Atlantic salmon and sturgeon, site location will play an important role in 

selecting criteria: 

8.1 Facilities should use 3 inch trash rack spacing, in addition to screening 

requirements required by the NMFS Regional Office.

8.2 Facilities located in upstream freshwater tidal portions of a river must address 

impingement and entrainment of eggs/larvae, as well as impingement of older life 

stages, as determined in coordination with the appropriate NMFS Regional 

Office.
8.3. Facilities in lower brackish-saline stretches of tidal rivers and in marine 

habitat must address impingement of older life stages but do not need to address 

eggs/larvae, as they cannot survive saline conditions. 

For sturgeon you must also: 

8.4 Use diversion structures near the intake canal to block sturgeon from entering 

the cooling water intake structure.

8.5 Use mechanisms to reduce approach-flow velocity (i.e., the V-shaped screen) 

that will allow sturgeon to avoid impingement on their own power should they 

make it into the canal.

8.6 Use full time staff to maintain (i.e., inspect, clean, and repair) the diversion 

structure on a daily basis.