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Memorandum to the Record of EPA’s Final Regulations to Establish Requirements for 

Cooling Water Intake Structures at Existing Facilities and Amend Requirements at Phase I 

Facilities – May 16, 2014

I. Introduction

Today’s Cooling Water Intakes Final Rule establishes requirements for cooling water 

intake structures (CWISs) at existing facilities. The regulation reduces impingement and 

entrainment of fish and shellfish and other aquatic organisms at CWISs which withdraw cooling 

water from waters of the United States. This rule is established under section 316(b) of the Clean 

Water Act (CWA); the rule establishes standards that require the location, design, construction, 

and capacity of CWISs reflect the best technology available (BTA) for minimizing adverse 

environmental impact. With regard to this rulemaking, “adverse environmental impact” is the 

impingement of fish and shellfish or T&E species and designated critical habitat (e.g. prey base) 

on components of an intake structure or entrainment in a CWIS. 

In addition to the EPA’s duty under the CWA to establish a standard(s) for CWISs that 

will minimize adverse environmental impacts, Section 7 of the ESA imposes substantive and 

procedural obligations on Federal agencies. Particularly, Section 7(a)(2) states that Federal 

agencies shall, in consultation with, and with the assistance of the Services, ensure that any 

action authorized, funded or carried out by the Federal agency is not likely to jeopardize the 

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

habitat that has been designated as critical to the species. 16 U.S.C. 1536(a)(2). There are many 

provisions in today’s rule that are protective of T&E species and designated critical habitat; 

collectively, these protections insure that the EPA’s action (issuance of this regulation) is not 

likely to jeopardize the continued existence of any listed species or result in the destruction or 

adverse modification of designated critical habitat. 
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The EPA chose to consult under the ESA on this federal action (issuance of the 316(b) 

final rule) under Section 7 of the ESA.

1 The EPA began informal consultation on this rule with 

the National Marine Fisheries Service (NMFS) in July 2012. In October 2012, the EPA began 

informal consultation with the U.S. Fish and Wildlife Service (FWS) (together “the Services”). 

As part of the informal consultation, the EPA prepared a draft biological evaluation of the effects 

of this rule on threatened and endangered (T&E) species. The EPA concluded in the draft 

biological evaluation that the rule was not likely to adversely affect listed species or designated 

critical habitat due to the many beneficial effects on species and concluded that the rule was not 

likely to adversely affect listed species or designated critical habitat. The EPA did not receive the 

Services’ concurrence in the Agency’s “not likely to adversely affect” finding. On June 18, 2013, 

the EPA requested formal consultation with the Services and submitted a final biological 

evaluation. 

During the two years of informal and formal consultation, the EPA and the Services 

engaged in extensive dialogue about CWISs, the scope of the rulemaking, NPDES permitting, 

and the many factors and considerations relevant to T&E species and designated critical habitat. 

The three agencies engaged in a thorough discussion and consideration of potential provisions to 

protect T&E species and designated critical habitat for possible inclusion in the rule. The 

regulation benefited substantially from these conversations and from the Services’ analysis of

listed species and designated critical habitat and how these resources will be impacted by today’s 

rule. Through this consultation with the Services and after careful consideration, the EPA crafted 

																																																												 1 The Services’ ESA regulations define the term “action”. “Action means all activities or programs of any kind 

authorized, funded, or carried out, in whole or in part, by Federal agencies in the United States or upon the high 

season. Examples include, but are not limited to: (a) actions intended to conserve listed species or their habitat; (b) 

the promulgation of regulations; (c) the granting of licenses, contracts, leases, easements, rights-of-way, permits, or 

grants-in-aid; or (d) actions directly or indirectly causing modifications to the land, water, or air.” 50 CFR 402.02.
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a rule that minimizes adverse environmental impacts, including impacts to T&E species and 

designated critical habitat. The rule provides significant protections to listed species and 

designated critical habitat and – as the Services concluded in their joint Biological Opinion –

insures that the rule is not likely to jeopardize the continued existence of listed species or result 

in the destruction or adverse modification of designated critical habitat. 

Prior to today’s rule, NPDES permitting directors have evaluated CWISs with a sitespecific analysis based on the permit writer’s best professional judgment (BPJ). 40 CFR Part 

125.90(b). This BPJ analysis resulted in 316(b) NPDES permitting requirements; often these 

requirements inherently protect T&E species or are developed with the intent to protect listed

species and designated critical habitat. In addition, a number of facilities with CWISs have dealt 

with the intersection of T&E species and CWIS through the Section 9 ESA “take permit” process

or through involvement in other federal actions (such as relicensing with the Nuclear Regulatory 

Commission) where the federal agency issuing the license may have consulted with the 

Service(s). These separate processes have produced numerous instances where permit 

requirements have been protective of listed species or designated critical habitat. Examples of 

these case-by-case permit requirements are discussed below.

This case-by-case structure has produced protective measures for listed species and 

designated critical habitat in specific instances. This rule, however, benefits T&E species and 

designated critical habitat by requiring a structured process for consideration of appropriate and 

relevant data and an opportunity for the Services to make suggestions prior to the NPDES 

permitting decision. Today’s national rule includes a number of provisions that create a process

whereby NPDES permitting directors, the Services, and facilities will produce and evaluate 

information about T&E species, designated critical habitats, and CWISs. This process and the 
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rule’s substantive requirements will ultimately produce NPDES permitting requirements that 

protect listed species and designated critical habitat. Some provisions apply broadly to aquatic 

organisms beyond federally-listed species. Other provisions were included to specifically protect 

T&E species and designated critical habitat. The combined effect of these provisions will protect

T&E species and designated critical habitat and ensure that the rule is not likely to jeopardize the 

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

designated critical habitat. 

There are a number of overarching themes evinced throughout the rule. First, during the 

consultation, the EPA and the Services recognized the important role of quality data and 

information in any site-specific evaluation of impacts to protected species and designated critical 

habitat. With the goal of producing valuable information, the rule requires facilities provide an 

abundance of information about their CWISs and about the organisms and listed species and 

designated critical habitat near their intakes. With the goal of sharing the information with all the 

relevant entities, the rule requires an information exchange between the facilities, Directors and 

the Services. Second, a careful review of the information and consideration of how CWIS impact 

protected species is vital to ultimately protecting the species and designated critical habitats. 

Therefore, the rule allows the Director and the Services the opportunity to review and consider 

this information before the NPDES permit is drafted. The Services – the federal agencies with

critical expertise on T&E species and designated critical habitat – will under the procedure 

established in today’s rule, receive the facility’s permit application (which will include

information about listed species and designated critical habitat), have the opportunity to review

the permit application, and suggest protective measures to the Director for inclusion in the 

permit. The permitting director will then determine what requirements will be included in the 
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draft NPDES permit based on all of the information from the facilities and any additional 

information and suggested measures provided by the Services. After the permit is drafted and 

released for public comment, the public and once again the Services, will have an opportunity to 

provide additional information to the Director, suggest control measures, or other protective 

requirements, and call attention to any relevant factors that the Director may have not yet 

considered during the development of the draft permit. Therefore, the Director will have 

sufficient information to address potential detrimental effects to listed species and designated 

critical habitat prior to finalization of the NPDES permit. Finally, after the permit is finalized, the 

public will have access to the information provided by the facilities and the Services via the 

administrative record. 

The permitting director must create a public administrative record for the permitting 

decisions. Furthermore, the Director’s decisionmaking must be reasoned. Facilities have a strong 

interest in providing accurate information to Directors so that Directors have access to accurate 

and complete information that informs the decisionmaking and is part of the permit’s 

administrative record. Permitting Directors will need to consider that information, record the 

rationale for permitting decisions, and include any needed protections for T&E species and 

designated critical habitat in NPDES permits. Strong administrative records bolstered by quality

information will ensure that the state’s decisions are reasonable and supported by the 

administrative record, and thereby help facilities and permitting directors to withstand any legal 

challenges in any state judicial proceeding. 

The entire rule provides a framework for protecting fish and shellfish and T&E species and 

designated critical habitat. There are key provisions, however, that establish a process that 

includes specific requirements for facilities with CWIS and requirements for NPDES permitting 
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authorities. These rule provisions will allow permitting directors, facilities, the Services, and 

affected communities to identify potential effects CWIS will have on T&E species, address

detrimental effects (including effects that rise to the level of jeopardizing species), and identify 

control measures for inclusion in NPDES permits that will protect species. These key provisions 

are summarized below and fall into five categories. 

II. Permitting Application Requirements

The first category includes permit application information. As noted above, information in 

the permit application will likely provide much of the information used by the Director, the 

Services, and the public when considering appropriate control measures and requirements in the 

NPDES permit. Overall, these rule provisions aim to give the Director adequate and accurate 

information to make well-reasoned NPDES permitting decisions. Information requirements that 

pertain to all species of fish and shellfish provide information on T&E species and designated 

critical habitat as well. The following section summarizes the key provisions pertaining to permit 

application information. 

• Pursuant to 122.21(r)(1)(H), the owner or operator of any existing facility or new unit at 

any existing facility must submit (with its permit application) all information received 

from any communication with the Services. 

• Pursuant to 125.95(f), the owner or operator of an existing facility or new unit at an 

existing facility must identify all Federally-listed threatened and endangered species 

and/or designated critical habitat that are or may be present in the action area. This 

identification must be based on readily available information at the time of the permit 

application and is in lieu of the information required at 122.21(r)(4)(vi). 
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This provision specifically requires identification of T&E species and designated critical 

habitat. Facilities must provide this information to the Director for the Director’s consideration. 

Since this information is in the permit application, the Services will have the opportunity to 

review the list of species and designated critical habitat prior to the draft permit release and again 

during the public notice and comment period on the draft permit. The Director may include 

appropriate control measures to protect listed species and designated critical habitat and these 

may include the Services’ suggested control measures or other requirements to address any 

concerns about listed species and designated critical habitat. 

• Pursuant to 122.21(r)(5), facilities must submit cooling water system data in the permit 

application. This includes a narrative description of the CWIS operation, the proportion 

of the design intake flow that is used in the system and the proportion of the source 

waterbody withdrawn on a monthly basis. Existing facilities must also include in their 

permit application a description of existing impingement and entrainment technologies or 

operational measures and a summary of their performance, including reductions in 

impingement mortality and entrainment. 

• Pursuant to 122.21(r)(6), facilities must identify their chosen compliance method(s) for 

their facility or identify the chosen compliance method under 40 CFR 125.94(c) (the 

national BTA standard for impingement mortality). Under 125.94(c), facilities have to 

comply with one of seven options, for example, operating a closed-cycle recirculating 

system or operating a system with a maximum through-screen design intake velocity or 

through-screen intake velocity of 0.5 fps, or operating any other combination of 

technologies, management practices, and operational measures that the Director 

determines is BTA for impingement reduction. 
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• Pursuant to 122.21(r)(7), existing facilities must submit any previously conducted studies 

or studies obtained from other facilities addressing technology efficacy, through-plant 

entrainment survival, and other entrainment studies. 

• Pursuant to 122.21(r)(8), existing facilities must submit a description of the operational 

status of each generating, production, or process unit that uses cooling water, including 

(for power production or steam generation) descriptions of individual unit operating 

status, Nuclear Regulatory Commission relicensing status of each unit at nuclear 

facilities, descriptions of current and future production schedules, descriptions of plans or 

schedules for any new units planned within the next 5 years.

These provisions alert the Director and the Services to the facilities’ status. Also, because 

NRC relicensing may be subject to the requirements of the ESA, then the facility may have an 

NRC license that includes provisions that are protective of listed species and designated critical 

habitat. This is important information for the Director, the Services, and the public when 

determining whether additional measures are necessary to protect species in the 316(b) NPDES 

permit. 

• Pursuant to 122.21(r)(9), existing facilities that withdraw greater than 125 mgd actual 

intake flow (AIF) must develop an Entrainment Characterization Study that includes a 

minimum of two years of entrainment monitoring. This study must include identification

and documentation of all life stages of fish and shellfish in the vicinity of the CWISs and 

are susceptible to entrainment (this includes any listed species with a habitat range that 

includes waters in the vicinity of the CWIS). In addition, the study must include a 

characterization of all life stages of fish, shellfish, and any species protected under 

Federal, State or Tribal law, including a description of their abundance and their temporal 
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and spatial characteristics in the vicinity of the cooling water intake structure(s), based on 

sufficient data to characterize annual, seasonal, and diel variations in entrainment, 

including but not limited to variations related to climate and weather differences, 

spawning, feeding, and water column migration. In addition, the facility must provide 

documentation of the current entrainment of all life stages of fish, shellfish, and any 

species protected under Federal, State, or Tribal law (including threatened or endangered 

species).

These provisions place a focus on entrainment of T&E species and designated critical 

habitat, alert the Director about protected species, and provide necessary information to the 

Director for consideration during development of the permit. In addition, this requirement to 

study T&E species in the vicinity of the CWIS provides information to the facility, 

specifically whether the facility may require separate take authorization from the Services 

under the ESA. 

• Pursuant to 122.21(r)(11), existing facilities that withdraw greater than 125 mgd must 

develop and submit to the Director a benefits valuation study. This study must evaluate 

the benefits of the candidate entrainment reduction technologies and operational 

measures. The facilities must include incremental changes in the numbers of individual 

fish and shellfish, for all life stages, lost due to impingement mortality and entrainment. 
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III. Monitoring, Reporting, and Recordkeeping Requirements 

The second category of rule provisions includes requirements for facilities with CWISs to 

monitor and report impacts to fish and shellfish and impacts to T&E species. The monitoring and 

reporting requirements are important components of the rule. EPA considered many options

when developing the monitoring and reporting requirements in the rule. The rule requires 

monitoring and reporting that is essential to the 316(b) permitting process and protection of listed 

species and designated critical habitat, while also not being overbroad and unduly burdensome. 

The EPA has selected monitoring and reporting requirements that are reasonable and appropriate 

balancing the need for the information and the costs of generating, reporting, and collecting it. 

For instance, the EPA considered mandating continuous monitoring for impingement and 

entrainment of T&E species, regardless of whether the facility was within the vicinity of T&E 

species or designated critical habitat, facility location, or existing control measures, or new 

316(b) control measures required by the Director. The EPA determined, however, that mandating

continuous monitoring and reporting of this type of information could be unnecessary, 

burdensome, and over-inclusive to assess what is happening at particular intakes. Instead, the 

EPA chose to mandate certain key monitoring and reporting requirements in order to target the 

specific monitoring information and reporting that will provide accurate and specific 

information. Further, the Director will need to consider the views of the Services provided to the 

Director during the permitting decision to determine if additional monitoring is warranted. 

Monitoring and reporting of a class of species, regardless of the organisms’ protected status, 

inherently is a monitoring and reporting requirement that pertains to protected species and 

critical habitat; therefore, general monitoring and reporting requirements are summarized below, 

in addition to requirements that are specific to T&E species and designated critical habitat. 
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• Pursuant to 125.96, the Director may establish monitoring requirements. For example, the 

Director may establish monitoring requirements for impingement mortality at an existing 

facility, such as biological monitoring (125.96(a)); entrainment monitoring for existing 

units on a site-specific basis (125.96(b)); or additional monitoring at existing units, for 

example, if there are changes in operating conditions at the facility or in the source water 

body that warrant a re-examination of the operational conditions identified at 40 CFR 

122.21(r)) (125.96(c)). Monitoring is also required to demonstrate compliance with the 

requirements of § 125.94(c) and § 125.94(e) (125.96(d)). For instance, the Director may 

establish monitoring requirements for impingement mortality in addition to those 

specified at § 125.94(c), including, for example, biological monitoring, intake velocity 

and flow measurements. In addition, visual or remote inspections are required during the 

period the CWIS is in operation (125.96(e)). These inspections must occur at least 

weekly to ensure that any technologies operated to comply with § 125.94 are maintained 

and operated to function as designed including those installed to protect Federally-listed 

threatened or endangered 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). Facilities where the CWIS 

does not directly or indirectly affect Federally-listed T&E species or designated critical 

habitat may request the Director reduce monitoring requirements after the first full permit 

term in which these monitoring requirements are implemented (125.96(f)). Where the 

Director requires additional measures to protect Federally-listed threatened or endangered 

species pursuant to 125.94(g), the Director shall require monitoring associated with those 

measures (125.96(g)). 
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• Pursuant to 125.97, facilities are subject to certain reporting and recordkeeping 

requirements, including submission to the Director of Discharge Monitoring Reports or 

equivalent State reports, results of all monitoring, demonstrations, and other information 

required by the permit sufficient to determine compliance with the permit conditions and 

requirements (125.97)(a)), any status reports required by the Director (125.97)(b)), an 

annual certification statement signed by the responsible corporate officer (125.97)(c). The 

Director may require supplemental recordkeeping, data collection, or additional 

monitoring or data collection (125.97)(e)). The Director also may require additional 

reporting when necessary to establish permit compliance and may provide for periodic 

inspection of the facility. Where the Director requires additional measures to protect 

Federally-listed threatened or endangered species or critical habitat pursuant to 125.94(g), 

the Director shall require reporting associated with those measures (125.97)(g)).

The general reporting and recordkeeping requirements of this section insure that 

information about T&E species and designated critical habitat collected in preparing the permit 

application is provided to the Director so that the information can be considered during 

development of the permit requirements. The reporting and recordkeeping requirements of this 

section also serve to insure that information subsequently collected during the term of the permit 

is available to the Director and the public for review to determine if the facility is in compliance 

with the permit’s requirements. This reporting and recordkeeping will insure that the 

technologies upon which the permit is based are properly operated and maintained to afford the 

level of protection intended by the Director. It will provide communities with access to the 

information about how well the facility is performing and whether the facility is in compliance 

with its permit. Citizens are an important part of the Clean Water Act as they have the ability to 
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enforce Clean Water Act requirements and they inform permitting decisions each time the permit 

is issued.

IV. Director Requirements

The third category of rule provisions includes substantive requirements for the Director. 

The Director’s required review of the permit application and establishment of standards and 

requirements will provide opportunities for the Director to exercise her authority to include 

protective measures and requirements for listed species and designated critical habitat. The 

Director will also be required to consider the expert views of the Services provided during the 60 

day permit application review period in development of permit requirements. These requirements

established by the Director will reduce impingement and entrainment, which will overall reduce 

impacts to listed species and designated critical habitat, reducing or removing more than minor 

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

jeopardizing Federally-listed species or destroying or adversely modifying designated critical 

habitat. 

• Pursuant to 125.89 (including existing sections of the regulations that are not changed by 

this rule), the Director must review the permit application and materials submitted along 

with the permit application. 

• Pursuant to 125.92 (definition of modified traveling screen), 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. 
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This provision is protective of T&E species because releasing these organisms into other 

source waters may cause adverse impacts to the species or the surrounding environment. In 

situations where the Director is considering approving fish returns to other waters, the Director’s 

decision should take into account the Services’ recommendations regarding potential fish returns. 

The Services’ expertise will inform the Director of potential adverse impacts to species. 

• Pursuant to 125.94(d), the Director must establish BTA standards for entrainment for 

each intake at existing facilities on a site-specific basis.

• Pursuant to 125.94(e), new unit(s) at an existing facility must achieve entrainment 

standards in (e)(1) (the facility must reduce the design intake flow for the new unit, at a 

minimum, to a level commensurate with that which can be attained by use of a closedcycle recirculating system) or (e)(2) (the owner or operator of a new unit at an existing 

facility must demonstrate entrainment reductions equivalent to 90 percent or greater of 

the reduction that could be achieved through compliance with paragraph (e)(1) of this 

section. 

• Pursuant to 125.94(g), in addition to the other provisions of 125.94, the Director may 

establish additional control measures, monitoring requirements, and reporting 

requirements in the permit. These control measures and requirements may be designed to 

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

Federally-listed species and designated critical habitat, or avoid jeopardizing Federallylisted species or destroying or adversely modifying designated critical habitat. These 

control measures and requirements may include measures or requirements that have been 

suggested by the Services when they receive the permit application or draft permit for 

review.
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Section 125.94(g) provides additional protection to listed species and designated critical 

habitat, in addition to the other provisions of 125.94 and elsewhere in the rule. Before the 

Director makes a permit decision, the Director will have all of the permit application 

information, including identification of T&E species and designated critical habitat, cooling 

water system data, the facility’s chosen method of compliance with the impingement mortality 

standard, the impingement technology performance optimization study (if applicable) and 

biological monitoring data, the operational status of the facility’s CWISs, the facility’s 

entrainment characterization study (if applicable), biological entrainment characterization, and 

other information included in the permit application. 

The Director has explicit authority under 125.94(g) to require additional measures to protect 

Federally-listed T&E species and designated critical habitat. Thus, for example, if the 

impingement mortality standard that the facility chooses pursuant to 122.21(r)(6) does not 

minimize incidental take, reduce or remove more than minor detrimental effects to Federallylisted species and designated critical habitat, or avoid jeopardizing Federally-listed species or 

destroying or adversely modifying designated critical habitat, the Director may establish 

additional control measures, monitoring requirements or reporting requirements that the Director 

determines are appropriate. In addition, the Director may receive input from the Services on 

control measures and monitoring and reporting requirements that the Services suggest to 

minimize take, reduce or remove more than minor detrimental effects, or avoid jeopardy to a 

species. The Director will have adequate information before her to develop control measures 

and monitoring and reporting requirements that will provide adequate protections to species. 

• Pursuant to 125.95(a)(3) the Director may waive some or all of the information 

requirements of 40 CFR 122.21(r) if the intake is located in a manmade lake or reservoir 
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and the fisheries are stocked and managed by a State or Federal natural resources agency 

or the equivalent; however, if the manmade lake or reservoir contains Federally-listed 

threatened and endangered species, or is designated critical habitat, the Director shall not 

grant such a waiver.

Therefore, even in situations where the Director would otherwise waive information 

requirements, if there are T&E species or designated critical habitat, the Director shall not waive 

the requirements. The Director will receive information under 122.21(r) if there are T&E species 

or designated critical habitat in the manmade lake or reservoir. As with other information 

requirements, the Director will consider this information when developing permit terms, 

including control measures and requirements that will protect T&E species and designated 

critical habitat. 

• Pursuant to 125.95(d), the Director has the discretion to request additional information to 

supplement the permit application, including a request to inspect a facility. 

• Pursuant to 125.98(b)(2), the Director must determine the requirements and conditions 

included in the NPDES permit based on the information in the permit application. The 

Director must include permit conditions to implement and ensure compliance with the 

impingement mortality standard at § 125.94(c) and the entrainment standard at § 

125.94(d), including any measures to protect Federally-listed threatened and endangered 

species and designated critical habitat required by the Director. In addition, the permit 

must include conditions, management practices and operational measures necessary to 

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

mortality standard at § 125.94(c) and the entrainment standard at § 125.94(d). 
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• 125.98(b)(2) also provides that pursuant to § 125.94(g), the permit may include 

additional control measures, monitoring requirements, and reporting requirements that 

are designed to minimize incident 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 

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

C.F.R. 124.10. The Director may include additional permit requirements if based on 

information submitted to the Director by any fishery management agency or other 

relevant information, there are migratory or sport or commercial species subject to 

entrainment that may be directly or indirectly affected by the cooling water intake 

structure, or it is determined by the Director, based on information submitted by any 

fishery management agencies or other relevant information, that operation of the facility, 

after meeting the entrainment standard of this section, would still result in undesirable 

cumulative stressors to Federally-listed and proposed, threatened and endangered species, 

and designated and proposed critical habitat.

• Pursuant to 125.98(b)(3), at a minimum, the permit must require the permittee to monitor 

as required at § 125.94 and § 125.96 and the permit must require the permittee to report 

and keep the records specified at § 125.97.

• Pursuant to 125.98(d), the Director may require additional technologies for protection of 

fragile species, and may require additional monitoring of species of fish and shellfish not 
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already required under § 125.95(c). The Director may consider data submitted by other 

interested parties. The Director may also require additional study and monitoring if a 

threatened or endangered species has been identified in the vicinity of the intake. 

• Pursuant to 125.98(e), if the owner or operator of a facility chooses to comply with § 

125.94(c)(5) or (6), the owner or operator must demonstrate that the impingement 

technology performance optimization study has been optimized to minimize impingement 

mortality of non-fragile species. The Director may request further data collection as part 

of the study, including extending the study period. 

• Pursuant to 125.98(f), the Director must establish site-specific requirements for 

entrainment after reviewing the information submitted under 40 CFR 122.21(r) and § 

125.95. These 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 entrainment requirements may also reflect any control measures to

reduce entrainment of Federally-listed threatened and endangered 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 there are 

unacceptable adverse impacts including impingement, entrainment, or other adverse 

effects to Federally-listed threatened or endangered species or designated critical habitat. 

Prior to any permit reissuance after the date specified in 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 § 125.94(d). 
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This provision provides the Director with the discretion to impose entrainment 

requirements that reduce entrainment of listed species or designated critical habitat. This is 

an important provision as it allows for the reduced entrainment of these protected species. 

• Pursuant to 125.98(f)(1), the Director must provide a written explanation of the proposed 

entrainment determination in the fact sheet or statement of basis for the proposed permit 

under 40 CFR 124.7 or 124.8. 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. 

• Pursuant to 125.98(f)(2), the proposed determination in the fact sheet or statement of 

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

Director at 125.98(i) and a number of factors, for example the numbers and types of 

organisms entrained, including, specifically, the numbers and species (or lowest 

taxonomic classification possible) of Federally-listed, threatened and endangered species, 

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

The requirements at 125.98(f)(1-2) insure that the Services, the public, and EPA will 

have an explanation of the Director’s rational for including or rejecting certain control 

technologies or measures and will provide further opportunity for the Services and others to 

examine that reasoning and suggest alternative measures that are protective of listed species and 

designated critical habitat.

• Pursuant to 125.98(h), the Director must transmit all permit applications for facilities 

subject to Subpart J to the appropriate Field Office of the U.S. Fish and Wildlife Service 
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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. The Director shall provide 

the public notice and comment period as required under 40 CFR 124.10 and must 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 Fish 

and Wildlife Service and/or Regional Office of the National Marine Fisheries Service. 

This includes notice of specific cooling water intake structure requirements at 

124.10(d)(1)(ix), 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.

• Pursuant to 125.98(i), in implementing the Director’s responsibilities under the 

provisions of this subpart, the Director is authorized to inspect the facility and to request 

additional information needed by the Director for determining permit conditions and 

requirements, including any additional information from the facility recommended by the 

Services upon review of the permit application under paragraph (h). 

The transmission to the Services and the Services’ opportunity to review the permit 

application for 60 days insures that the Services – the federal agency with expertise in T&E 

species and designated critical habitat – have the opportunity to suggest control measures and 

other requirements that will minimize incidental take, reduce more than minor detrimental 

effects, or avoid likely jeopardy to listed species or destruction or adverse modification of 

designated critical habitat to the Director. The Director’s ability to request additional information 

under (i) would include information about listed species and designated critical habitat, which 
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will inform the Director and the Services as they develop permit terms or suggestions for control 

measures. The rule does not compel the Director to include the Services’ suggested control 

measures; the Director has the discretion to consider the Services’ suggestions and include them 

if the Director deems appropriate. This rule does, however, provide the opportunity for the 

Services to submit any relevant information to the Director and the Director must consider all 

relevant information in making his permit decisions. 

• Pursuant to 125.98(k), the Director must submit at least annually to the appropriate EPA 

Regional Office, facilities’ annual reports submitted pursuant to 125.97(g), for 

compilation and transmittal to the Services annually. 

This section insures that facilities’ annual reports are transmitted to the EPA and that 

information will be available to the Services. This process insures that the Services and EPA 

possess information that may indicate whether any permit has unexpected adverse impacts to 

T&E species or designated critical habitat. 

V. Facility Requirements 

The fourth category of rule provisions includes facility requirements. These requirements 

protect listed species and designated critical habitat by establishing standards and requirements 

for facilities that will reduce impingement and entrainment of fish and shellfish and T&E species 

and designated critical habitat. Since the Director may require additional control measures, and 

monitoring and reporting requirements, these provisions work in conjunction to provide a 

protective regime for listed species and designated critical habitat. 
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• Pursuant to 125.94(c), existing facilities or new units at existing facilities must comply 

with one of seven alternatives, except as provided by the Director pursuant to 

125.94(c)(1), (c)(12) or (c)(13). In addition, a facility may also be subject to the 

requirements of (c)(8) or (c)(9) if the Director requires such additional measures. 

1) Closed-cycle recirculating system

2) 0.5 feet per second through-screen design velocity

3) 0.5 feet per second through-screen actual velocity

4) Existing offshore velocity cap

5) Modified traveling screens

6) Systems of technologies as the BTA for impingement mortality

7) Impingement mortality performance standard – A facility must achieve a 12 

month impingement mortality performance standard of all life stages of fish and 

shellfish of no more than 24 percent mortality, including 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. The Director may prescribe an alternative holding period. 

8) Additional measures for shellfish - The owner or operator must comply with any

additional measures, such as seasonal deployment of barrier nets, established by 

the Director to protect shellfish.

9) Additional measures for other species - The owner or operator must comply with 

additional measures, established by the Director, to protect fragile species.

This section of the regulation protects T&E species by requiring facilities to choose control 

measures that overall reduce impingement mortality of fish and shellfish, which by logical 
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extension, reduce impingement mortality of T&E species and designated critical habitat. 

Compliance with such requirements may be sufficient to reduce more than minor detrimental 

effects, reduce or eliminate incidental take, or avoid jeopardizing species.

• Pursuant to 125.95(c), for subsequent permit applications, an owner or operator of a 

facility may request to reduce the required permit application information if conditions at 

the facility and in the waterbody remain substantially unchanged since the previous 

permit application, as long as the relevant previously submitted information remains 

representative. However, critical habitat designations or T&E species listings (in the 

waters where the facility’s intake is located) after issuance of the current permit 

constitutes potential for a substantial change that must be addressed in a subsequent 

permit application unless the facility receives an exemption under 16 U.S.C. 1536(o) or a 

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

Therefore, in areas where there are new T&E species listings or new critical habitat 

designations, the Director will receive the full body of permit application information in 

subsequent permit terms. 

• Pursuant to 125.95(g) – the owner or operator must certify that its application is true, 

accurate and complete pursuant to 122.22(d). 

This provision insures that facilities provide accurate and complete information in permit 

applications, including information about T&E species and designated critical habitat. 40 CFR 

122.22(d) provides that the signor of a certification certifies “under penalty of law”. There are 

penalties for submitting false information. These requirements make it significantly less likely 
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that an owner or operator will provide false information and provides an incentive for facilities to 

diligently prepare their permit applications. 

VI. Rule Provisions Prohibiting Take 

The rule also recognizes the ESA prohibition against take, found at 16 U.S.C. 1538(a)(1). 

Under ESA Section 9, it is unlawful for any person to take any endangered species of fish or 

wildlife except under defined circumstances, including receiving a permit from the FWS or 

NMFS. See 16 U.S.C. 1536(o) and 16 U.S.C. 1539(a). By expressing a prohibition on take in a 

note to the 316(b) rule, the EPA makes clear that other statutes, namely the ESA, govern take 

and a facility’s obligation to comply with the ESA is not fulfilled by obtaining an NPDES 

permit. In order to comply with Section 9 of the ESA, facilities that take endangered species of 

fish or wildlife must receive authorization from the Services. See 16 U.S.C. 1536(o) and 16 

U.S.C. 1539(a). The note in the Code of Federal Regulations helps to make the public aware of 

existing law and facilitates communication between the facilities, permitting directors, the 

Services, and the EPA concerning measures that may prevent unauthorized take.

• Sections 125.90 and 125.98(j) note that this regulation does not authorize take, as defined 

by the Endangered Species Act, 16 USC 1532(19). The provisions also state that the 

U.S. Fish and Wildlife Service and National Marine Fisheries Service have determined 

that any impingement (including entrapment) 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). 
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• Pursuant to 125.98(b)(1), permits 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.”

VII. EPA’s Commitment to Follow the 2001 Memorandum of Agreement with the 

Services

In addition to the permit requirements summarized above, the EPA has also affirmed in 

the preamble to the rule the Agency’s commitment to insure coordination of the EPA’s and the 

Services’ programs and appropriate protection of T&E species and designated critical habitat. 

The preamble affirms the Agency’s commitment to follow the procedures in the 2001 

Memorandum of Agreement (MOA) between the Services and the EPA. See 66 Fed. Reg. 11202. 

The MOA committed the EPA to a number of specific actions that are protective of listed 

species and designated critical habitat. Under the MOA, EPA committed, when contacted by the 

Services, to coordinate with the Services and the State/Tribe during the permit development 

process, in order to ensure that permits will comply with all applicable CWA requirements. 

EPA’s commitment to coordinate effectively with the Services includes following the procedures 

in section IX.A.6 and 7 of the MOA and are described in full in the preamble. The MOA 

describes a process whereby if an NPDES permit causes minor detrimental effects on listed 

species or designated critical habitat, the Services will work with the State or Tribe to reduce 

those detrimental effects. If the permit causes more than minor detrimental effects, the Services 

will work with the State or Tribe and if unable to address the detrimental effects in the permit, 

EPA would work with the State or Tribe to remove or reduce the detrimental effects of the 

permit. This step may include EPA objecting to the state permit, where appropriate. 
26

Where a permit is likely to jeopardize the continued existence of any listed species or 

result in the destruction or adverse modification of critical habitat, the MOA states that EPA will 

use the full extent of its CWA authority to object to the permit. If EPA objects to a NPDES 

permit, EPA will follow the permit objection procedures outlined in 40 CFR 123.44 and 

coordinate with the Services in seeking to have the State or Tribe revise its permit. A State or 

Tribe may not issue a permit over an outstanding EPA objection. If EPA assumes permit issuing 

authority for a NPDES permit, EPA will consult with the Service prior to issuance of the permit 

(as a Federal action) as appropriate under Section 7 of the ESA.

The preamble explains that the MOA applies to 316(b) NPDES permitting. EPA will use 

its oversight authority to object to proposed state permits where EPA finds (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 critical habitat. The process described in the MOA and in 

the Preamble provides an additional safeguard to ensure that today’s rule is protective of T&E 

species and designated critical habitat and ultimately, provides an additional assurance that

individual permits issued under this rule do not jeopardize species and therefore the rule itself, is 

not likely to jeopardize the continued existence of any listed species or result in the destruction 

or adverse modification of critical habitat. 

VIII. The Case-By-Case Approach Has Protected Listed Species

The cooperative approach EPA has adopted today in its final rule for ensuring protection 

of listed threatened and endangered species and designated critical habitat in 316(b) permitting is 

not a new one. Rather, it builds on the constructive engagement between EPA (and other 
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regulatory agencies), states and the Services in the case-by-case permit setting. It is a process 

that, for a number of years, in EPA’s understanding, has worked effectively to ensure protection 

of threatened and endangered species and listed critical habitat. Given the provisions of today’s 

rule that require detailed identification of potential concerns under the ESA and the participation 

of the Services in the permitting process, EPA expects, based on its historical experience, that 

this fruitful collaboration will continue. 

The record indicates that case-by-case NPDES permitting under the structure EPA has 

adopted for the final rule will provide the necessary protection under the ESA. EPA reviewed 

National Pollution Discharge Elimination System (NPDES) permit provisions and Nuclear 

Regulatory Commission (NRC) relicensing at 49 nuclear power plants that recently underwent 

NRC re-licensing subject to FWS and NMFS Section 7 consultation.

In the majority of permits and re-licensing documents reviewed by EPA, the Services 

concurred with applicants that there were no or negligible significant impact to T&E species. 

Eight of 49 nuclear power plants that sought NRC re-licensing were required to institute 

mitigative measures to protect T&E species, including structural changes, operational controls, 

enhanced reporting and monitoring, or combinations of measures. Examples of species for which 

enhanced monitoring and reporting were required include pallid sturgeon (Ft. Calhoun, NE ), and 

sea turtles (Brunswick, NC, Crystal River, FL, Diablo Canyon and San Onofre, CA, and Oyster 

Creek, NJ), and shortnose sturgeon (Indian Point, NY). Two other of the facilities are still 

undergoing ESA consultation (Columbia Generating Station, WA, and Edwin Hatch, GA).

The St. Lucie nuclear plant in Florida is an example of where structural mitigation 

measures were implemented to prevent incidental sea turtle take, including installation of turtle 
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nets, installation of exclusion devices at the velocity caps, a debris removal program, and sealing 

off dead-end sections of intake pipes. Ancillary operational measures include periodic 

examination of intake pipes to ensure that conditions that could adversely affect sea turtles be 

found and corrected. 

The Joseph Farley nuclear plant in Alabama is another example of where operational 

measures were required to reduce chemical discharges to the receiving water to better protect 

T&E freshwater mussel species. These measures included riparian buffer management to reduce 

local herbicide application and reduction of chlorine in plant discharge.

The Quad Cities nuclear power plant in Iowa is an example of where the FWS required,	

under a Habitat Conservation Plan, the development and implementation of a mussel habitat and

population monitoring program.

EPA also identified Florida State NPDES permits for 15 coastal power plants that include 

requirements for protection of manatees, a Federally-protected species under the Endangered 

Species Act. These conditions require the plants to develop and comply with a manatee 

protection plan. The plan includes provisions that call for the facility to provide warm water 

refuges for manatees during cold periods. The facility must also notify the state of Florida and 

the USFWS within four hours if they have an unplanned shutdown. The facility must monitor 

water temperature in their discharge areas, and must operate to the maximum extent practicable 

to maintain temperatures in the discharge area above 68 degrees. These conditions, which were 

reviewed and approved by the U.S. Fish and Wildlife Service, were developed in accordance 

with the USFWS’ Florida Manatee Recovery Plan, which was designed to maintain safe and 

reliable warm water refuges for wintering manatees.
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In the case of the EPA-issued NPDES permit for the Brayton Point facilities in 

Massachusetts, EPA consulted with the NMFS and the FWS concerning the 316(a) and 316(b) 

conditions of the NPDES permit. (40 C.F.R. § 125.72(d) requires consultation whenever EPA is 

considering an application for a variance under CWA § 316(a)). The Services concluded that the 

316(a) NPDES permit limits were consistent with the ESA. The permit also included BTA 

limitations on the capacity of cooling water intake structures under section 316(b). The NMFS 

agreed that these intake capacity limitations satisfied the requirements under the ESA. 

These examples demonstrate that even prior to this rule, where Directors were required to 

establish controls for CWISs on a best professional judgment basis under 40 CFR 125.90 or 

perhaps by the now remanded Phase II rule), Directors were able to protect listed species and 

designated critical habitat. Today’s regulation includes many provisions that are protective of 

listed species and designated critical habitat. These provisions build a process for facilities, 

Directors, and the Services and impose substantive requirements on facilities and Directors. The 

process provided in the rule, while not wholly a new concept, does provide an NPDES regulatory 

structure to insure that listed species and designated critical habitat are protected through 316(b) 

permits. The process and the substantive requirements combine to insure that the regulation is 

not likely to jeopardize the continued existence of any listed species or result in the destruction 

or adverse modification of critical habitat.