July 21, 2008 

MEMORANDUM

Subject: Endangered Species Act (ESA) Section 7(d) Determination for EPA’s Approval 

under CWA Section 303(c) of Site-Specific Water Quality Objectives for Cyanide 

for San Francisco Bay, within an Amendment to the San Francisco Regional 

Water Quality Control Board Basin Plan 

From: Diane E. Fleck, P.E., Esq.

Through: Janet Hashimoto

Chief, Standards, Assessment and TMDL Office

To: The Record

This memorandum documents EPA’s determination that our approval of the site-specific 

water quality objectives (criteria) for cyanide for San Francisco Bay, subject to the completion 

and outcome of an Endangered Species Act (ESA) section 7(a)(2) consultation with the U.S. Fish 

and Wildlife Service and National Marine Fisheries Service (U.S. FWS and NMFS, respectively, 

the Services collectively), is consistent with ESA section 7(d). The objectives are within an 

amendment to the San Francisco Regional Water Quality Control Board Basin Plan (the Basin 

Plan Amendment). The Basin Plan Amendment adopts site-specific marine aquatic life water 

quality objectives for cyanide in all segments of San Francisco Bay

1

, and establishes an 

implementation provision for the objectives. The site-specific objectives (SSOs) are: 2.9 ug/l for 

chronic conditions (4 day average) and 9.4 ug/l for acute conditions (1 hour average). Marine 

objectives apply to waters in which the salinity is equal to or greater than 10 parts per thousand 

95% of the time; in waters in which the salinity is between 1 and 10 parts per thousand, the 

applicable objectives are the more stringent of the freshwater or marine objectives. The 

implementation provision requires effluent limits for wastewater and selected industrial 

dischargers under the California State Water Resources Control Board’s (State Board’s) Policy

for Implementation of Toxics Standards for Inland Surface Waters, Enclosed Bays, and Estuaries 

of California (the SIP). The provision also requires strong pollution prevention and source 

control actions designed to prevent water quality degradation and ensure ongoing attainment of 

the SSOs, as well as a program for dilution credits for shallow water dischargers to be used to 

compute water quality-based effluent limits in permits. 

 

1 All segments of San Francisco Bay include: the Sacramento/San Joaquin River Delta (within the San Francisco 

Bay region); Suisun Bay; Carquinez Strait; San Pablo Bay; Central San Francisco Bay; Lower San Francisco Bay; 

and South San Francisco Bay.
This ESA section 7(d) determination relates only to our approval under CWA section 

303(c) of the SSOs for cyanide in San Francisco Bay. The ESA determination does not relate to 

the implementation provision for the SSOs, as it is not necessary for EPA to take any action on 

the implementation provision. Based on discussions with the State Board and Regional Board 

legal and technical staff, EPA’s understanding is that the implementation provision contained in 

the Basin Plan Amendment implements the existing State Board SIP’s mixing zones and dilution 

credits provision (Section 1.4.2), and is fully consistent with that provision. Therefore, EPA 

understands that the State is not submitting the implementation provision for approval to EPA as 

a water quality standard, and EPA is not taking action on that provision. 

The San Francisco Regional Water Quality Control Board (the Regional Board) adopted 

the amendment on December 16, 2006, under Resolution No. R2-2006-0086. The amendment 

was approved by the State Board on December 4, 2007 under Resolution No. 2007-0077, and by 

California’s Office of Administrative Law (OAL) on February 28, 2008. On May 28, 2008, the 

State Board requested EPA approval of the amendment to establish the SSOs for cyanide for San 

Francisco Bay, under Clean Water Act (CWA) Section 303(c)(2). EPA has determined that the 

SSOs are consistent with all applicable CWA and EPA regulatory requirements.

EPA promulgated the currently applicable water quality standards for cyanide in “Water 

Quality Standards; Establishment of Numeric Criteria for Priority Toxic Pollutants,” 57 FR 

60848, on Tuesday, December 22, 1992. This regulation, also known as the National Toxics 

Rule (NTR), is codified at 40 CFR Part 131.36. The saltwater, or marine, aquatic life water 

quality criteria are: 1.0 ug/l for chronic conditions (4 day average), and 1.0 ug/l for acute 

conditions (1 hour average). These criteria apply to waters in which the salinity is equal to or 

greater than 10 parts per thousand 95% or more of the time. For waters in which the salinity is 

equal to or less than 1 part per thousand 95% or more of the time, the freshwater criteria apply. 

The freshwater criteria are: 5.2 ug/l for chronic conditions (4 day average), and 22 ug/l for acute 

conditions (1 hour average). For waters in which the salinity is between 1 and 10 parts per 

thousand, the more stringent of the saltwater and freshwater criteria apply, which, in this case, 

are the saltwater criteria.

The adopted SSOs are consistent with EPA procedures for adoption of site-specific water 

quality criteria. Site-specific water quality criteria account for potential over-protectiveness and 

under-protectiveness of national criteria by using EPA-approved and published procedures. The 

Regional Board’s marine aquatic life site-specific objectives were developed using an EPAapproved procedure, the Recalculation Procedure. The goal of the Recalculation Procedure is to 

recalculate water quality criteria (objectives) using data that is representative of the sensitivities 

of the species that are found in the water body. Recalculation of the cyanide criteria, 

incorporating recent, peer-reviewed toxicity data, indicates that the cyanide criteria should be 

less stringent.
In the discussion of the SSOs, the State Board in its Summary dated December 4, 2007, 

stated:

Cyanide is a pollutant that chemically degrades to harmless by-products in natural surface 

waters over time, as opposed to pollutants like elemental metals, which are persistent in 

the environment. Degradation of cyanide is supported by observations that have been 

made of a relatively rapid decline in cyanide concentrations in the San Francisco Bay

away from points of discharge and attributed to the effects of tidal mixing, dilution, and 

degradation (this decline is termed “attenuation”). These observations support the 

adoption of less stringent SSOs for cyanide. The source of cyanide in municipal 

wastewater discharges is in part from small amounts of cyanide that are formed in 

municipal wastewater treatment plants as a by-product of disinfection processes, such as 

chlorination. Disinfection occurs at the end of the treatment process, prior to discharge to 

the San Francisco Bay. Some of the potential compliance issues for wastewater 

dischargers are related to the need for disinfection.

Section 7(a)(2) of the ESA requires that federal agencies, in consultation with the 

Services, insure that actions they authorize, fund or carry out are not likely to jeopardize the

continued existence of federally listed threatened or endangered species or result in the 

destruction or adverse modification of designated critical habitat of such species. Following 

initiation of section 7(a)(2) consultation, section 7(d) of the ESA prohibits irreversible or 

irretrievable commitments of resources by federal agencies or applicants that have the effect of 

foreclosing the formulation or implementation of reasonable and prudent alternatives which 

would not violate section 7(a)(2) of the ESA. 

EPA Region 9 first initiated informal consultation under section 7(a)(2) of the ESA with 

the Services regarding our potential approval of the Regional Board’s marine aquatic life SSOs

for cyanide on August 14, 2006 (correspondence from U.S. FWS, Sacramento Office, 

transmitting a species list specifically for the cyanide SSOs for San Francisco Bay, per request of 

Susan Hatfield of EPA) and continued the consultation on July 9-10, 2008 (phone contact 

between Diane Fleck of EPA, Joe Dillon of NMFS, and Tom Maurer of U.S. FWS), and will 

continue to consult with the Services on this action. EPA Region 9 is currently completing an 

analysis regarding this action and anticipates, based on the analysis to date, that a Not Likely to 

Adversely Affect (NLAA) federally listed species or critical habitat determination will be 

appropriate. The analysis will discuss the individual federally listed threatened and endangered 

species (listed species) that may be affected by cyanide. Based on prior interactions with the 

Services, we anticipate that the Services will concur with our determination. EPA Region 9’s 

approval of the State’s water quality standards changes will be made explicitly subject to the 

outcome of the section 7(a)(2) consultation. This memorandum discusses our preliminary

analysis of why a NLAA determination will be appropriate as well as other factors why
proceeding with approval of the SSOs subject to the outcome of section 7(a)(2) consultation is 

consistent with the requirements of section 7(d). 

From earlier discussions with the Services, it is EPA’s understanding that any potential

impact to listed species or critical habitat concerning the cyanide SSOs lie with the 

implementation of the objectives, and in particular, the allowable mixing zones for shallow water 

dischargers. This issue was discussed in EPA’s written comments to the Regional Board, dated 

September 29, 2006. EPA wrote:

We are still concerned that this proposal could jeopardize beneficial uses within 

the mixing zones. The calculated mixing zone surface areas are quite extensive for most 

of the shallow water dischargers, and range from a median of 4.2 acres to the largest 

mixing zones for San Jose and Hayward Marsh of 41 acres. In general, we accept the 

staff report’s conclusion that acute water quality objectives will be met within the mixing 

zones and that the “main” body of the Bay will not exceed the site-specific objectives. 

However, we are concerned that given the extent of the mixing zones, aquatic organisms 

including swimming fish as well as drifting and sessile organisms are likely to live out 

their lives within these mixing zones. The chronic objectives were developed to protect 

organisms from chronic effects on a frequency of an average of 4 days once every 3 

years. This proposal, however, would allow exceedences of the chronic objectives at all 

times within the mixing zones.

The Regional Board, in its Response to Comments document, dated December 4, 2006, replied: 

In response to this comment, Board Staff reevaluated the mixing zones associated 

with each shallow water discharger. The mixing zones for American Canyon, Fairfield 

Suisun Sewer District, Hayward March, Napa SD, City of Petaluma, City of San 

Jose/Santa Clara and Sonoma County Water Agency have been revised in accordance 

with the Policy for Implementation of Toxic Standards for Inland Surface Waters, 

Enclosed Bays and Estuaries of California (SIP) to make them as small as practicable. 

The resulting mixing zones vary in size from 0.1 acre to 19.8 acres and have a median 

size of 0.8 acre. The revisions are based on a reevaluation of existing data, new 

information provided by the dischargers, and high resolution satellite imagery data 

making it possible to more accurately estimate surface areas of the proposed mixing 

zones. Changes to the Staff Report that reflect the revised mixing zones have been made 

to Table 21, Appendix D Spatial Descriptions of Effluent Attenuation and include the 

addition of a new Table in Staff Report Appendix J, Basin Plan and SIP Requirements

for Approval of Dilution Credit for Shallow Water Dischargers. 
The Regional Board, in response to EPA’s comment on the size of the mixing zones possibly

affecting aquatic organisms and therefore beneficial uses, reevaluated the size of the mixing 

zones and reduced them to approximately half their original size. Thus, we believe the Services’

concerns have been addressed.

EPA Region 9’s approval decisions do not set into motion any circumstances that would 

cause an irreversible or irretrievable commitment of resources that would have the effect of 

foreclosing the formulation or implementation of reasonable and prudent alternatives that might 

be determined in the consultation to be needed to comply with section 7(a)(2). Such approval is 

thus consistent with section 7(d). By approving the standards action subject to the section 

7(a)(2) consultation, EPA has explicitly stated that it retains its discretion to take appropriate 

action if the consultation identifies deficiencies in the standards requiring remedial action by 

EPA. EPA retains the full range of options available under section 303(c) for ensuring water 

quality standards are environmentally protective. EPA can, for example, work with the Regional 

Board and State Board to ensure that the State revises its standards as needed to ensure listed 

species’ protection. Further, if clear and compelling information from the consultation indicates 

more immediate action is appropriate, EPA could pursue additional options including, in 

appropriate circumstances, revising its decision from approval to disapproval.

EPA believes that it is very unlikely that either of the Services will conclude that the 

portion of the State’s Basin Plan Amendment which includes the new aquatic life SSOs violates 

ESA section 7(a)(2); the aquatic life objectives are designed to “protect the public health or 

welfare, enhance the quality of water and serve the purposes” of the Clean Water Act, which are 

to “restore and maintain the chemical, physical, and biological integrity of the Nation’s waters.” 

CWA sections 303(c)(2)(A) and 101(a). Moreover, approval of the standards actions will 

continue to protect aquatic ecosystems, including the listed species dependent on them . 

Given all of the above, EPA believes it is appropriate from an environmental standpoint 

generally, and with regard to the protection of listed species/critical habitat in particular, to have 

the new water quality SSOs in place pending the completion of the consultation. EPA retains the 

full range of options to address any issues that may be identified during the consultation. In 

addition, our analysis is that the new provisions are protective of listed species and will not result 

in any impacts of concern pending completion of consultation, and we believe it is highly likely 

that the Services will agree. EPA’s approval of the SSOs subject to the outcome of consultation 

is thus consistent with ESA section 7(d).