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 Cy anide 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 qualit y 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, respectivel y, 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 Ame ndment adopts site

- specific marine aquatic life water quality objectives for cyanide in all segments of San Francisco Ba y 1 , and establishes an implementation provision for the objectives. The site

- specific objec tives (SSOs) are: 2.9 ug/l f or chronic conditions (4 day average) and 9.4 ug/l for acute conditions (1 hour average). Marine objectives appl y 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 Wate r Resources C ontrol Board’s (State Board’s) Policy for Implementation of Toxics Standards for Inland Surface Waters, Enclosed Bay s, and Estuaries of California (the SIP). The provision also requires strong pollution prevention and source control acti ons designed to prevent water qualit y 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 B ay region); Suisun Bay; Carquinez Strait; San Pablo Bay; Central San Francisco Bay; Low er San Francisco Bay; and South San Francisco Bay.This ESA section 7(d) determination relates onl y t o our approval under CWA section

303(c) of the SSOs for cy anide in San Francisco Ba y. 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 provisi on contained in the Basin Plan Am endment implem ents the existing State Board SI P’s mixing zones and dilution credits provision (Section 1.4.2) , and is fully consistent with that p rovision . Therefore, EPA understands that the State is not submitting th e implementation pr ovision for approv al 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 Resolut ion No. R2

- 2006

- 0086. The amendment was approved b y the State Board on December 4, 2007 under Resolution No. 2007

- 0077, and b y California’s Office of Administrative L aw (OAL) on February 28, 2008. On May

28, 2008, the State Board requested EPA approval of the amendme nt to establish the SSOs for cyanide for San Francisco Ba y, 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 th e current ly applicable water quality standards for cy anide 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 appl y 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 appl y, which, in this case,
are the saltwater criteria. The adopted SSOs are consistent with EPA procedures for adoption of site

- specifi c water quality criteria. Site

- specific water quality criteria account f

or potential over

- protectiveness and under

- protectiveness of national criteria b y using EPA

- approved and published procedures. The Regional Board’s marine aquatic life site

- specific objectives were developed using an EPA

approved procedure, the Recalculat ion Procedure. The goal of the Recalculation Procedure is to recalculate water qualit y 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, in corporating 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 relativel y 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 cy anide. The source of cy anide in municipal wastewater discharges is in part from small amounts of cyanide that are formed in municipal wastewater treatment plants a s a b y - product of disinfection processes, such as chlorination. Disinfection occurs at the end of the treatment process, prior to discharge to the San Francisco Ba y. Some of the potential compliance issues for wastewater dischargers are related to the need for disinfection. Section 7(a)(2) of the ESA req uires 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 federall y 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 Service s 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 specificall y for the cyanide SSOs for San Francisco Bay, per r equest of Susan Hatfield of EPA) and continued the consultation on July 9

- 10, 2008 (phone contact between D iane 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 anal ys is regarding this action and anticipates , based on the anal ys is to date, that a Not L ikely to Adversel y Affect (NLAA) federall y listed species or critical habitat determination will be appropriate. The analy si s will discuss the individual federall y 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 Regi on 9’s approval of the State’s water qualit y standards changes will be made explicitly subject to the outcome of the section 7(a)(2) consultation. This memorandum discusses our preliminary anal ys is of why

a NLAA determination will be appropriate as well a s other factors wh yp roceeding 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 Hay ward Marsh of 41 acres. In general, we accept the staff report’s conclusion that acute water qualit y objectives will be met w ithin 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 likel y 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 day s once every 3 ye ars. This proposal, however, would allow exceedenc es 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, Hay ward 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 Bay s 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. T he revisions are based on a reevaluation of existing data, new information provided b y the dischargers, and high resolution satellite imagery data making it possible to more accuratel y 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 Di lution Credit for Shallow W ater 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 d etermined in the consultation t o 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 b y 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 standar ds 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 unlikel y 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 aquati c 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, phy sical, and biological integrit y 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 ecos ys tems, including the listed species dependent on them .

Giv en all of the above, EPA believes it is appropriate from an environmental standpoint generall y, and with regard to the protection of listed species/critical habitat in particular, to have the new water qualit y SSOs in place pending the completion of the consultation. EPA retains the full range of options t o address an y issues that may be identified during the consultation. In addition, o ur anal ys is 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 highl y 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).