C

Water Quality Challenges in the San Francisco Bay/ 

Sacramento-San Joaquin Delta Estuary:

EPA’s Action Plan 

United States

Environmental Protection

Agency

August 2012
Water Quality Challenges in the San Francisco Bay/ 

Sacramento-San Joaquin Delta Estuary: 

EPA’s Action Plan

 Table of Contents

Executive Summary.............................................................1

Background......................................................................2

Clean Water Act Regulatory Assessment.. ...................................6

EPA’s Action Plan...............................................................9

 

 1 - Strengthen estuarine habitat protection standards

 2 - Advance regional water quality monitoring and assessment 

 3 - Accelerate water quality restoration through Total Maximum Daily Loads 

 4 - Strengthen selenium water quality criteria 

 5 - Prevent pesticide pollution 

 6 - Restore aquatic habitats while managing methylmercury

7 - Support the Bay Delta Conservation Plan

Appendix I - Staff Report: analysis of water quality issues in EPA’s February 2011 ANPR

Appendix II - Synthesis of public comments in response to ANPR

Appendix III - Unabridged Advance Notice of Proposed Rulemaking, February 2011
1

Executive Summary

The U.S. Environmental Protection Agency (EPA) developed this Action Plan after assessing the 

effectiveness of current regulatory mechanisms designed to protect water quality in the San 

Francisco Bay Sacramento-San Joaquin Delta Estuary (Bay Delta Estuary) and its tributaries. 

EPA’s assessment concludes that Clean Water Act (CWA) programs currently are not adequately 

protecting aquatic resources of the Bay Delta Estuary. In this document, EPA recommends actions 

to restore water quality for aquatic species protection using existing EPA authorities and resources, 

as well as actions EPA believes are important and appropriate for the State Water Resources 

Control Board (State Water Board). 

The Bay Delta Estuary is one of the largest and most important estuarine systems on the Pacific 

Coast of the United States, supporting over 750 animal and plant species. The Estuary is the hub of 

California’s water distribution system, supplying drinking water to 25 million people and irrigation 

water to 4 million acres of farmland. For more than 25 years, the decline of aquatic resources in the 

Estuary, along with the corresponding impacts on urban and agricultural water districts who rely on 

water exported from the Estuary, has drawn increased attention from federal, state and local 

agencies responsible for addressing these related problems. The most recent drought (2006-2009) 

highlighted the increasing fragility of both ecosystem health and water supply reliability. 

EPA is one of more than 25 state and federal governmental agencies with responsibilities in the Bay 

Delta Estuary. EPA’s major statutory mission in the Estuary is to implement the CWA. EPA has 

delegated many CWA program authorities to the State Water Board while providing financial 

support,

1

technical assistance, and oversight (including, in some cases, review and approval of State 

actions). Much of EPA's work in this Action Plan (as well as elsewhere in California) is done in 

support of and in partnership with the State. For example, water quality standards, which define 

water quality goals for our waterbodies, are typically developed and adopted by the State with EPA 

assistance, review, and ultimately, approval or 

disapproval.

In the Bay Delta Estuary, EPA focuses on assuring that 

the many designated uses of the Estuary’s aquatic 

resources are protected. EPA emphasizes the CWA 

goals of maintaining and improving water quality – the 

chemical, physical, and biological integrity of the water 

– to ensure the Bay Delta Estuary can function as a 

vibrant, healthy estuary. About 90 species of fish are found in the Delta. The Delta’s channels serve 

as a migratory route and nursery area for Chinook salmon, striped bass, white and green sturgeon, 

American shad, and steelhead trout. These anadromous fish spend most of their adult lives either in 

 

1

In federal fiscal year 2012, EPA grants to the State Water Resources Control Board totaled $123,547,800, including a 

$101 million State Revolving Fund capitalization grant and other grants under the authority of CWA Sections 106, 319 

and 604.

To learn more about the San 

Francisco Bay Delta watershed 

and EPA activities, go to:

www.epa.gov/sfbaydelta
2

the lower bays of the Estuary or in the ocean. Resident fish in the Estuary include delta smelt, 

longfin smelt, Sacramento splittail, catfish, largemouth bass, black bass, crappie, and bluegill. All 

Bay Delta Estuary waters are impaired by one or more contaminants. In addition, the reduction in 

the quantity and quality of estuarine habitat limits the Estuary’s ability to support aquatic species. 

EPA’s Action Plan describes a suite of activities to: 

1. Strengthen water quality standards to protect estuarine habitat 

2. Advance regional water quality monitoring and assessment 

3. Accelerate water quality restoration through Total Maximum Daily Loads 

4. Strengthen selenium water quality criteria

5. Prevent pesticide pollution 

6. Restore aquatic habitats while managing methylmercury

7. Support the Bay Delta Conservation Plan

Collectively, these activities will contribute to the restoration of the Bay Delta Estuary. Even if 

they are all successfully implemented, however, they are not sufficient to resolve the complex

problems that have stressed the ecosystem to the point of collapse. Any solution to the ecological 

problems of the Bay Delta Estuary must be multi-faceted, including providing sufficient flows, 

physical habitat which is sufficiently large, connected, diverse, and self-sustaining, as well as a 

reduction of many types of stressors, such as contaminants, invasive species, and predation. 

Background

In response to the most recent drought and resulting conflicts in California water resource 

management, EPA joined five other federal agencies in issuing the Interim Federal Action Plan 

(IFAP) in December 2009.2 The IFAP described actions each agency would take, in partnership 

with the State of California, to address the many interrelated water issues associated with the Bay 

Delta Estuary. As part of this interagency effort, EPA committed in the IFAP to “assess the 

effectiveness of the current regulatory mechanisms designed to protect water quality in the Delta 

and its tributaries, including standards for toxics, nutrients, and estuarine habitat protection.” 

As a first step in this assessment, on February 10, 2011, EPA issued an Advance Notice of Proposed 

Rulemaking for Water Quality Challenges in the San Francisco Bay/Sacramento-San Joaquin Delta 

Estuary (ANPR)3(attached as Appendix III). This ANPR summarized the status of aquatic species 

of concern in the Bay Delta Estuary; the current scientific and technical understanding of seven 

major stressors affecting those aquatic resources; and the state of the regulatory response to the 

 

2

Interim Federal Action Plan for the California Bay-Delta (Dec. 22, 2009), available at

http://www.doi.gov/documents/CAWaterWorkPlan.pdf. (last visited 08/17/12).

3

U.S. ENVTL. PROT.AGENCY, WATER QUALITY CHALLENGES IN THE SAN FRANCISCO BAY/SACRAMENTO –SAN 

JOAQUIN DELTA ESTUARY, 76 Fed. Reg. 9709 (Feb. 22, 2011). The unabridged version of this notice is available at 

http://www.epa.gov/sfbay-delta/pdfs/BayDeltaANPR-fr_unabridged.pdf .
3

dramatic decline in those resources. The seven stressors EPA considered of most significance

included: ammonia, selenium, pesticides, contaminants of emerging concern, declining estuarine 

habitat, fragmented migratory corridors and wetlands loss. The purpose of the ANPR was to solicit 

comment from the public and other agencies on what EPA might do differently to implement the 

programs under its purview – most notably the CWA – to address these named stressors for which 

EPA has existing authority.4

EPA received 55 comments from state, local and federal agencies, nongovernmental organizations 

and individuals in response to the ANPR. Some of these comments provided technical information 

or scientific research not reflected in the ANPR. Some comments included suggestions for new or 

augmented EPA activities in the Bay Delta Estuary. Other comments disagreed with EPA’s 

findings and suggested that further regulatory action was unnecessary. The comments are 

summarized in Appendix II.

5

 

Based on the ANPR and the comments received, as well as on more recent scientific and technical 

information, EPA is now: (1) summarizing certain conclusions about the current regulatory 

mechanisms protecting water quality in the Bay Delta Estuary; and (2) setting forth EPA’s priorities 

and commitments to improve water quality for aquatic species in the Bay Delta Estuary. This 

document does not answer all of the questions raised in the ANPR, nor does it attempt to provide a 

comprehensive blueprint for solving all of the problems in the Bay Delta Estuary. Instead, this 

document defines EPA’s priorities in the Bay Delta Estuary and recommends changes in EPA (or 

other agency) activities or policies, given our current authorities and our understanding of the 

threats to aquatic resources.

EPA’s Action Plan focuses on the CWA, the primary federal statute protecting water quality. 

Where relevant, other federal laws which provide EPA additional tools are discussed. These 

include pesticide regulation under the Federal Insecticide, Fungicide and Rodenticide Act (FIFRA); 

chemical regulation under the Toxic Substances Control Act (TSCA); remediation of sites 

contaminated with hazardous substances under the Comprehensive Environmental Response, 

Compensation, and Liability Act (CERCLA, or “Superfund”); and the review of Environmental 

Impact Statements for federal projects under the National Environmental Policy Act (NEPA).

6

 In 

addition, California has significantly broader authority under its Porter-Cologne Act (such as the 

authority to regulate agricultural discharges and discharges to ground water) and under state 

 

4 EPA’s review was focused on the most significant water quality factors adversely affecting aquatic species in the Bay 

Delta Estuary. This document does not address water quality issues related to other designated uses, including uses 

related to drinking water (which is also protected under the Safe Drinking Water Act which EPA implements with the 

California Department of Public Health), recreation, fish consumption, agriculture, etc. EPA acknowledges the ongoing 

need to evaluate and address these other critical water quality issues. 

5 Also posted at http://www.epa.gov/sfbay-delta/anpr-pubcomments.html.

6 NEPA requires Environmental Impact Statements (EIS) for major federal actions significantly affecting the 

environment. Clean Air Act Section 309 mandates EPA’s review and comment on EISs prepared by other federal 

agencies.
4

pesticide law, which provide authorities to control pesticide use and protect surface water from 

pesticide residues. These California authorities provide critical tools to supplement federal law.

As discussed in detail in the ANPR, the regulatory response to water quality issues in the Bay Delta 

Estuary is complex. This is due in part to the nature of the problem and in part to the multi-layered 

and sometimes fragmented regulatory structure in California, where the task of identifying water 

quality goals and defining and implementing regulatory solutions is shared by the State Water 

Board and the nine Regional Water Quality Control Boards (Regional Water Boards), as well as 

between the water quality and water rights functions of the State Water Board.7 

Other state and federal agencies perform vital functions which intersect or impact programs of EPA 

and the Water Boards. The California Department of Water Resources (DWR) and the federal 

Bureau of Reclamation (USBR), as water management agencies, provide water to their contractors 

and are subject to water quality and endangered species laws. The natural resource agencies 

(California Department of Fish and Game (DFG) and the federal Fish and Wildlife Service (FWS)

and National Marine Fisheries Service (NMFS) have responsibility and authority to recover 

threatened and endangered species. As the CWA (and California water quality law) protects all 

beneficial uses of water, including aquatic habitat, Endangered Species Act (ESA) measures to 

protect threatened and endangered aquatic species can overlap with state and/or federal CWA 

requirements. In addition, the California Department of Pesticide Regulation (DPR) implements

programs to protect surface water from the impacts of pesticides, a role which they undertake in 

coordination with the Water Boards. The U.S. Army Corps of Engineers (Corps), with assistance 

and oversight by EPA, issues permits for activities that unavoidably fill waters and wetlands. The 

Natural Resources Conservation Service supports voluntary conservation on private agricultural 

lands with the goal of addressing water supply, water quality, and habitat restoration needs.

There are several processes underway to improve Bay Delta Estuary resources and stabilize water 

supplies. Notable among these are the Bay Delta Conservation Plan (BDCP) and the Delta Plan. 

The BDCP is a multi-agency (state and federal agencies and local water districts) effort to recover 

endangered species and ensure a reliable water supply through reconfiguring water conveyance 

facilities and restoring large-scale aquatic habitat. EPA is supporting development of the BDCP by

participating as a cooperating agency in its environmental review process. EPA’s input is focused 

on ensuring that water quality impacts of conveyance and operations changes are analyzed and 

appropriately considered and that information needed for CWA permitting is developed as early as 

possible. (See page 21 for additional comments related to the BDCP.)

Another significant effort, the Delta Plan, will be finalized by the Delta Stewardship Council (DSC)

in 2013 and includes a set of legally enforceable policies to achieve California’s policy of “co-equal 

goals”, i.e., a more reliable water supply and a restored, enhanced Delta ecosystem. Although the 

role of the Delta Plan in regulatory activities affecting the Bay Delta Estuary is evolving, EPA 

 

7 Noting this complex structure is not intended as criticism. Under the federalism concept of the Clean Water Act, EPA 

is respectful of how each state organizes its various water quality functions, as long as the goals of the Clean Water Act 

are attained.
5

supports the DSC’s effort to comprehensively address the multiple goals inherent in Delta 

protection, and especially the importance it places on the State Water Board’s work to promulgate 

new Delta water quality standards. 

In addition, many other agencies and organizations are working to improve Bay Delta Estuary water 

quality and aquatic species protection, pursuant to their authorities and responsibilities. In 

developing this Action Plan, EPA considered these activities and processes. EPA’s intent is to 

complement and, where possible, support the efforts of these other organizations. Some of these 

efforts include:

DFG’s draft Conservation Strategy for Restoration of the Sacramento-San Joaquin Delta 

Ecological Management Zone; and Quantifiable Biological Objectives and Flow Criteria 

for Aquatic and Terrestrial Species of Concern Dependent on the Delta;

8

Sacramento-San Joaquin Delta Conservancy’s Strategic Plan;

9

San Joaquin River Restoration Program (as authorized in 2009);

10

Central Valley Flood Protection Board’s Central Valley Flood Protection Plan;

11 and 

Natural Resource Conservation Service’s Bay-Delta Initiative12.

EPA’s Action Plan was also informed by several recent efforts to assess the health of the ecosystem 

and the success of efforts to address Delta issues, from policy and scientific perspectives, including:

Delta Regional Monitoring Program’s first annual Pulse of the Delta, issued by the 

Central Valley Regional Water Board;

13

 

8 CAL. DEPT. OF FISH AND GAME, CONSERVATION STRATEGY FOR RESTORATION OF THE SACRAMENTO-SAN JOAQUIN 

DELTA ECOLOGICAL MANAGEMENT ZONE AND THE SACRAMENTO AND SAN JOAQUIN VALLEY REGIONS (Draft July 

2011), available at http://www.dfg.ca.gov/ERP/reports_docs.asp (last visited 06/26/12); CAL. DEPT. OF FISH AND 

GAME, QUANTIFIABLE BIOLOGICAL OBJECTIVES AND FLOW CRITERIA FOR AQUATIC AND TERRESTRIAL SPECIES OF 

CONCERN DEPENDENT ON THE DELTA (November 23, 2010), available at

http://www.dfg.ca.gov/water/water_rights_docs.html (last visited 06/26/12).

9

SACRAMENTO-SAN JOAQUIN DELTA CONSERVANCY 2012 STRATEGIC PLAN (adopted June 27, 2012), available at 

http://deltaconservancy.ca.gov/docs/meeting_materials/june_2012/Delta_Conservancy_Strategic_Plan_Designed_20Jun

e2012.pdf (last visited 08/21/12).

10 CAL. DEPT. OF WATER RES., SAN JOAQUIN RIVER RESTORATION PROGRAM, available at

http://www.water.ca.gov/rivers/sanjoaquin/program/ (last visited 06/26/12).

11 CENT. VALLEY FLOOD PROTECTION BD., 2012 CENTRAL VALLEY FLOOD PROTECTION PLAN (adopted June 29, 2012) 

available at http://www.cvfpb.ca.gov/ (last visited 07/16/12).

12 NATURAL RES. CONSERVATION SERVICE, BAY DELTA INITIATIVE, available at

http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/national/programs/farmbill/initiatives/?&cid=stelprdb1047519 (last 

visited 06/26/12).

13 CENT. VALLEY REG’L WATER QUALITY CONTROL BD, THE PULSE OF THE DELTA – RE-THINKING WATER QUALTY 

MONITORING(2011), available at
6

San Francisco Estuary Partnership’s State of the Estuary report;

14

Public Policy Institute of California’s series of reports;

15

Delta Vision Foundation’s Delta Vision Report Card series;

16

National Research Council’s three scientific reviews of the basis of the actions taken and 

those that could be taken to achieve a sustainable ecosystem and a reliable water 

supply;

17

Interagency Ecological Program’s Pelagic Organism Decline Synthesis (December 

2010);

18 and

Report to the California Fish and Game Commission on Stressors Impacting Delta 

Related Organisms.

19

Clean Water Act Regulatory Assessment

The ANPR describes federal and state water quality programs to protect aquatic species in the Bay 

Delta Estuary, from establishing water quality standards to using various programs and regulatory 

tools (e.g., discharge permits, enforcement, total maximum daily loads (TMDLs), financial 

 

http://www.swrcb.ca.gov/rwqcb5/water_issues/delta_water_quality/comprehensive_monitoring_program/ (last visited 

06/28/12).

14 SAN FRANCISCO ESTUARY PARTNERSHIP, STATE OF SAN FRANCISCO BAY 2011 REPORT, available at 

http://sfestuary.org/StateofSFBay2011/ (last visited 06/26/12).

15 PUBLIC POLICY INSTITUTE OF CALIFORNIA, ENVISIONING FUTURES FOR THE SACRAMENTO-SAN JOAQUIN DELTA 

(2007); COMPARING FUTURES FOR THE SACRAMENTO-SAN JOAQUIN DELTA (2008); MANAGING CALIFORNIA’S WATER:

FROM CONFLICT TO RECONCILIATION (2011); AND WATER AND THE CALIFORNIA ECONOMY (2012). Available at 

http://www.ppic.org/main/policyarea.asp?i=15 (last visited 06/26/12). PPIC has also published a number of other 

reports and monographs on California water issues, as noted on the website.

16 DELTA VISION FOUNDATION, DELTA VISION REPORT CARDS (2012 and earlier), available at

http://www.deltavisionfoundation.org/(last visited 06/26/12).

17 NATIONAL RESEARCH COUNCIL: A SCIENTIFIC ASSESSMENT OF ALTERNATIVES FOR REDUCING WATER MANAGEMENT 

EFFECTS ON THREATENED AND ENDANGERED FISHES IN CALIFORNIA’S BAY DELTA (2010)(available at 

http://dels.nas.edu/Report/Scientific-Assessment-Alternatives/12881); A REVIEW OF THE USE OF SCIENCE AND 

ADAPTIVE MANAGEMENT IN CALIFORNIA’S DRAFT BAY DELTA CONSERVATION PLAN (2011) (available at 

http://dels.nas.edu/Report/Review/13148); SUSTAINABLE WATER AND ENVIRONMENTAL MANAGEMENT IN THE 

CALIFORNIA BAY/DELTA (2012) (available at http://dels.nas.edu/Report/Sustainable-Water-EnvironmentalManagement/13394) (last visited 06/26/12).

18 Baxter, R., R. Breuer, L. Brown, L. Conrad, F. Feyrer, S. Fong, K. Gehrts, L. Grimaldo, B. Herbold, P. Hrodey, A. 

Mueller-Solger, T. Sommer, and K. Souza. Interagency Ecological Program 2010 Pelagic Organism Decline Work Plan 

and Synthesis of Results. Available at http://www.water.ca.gov/iep/docs/FinalPOD2010Workplan12610.pdf (last 

visited 06/26/12).

19 CAL. DEPT. OF FISH AND GAME, A REPORT TO THE CALIFORNIA FISH AND GAME COMMISSION ON STRESSORS 

IMPACTING DELTA RELATED ORGANISMS (September 1, 2010) , available at http://www.dfg.ca.gov/delta/reports/DeltaOrganisms-Stressors-Report-20100728.pdf (last visited 06/27/12).
7

assistance) to ensure those standards are met. EPA considered the information in the ANPR and the 

subsequent public comments in identifying water quality issues which are not effectively being 

addressed. EPA also considered the 2009 Periodic Review of the Water Quality Control Plan for 

the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (Bay-Delta WQCP) completed by the 

State Water Board and the 2011 Triennial Review of the Sacramento River-San Joaquin River 

Basin Plan completed by the Central Valley Regional Water Board in 2011. The conclusions of 

these reviews are generally consistent with EPA’s findings.

Despite much ongoing activity, CWA programs are not adequately protecting Bay Delta Estuary 

aquatic resources, as evidenced by the pelagic organism decline. That said, the Water Boards have 

initiated work on the most significant tasks and are making steady progress. Other agencies have 

also strengthened relevant regulatory programs. Most notably, the Department of Pesticide 

Regulation recently finalized regulations designed to prevent surface water contamination by 

pesticides in non-agricultural settings. 

In 2008, in response to the Bay Delta Estuary aquatic resource decline, the State Water Board, with 

the Central Valley and San Francisco Bay Regional Water Boards, adopted a five-year Strategic 

Workplan20 targeting their collective efforts towards a suite of priority activities to help address the 

ecological crisis. The Strategic Workplan included flow-related and water quality actions, 

deploying CWA tools as well as California’s broader authorities. For instance, the State Water 

Board’s administration of water rights goes well beyond CWA authority and is a critical component 

of ensuring flow of adequate quality, quantity, and timing to sustain aquatic species. Development 

of the Strategic Workplan was an important effort to articulate the Water Boards’ priorities and 

reinforce collaboration between the three Water Board offices. 

The Water Boards have accomplished much since the Strategic Workplan was adopted.

21

 Several 

major actions in the Strategic Workplan have been completed, notably: 

The Central Valley Regional Water Board studied the potential effects of ammonia on 

aquatic species and issued a new discharge permit to the Sacramento Regional County 

Sanitation District wastewater treatment facility requiring advanced treatment; 

The challenging Delta Methylmercury TMDL was adopted and implementation is under

way;

 

20 STATE WATER RES. CONTROL BD., STRATEGIC WORKPLAN FOR ACTIVITIES IN THE SAN FRANCISCO 

BAY/SACRAMENTO-SAN JOAQUIN DELTA ESTUARY (July 2008), available at

http://www.swrcb.ca.gov/waterrights/water_issues/programs/bay_delta/strategic_plan/docs/baydelta_workplan_final.pd

f (last visited 06/26/12).

21 STATE WATER RES. CONTROL BD., BAY-DELTA STRATEGIC WORKPLAN UPDATE TO THE BOARD (May 17, 2011), 

available at http://www.swrcb.ca.gov/waterrights/water_issues/programs/bay_delta/element_actions/ (last visited 

06/26/12).
8

Key steps were taken toward developing a Delta Regional Monitoring Program (RMP), 

including publishing the first Pulse of the Delta report; 

New flow objectives to support migratory fish populations for the San Joaquin River and 

tributaries were proposed and are slated for adoption in 2013; and

Water quality improvements were made through implementing TMDLs for selenium, 

organophosphate pesticides, and low dissolved oxygen (see Table 1 on page 23). 

Although not in the Strategic Workplan, the Board also produced the Delta Flow Criteria Report22

in August 2010, as mandated by the State’s 2009 Delta Reform legislation. This significant effort 

drew upon the best available science to develop useful recommendations, though other activities 

were necessarily delayed due to the Water Board’s finite resources.

Notwithstanding the Water Boards’ comprehensive water quality program and the progress made, 

several efforts have fallen behind the original Strategic Workplan schedule, either due to resource 

constraints, unforeseen tasks (such as the Flow Criteria), or lengthy public process. Of most 

significance, the State Water Board only recently initiated its comprehensive review of the 2006 

Bay-Delta WQCP, including Delta flow objectives. This was originally scheduled for completion 

in mid-2010, with implementation to begin by the end of 2011. The development of financial and 

governance options for the long-term Delta RMP has also been delayed. Lastly, though the 

Strategic Workplan set priorities for TMDL development and implementation, resources have not 

been sufficient to aggressively implement all of the adopted TMDLs (27) while concurrently

developing new TMDLs (15 underway) to address other impairments. The Water Boards lack 

protocols for tracking TMDL implementation, providing regular updates on the status of achieving 

load limits, or connecting water quality monitoring data with TMDL progress. 

EPA recommends the Water Boards update the 2008 Strategic Workplan, as it was envisioned as a 

five-year plan. Current knowledge of ecosystem stressors may suggest different or additional 

priorities. For example, the Board might consider prioritizing the development of site-specific 

temperature criteria, given how critical temperature is to fish viability in the San Joaquin watershed. 

During the 2011 Triennial Review, the Central Valley Regional Water Board noted concerns that its 

current narrative temperature objective is not adequately protective of anadromous fish, particularly 

during early life stages,

23 a conclusion also supported by DFG and NMFS. An updated Strategic 

 

22 STATE WATER RES. CONTROL BD., DEVELOPMENT OF FLOW CRITERIA FOR THE SACRAMENTO-SAN JOAQUIN DELTA 

ECOSYSTEM PREPARED PURSUANT TO THE SACRAMENTO-SAN JOAQUIN DELTA REFORM ACT OF 2009 (August 3, 2010) 

available at 

http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/deltaflow/docs/final_rpt080310.pdf (last 

visited 06/27/12).

23 CENT. VALLEY REG’L WATER QUALITY CONTROL BD., ISSUE LIST AND WORKPLAN FOR THE 2011 TRIENNIAL REVIEW 

OF THE WATER QUALITY CONTROL PLAN FOR THE SACRAMENTO RIVER AND SAN JOAQUIN RIVER BASINS (2011) at page 

35. Available at http://www.waterboards.ca.gov/centralvalley/water_issues/basin_plans/2011_tr_workplan.pdf (last 

visited 06/26/12).
9

Workplan might also reflect the Irrigated Lands Regulatory Program (ILRP), where the Central 

Valley Regional Water Board is working with water quality coalitions throughout the Central 

Valley to control farm run-off through water quality monitoring of receiving water and corrective 

actions when impairments are found. The ILRP goes beyond the authorities of the CWA in 

addressing agricultural discharges to surface water and groundwater and is critical to addressing the 

biggest source of nonpoint source pollution to the Estuary.

In addition, EPA encourages the Water Boards to more fully and specifically identify impairments 

to Bay Delta Estuary water quality where a designated use is impaired or a narrative standard is 

violated. One of the foundations of the CWA program is the biennial evaluation of water quality 

impairments included in the Integrated Water Quality Monitoring and Assessment Report under 

Sections 303(d) and 305(b)(“Integrated Report”). The Integrated Report identifies waterbodies with 

water quality problems, assesses the cause of the problems, and proposes a remedial approach. 

Integrated Reports have tended to focus on impairments measurable by numeric objectives. In the 

Bay Delta Estuary, many of the beneficial uses are defined by ecological function (fish migration, 

warm freshwater habitat, etc.) or are protected by narrative objectives (anadromous fish doubling). 

Identifying impairments of these beneficial uses or violations of narrative objectives is complex. 

Nevertheless, the failure to do so results in a distorted picture of the status of water quality in the 

Bay Delta Estuary. EPA will work with the Water Boards to address this problem during the next 

(2014) Integrated Report cycle. As the information in the ANPR and this Action Plan suggests, 

many of the designated uses in the Bay Delta Estuary are impaired. Identifying those impairments 

and identifying the cause (whether it is a “pollutant” for purposes of Section 303(d) or some other 

cause) is a critical part of the Clean Water Act response to the Estuary’s problems.

The State Water Board is also developing state-wide policies and general permits that will benefit 

the Bay Delta Estuary. In some areas, the Water Boards are undertaking groundbreaking work. For 

example, California's draft Toxicity Policy proposes new toxicity evaluation methods (“whole 

effluent toxicity”) which will more consistently and effectively diagnose water quality problems 

caused by pesticides and other toxicants. Other state-wide policies are being developed related to 

nutrients (including guidance on developing numeric nutrient endpoints); biocriteria (i.e., biological 

objectives that will provide narrative and numeric benchmarks to describe conditions necessary to 

protect aquatic life beneficial uses); and methylmercury (including water quality criteria based on 

fish-tissue concentrations protective of human health).

In the face of complex ecological problems, declining budgets and a high degree of public and 

political interest, the Water Boards have accomplished much. They have targeted their efforts at the 

most crucial tasks and are making steady progress. EPA supports the State in these priority areas, 

which constitute much of EPA’s Action Plan, below.

EPA’s Action Plan

EPA believes the activities highlighted below are the most significant steps, within EPA’s 

authorities and resources, toward restoring water quality and aquatic species health in the Bay Delta 

Estuary. Prioritizing the many Bay Delta Estuary stressors is difficult. The scientific community 

has not identified any single stressor as primarily responsible for diminishing fish populations. 

Instead, scientists on the Delta Stewardship Council's Independent Science Board, the Interagency 
10

Ecological Program, and the National Research Council describe contaminant and habitat stressors 

in the Bay Delta Estuary as interactive and highly dynamic. Informed by these experts, EPA 

concludes, from the perspective of the Clean Water Act, that updating and implementing the 

estuarine habitat water quality standard in the Bay-Delta WQCP is the most critical action for 

protecting aquatic life in the Bay Delta Estuary. EPA is committed to supporting the State Water 

Board in this important work. 

Over the last decade, there has been much regulatory activity related to contaminant stressors,

including pesticides, selenium, mercury, and ammonia. By contrast, the estuarine habitat water 

quality standard has not been updated for 17 years. Flow is a primary driver of physical habitat 

conditions, including turbidity, temperature, dissolved oxygen, and nutrient loading. In addition, 

the impacts of contaminant stressors are significantly altered by flow, as flows determine residence 

time, concentrations of contaminants, exposure duration and the salinity, temperature, and turbidity 

conditions that alter the chemistry and biological availability of contaminants. 

This Action Plan relies on complementary State and EPA actions. EPA works closely with the 

Water Boards to develop a common understanding of how the resources and authorities of the 

CWA, supplemented by California’s additional resources and authorities, can achieve mutual goals. 

EPA has consulted with the Water Boards in developing these recommendations and will continue 

this collaboration to address the priority water quality issues in the Estuary. EPA will evaluate 

progress on the proposed actions, as well as the underlying science and evolving understanding of 

aquatic resource protection in the Bay Delta Estuary, to ensure our resources are focused on the 

most critical needs.

EPA recognizes that the next 20 years will see significant change in the Bay Delta Estuary. Some 

changes will be the result of human decision (or non-decision) and are controllable – Delta 

conveyance, pollution, future invasive species, land use. Other changes are largely beyond local 

control – climate change, earthquakes, legacy pollution, existing invasive species, and population

growth. While our response to these uncontrollable stressors will be mainly adaptive, any plans to 

restore the Estuary need to consider these likely threats.

Appendix I is a more complete discussion of each of the water quality issues in the ANPR, 

including highlights from public comments, EPA’s assessment of the regulatory response to each 

issue, and areas where EPA believes additional focus would be helpful. Highlighted below are

EPA’s seven priority areas to help restore the aquatic resource beneficial uses of the Bay Delta 

Estuary.

1. Estuarine habitat water quality standards 

The State Water Board should expeditiously review, modify, and implement estuarine habitat 

standards in the Bay Delta Water Quality Control Plan to more fully protect aquatic species. 

EPA concurs with the timeframe set for this action by the Delta Stewardship Council of June 
11

2014.24 EPA will provide assistance and recommendations to the State Water Board as it 

considers new standards to protect estuarine habitat. 

In 1991, the State Water Board designated Estuarine Habitat as a beneficial use of the waters in the 

Bay Delta Estuary. In 1995, the State Water Board established a Delta outflow standard designed to 

protect estuarine habitat and fisheries. This outflow standard25 was designed to mimic the 

relationship between springtime precipitation and the geographic location and extent of estuarine 

habitat as had occurred in the late 1960s and early 1970s and was adopted as a springtime standard 

only; no attempt was made at that time to define standards explicitly protecting the estuarine habitat 

designated use during other times of the year.

From 1995 to 1999, there was a significant recovery of migratory and resident Delta fish 

populations, probably due primarily to a series of wet springs and probably helped by the newly 

implemented water quality standards. In about 2000, however, many critical pelagic species 

suffered an unexpected and dramatic decline (the “pelagic organism decline” or “POD”). This time 

period coincided with increases in fall pumping in the south Delta. Since then, during fall (except 

2011), the low salinity zone has been consistently in the western Delta where poor quality estuarine 

habitat is compressed into modified, inhospitable river channels. Consequently, no matter how 

favorable conditions might be for pelagic fishes during the winter and spring, they have been forced 

into unfavorable habitat during the fall. The POD prompted wide-ranging scientific investigations.26

In 2009, the State Water Board conducted a Periodic Review of the 2006 Bay-Delta WQCP. The 

Periodic Review concluded that “[t]he available information indicates that further review and 

change of Delta outflow objectives may be required. Changes to Delta outflow patterns have likely 

contributed to the POD and are likely having an impact on the abundance of other species of 

concern...Based on current scientific information, recent regulatory actions, and expected 

recommendations from agencies and stakeholder groups, staff recommends the State Water Board

conduct a detailed review of the Delta outflow objectives for possible revisions to the Bay-Delta 

Plan. Any revisions should also consider the need for Delta inflows.”

27

 

 

24 DELTA STEWARDSHIP COUNCIL, FINAL STAFF DRAFT OF THE DELTA PLAN (MAY 2012), available at 

http://deltacouncil.ca.gov/delta-plan/current-draft-of-delta-plan, at page 146 (last visited 6/28/12).

25 The history and background of the X2 standard is discussed at length in the ANPR at pp. 52-56 and the associated 

footnotes.

26 Baxter, R., R. Breuer, L. Brown, L. Conrad, F. Feyrer, S. Fong, K. Gehrts, L. Grimaldo, B. Herbold, P. Hrodey, A. 

Mueller-Solger, T. Sommer, and K. Souza. Interagency Ecological Program 2010 Pelagic Organism Decline Work Plan 

and Synthesis of Results, available at http://www.water.ca.gov/iep/docs/FinalPOD2010Workplan12610.pdf (last visited 

06/26/12).

27 STATE WATER RES. CONTROL BD. Staff Report, Periodic Review of the 2006 Water Quality Control Plan for the San 

Francisco Bay/Sacramento-Estuary, at p. 19, available at 

http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/periodic_review/docs/periodicreview2009

.pdf (last visited 06/27/12). 
12

Over the last several years, the State Water Board has focused on the initial phase of the WQCP 

revision related to the Southern Delta Salinity and San Joaquin River Flow Objectives. Now that 

this first phase is well underway, on January 24, 2012, the Board initiated the process to review the 

remaining parts of the WQCP, including Delta outflow objectives (i.e., “X2”), with a goal of Board 

adoption of a revised WQCP by June 2014. Although this lags significantly behind the late 2011 

date established in the Board’s Strategic Workplan, EPA is encouraged by and supportive of the 

Board’s commitment to this task.

The State Water Board’s WQCP review has received significant attention. For example, the Delta 

Stewardship Council’s draft Delta Plan includes a policy requiring the State Water Board (a) adopt 

and implement updated flow objectives for the Delta by June 2014; and (b) develop flow criteria for 

high-priority tributaries to the Delta by June 2018.

To assist the Board in harnessing the considerable scientific research done since 1995, EPA 

convened a technical workshop in March 2012 to assemble information on how biological 

indicators and ecological processes change in response to different locations of the low salinity 

zone. Input received at the Workshop was compiled and submitted to the State Water Board for use 

during their upcoming proceedings.

28

 EPA provided initial scoping comments in April 

recommending that the Board consider standards to protect year-round conditions of physical 

factors that directly affect aquatic resources and which can be monitored and assessed in a way that 

will facilitate future review. An important aspect of this is developing metrics/performance 

measures to determine if the water quality objectives are contributing to a healthier ecosystem, and 

an adaptive management plan to support future revisions. Most recently, EPA submitted comments 

for the first of three State Water Board workshops on technical topics associated with the WQCP 

review.29 EPA will continue to provide assistance and recommendations as the Board review 

proceeds. Additional discussion on this topic may be found in Appendix I beginning at page 20.

2. Regional Water Quality Monitoring and Assessment Program

EPA supports the establishment of Regional Water Quality Monitoring and Assessment 

Programs in the Central Valley. EPA applauds the Central Valley Regional Water Board’s 

commitment to develop a Delta RMP, and has provided funding toward the Pulse of the Delta 

reports. With the Water Board, EPA will continue its support of an RMP in the San Joaquin

River Watershed. 

A significant impediment to improving water quality in the Delta and in the larger Central Valley is 

the lack of an effective, efficient system for collecting and assessing water quality data. There are 

many active monitoring programs in the Delta and its watersheds, most of which are narrowly 

 

28 BROCK B. BERNSTEIN, FACILITATOR, U.S. ENVTL. PROT. AGENCY, WORKSHOP SUMMARY: TECHNICAL 

WORKSHOP ON ESTUARINE HABITAT IN THE BAY DELTA ESTUARY (March 27, 2012) available at:

http://www.epa.gov/sfbay-delta/activities.html.

29 http://www.epa.gov/sfbay-delta/activities.html
13

focused to satisfy specific regulatory requirements. Some contaminants are monitored regularly;

others occasionally or not at all. There is little standardization of monitoring procedures, data 

quality assurance or presentation protocols. Data is not accessible through a single database and 

some data are not accessible electronically. Most significantly, there is no regular attempt to 

integrate data into a meaningful assessment of water quality. The current situation makes it difficult 

to obtain timely access to monitoring results, to combine data for broader analyses and to strategically 

target and assess the effectiveness of corrective measures. 

California has seen the success of regional monitoring programs in the San Francisco Bay, in 

Southern California, and elsewhere. In the Bay Delta Estuary, since 1970, the Interagency 

Ecological Program (IEP) has provided the foundational science for water management activities. 

Though its contributions to understanding aquatic resources in the Estuary have been invaluable, the 

IEP has not historically focused on contaminants. When IEP launched its POD investigations in 

2005, the lack of any comprehensive assessment of water quality information impeded the 

understanding of the causes of the decline. In response, IEP directed numerous studies on fish 

health and contaminant effects and the Water Boards commissioned a University of California at

Davis study to synthesize existing contaminants data. The UC Davis study concluded there were 

insufficient high-quality data to make conclusions about the potential role of specific contaminants 

in the POD.30 A functioning RMP would include regular data collection and assessment, better 

preparing us to answer critical management questions.

The goals of a regional monitoring program are supported by many. The federal agencies, in their 

December 2009 Interim Federal Action Plan, committed to work together and with California to 

develop a comprehensive regional water quality monitoring and assessment program in the Delta 

and its tributaries.

31

 In 2006, the California legislature established a Water Quality Monitoring 

Council to improve the State’s system for collecting information on its water resources and make 

that information available to decision makers and the public. In its 2010 Comprehensive Water 

Quality Monitoring Program Strategy for California, the Council endorsed the California 

Environmental Data Exchange Network (CEDEN) as the mechanism for bringing monitoring data 

together from a wide variety of sources. The Council also committed to developing a series of 

internet portals (MyWaterQuality.com) to provide these data to the public. A Bay Delta Estuary 

portal is being developed jointly by the Water Board, IEP and the state and federal water 

contractors. The DSC also supports regional monitoring in its draft Delta Plan, identifying 2017 as 

a target date for developing and implementing a Delta RMP.32

 

30 Michael L. Johnson, et al., Evaluation of chemical, toxicological, and histopathologic data to determine their role in 

the pelagic organism decline (April 20, 2010) available at: 

http://www.swrcb.ca.gov/rwqcb5/water_issues/delta_water_quality/comprehensive_monitoring_program/contaminant_s

ynthesis_report.pdf (last visited 06/27/12).

31INTERIM FEDERAL ACTION PLAN (December 22, 2009) at page 15, available at

http://www.doi.gov/documents/CAWaterWorkPlan.pdf (last visited 06/27/12).

32 DELTA STEWARDSHIP COUNCIL, FINAL STAFF DRAFT OF THE DELTA PLAN (MAY 2012), available at 

http://deltacouncil.ca.gov/delta-plan/current-draft-of-delta-plan (last visited 06/27/12).
14

Development of a water quality RMP for the Delta and its watersheds will be an incremental 

process. In the Delta, the Central Valley Regional Water Board has taken initial steps, focusing on 

the contaminants-related monitoring under its direct control. In March 2011, the Central Valley 

Regional Water Board issued the first Pulse of the Delta report, an accessible summary of recent 

Delta water quality information related to ammonia, pyrethroid pesticides and other contaminants of 

emerging concern. The second “Pulse”, scheduled for publication in September 2012, will 

highlight mercury, sediment quality and nutrients. The Central Valley Regional Water Board is 

developing governance and finance options for the RMP and working with dischargers to achieve 

more integrated monitoring. In June 2012, they released a draft "Regional Monitoring and 

Assessment Framework and its Implementation" describing proposed monitoring questions and 

design principles for the Delta RMP.

In the San Joaquin watershed, EPA has made a similar investment, in collaboration with the Water 

Boards and others. The Central Valley Watershed Monitoring Directory was built to promote and 

facilitate improved coordination of water quality monitoring across the basin. In March 2010, EPA 

produced a “Proposed Strategy for San Joaquin River Basin Water Quality Monitoring and 

Assessment” and is currently funding the Coalition for Urban and Rural Environmental Stewardship 

(CURES) to implement this strategy. As part of that effort, in February 2012, CURES convened a 

workshop “Who’s Watching the San Joaquin River.” This forum brought together agricultural and 

municipal water districts and federal and state agencies to discuss their respective water quality 

monitoring programs, the questions they are trying to answer, what they’re learning from the data, 

and the potential benefit of increasing regional 

collaboration. A second workshop will focus on the next 

steps for setting up a San Joaquin Watershed RMP.

As the San Joaquin and Delta RMP efforts proceed, 

coordination with the IEP and the Delta Science Program is 

essential, especially as the IEP considers expanding its role 

to include more contaminant monitoring and/or additional 

monitoring upstream. Recently, IEP formed a Management, 

Assessment, and Synthesis Team (MAST) to conduct more 

timely synthesis and assessment of data. The nascent RMPs should consider supporting MAST and 

leveraging its expertise. Inclusion of the Central Valley Regional Water Board in the IEP 

Memorandum of Understanding would foster this collaboration. Recent work funded by the 

CALFED and Delta Science Programs, “Framework for a Unified Monitoring, Assessment and 

Reporting Program (UMARP) for the Bay-Delta”33 provides guidance to help unite monitoring 

efforts to be more responsive to management needs. 

 

33 S. Luoma, Chair, Framework for a Unified Monitoring, Assessment and Reporting Program (UMARP) for the BayDelta 2010 Report (Draft November 4, 2011), available at http://deltacouncil.ca.gov/science-program-event-products

(last visited 06/27/12).

EPA recently awarded $59,660 

to Revive the San Joaquin to 

establish a citizen-based water 

quality monitoring and 

pollution prevention education 

program in the Fresno area.

www.revivethesanjoaquin.org/
15

3. Total Maximum Daily Load Implementation

EPA will work with the Water Boards to accelerate Bay Delta Estuary water quality 

restoration through strengthening the implementation of Total Maximum Daily Loads 

(TMDLs). 

TMDLs are an important catalyst for restoring impaired water quality. They establish a technical 

foundation for identifying pollutant load reductions and actions needed to achieve water quality 

standards. EPA provides financial and technical assistance to the Water Boards to develop and 

implement TMDLs for impaired water bodies. EPA reviews and, if the TMDL complies with the 

CWA, approves final TMDLs. California has strong TMDL implementation plans and regulatory 

authorities, relative to other states, to address polluted runoff, habitat loss, and habitat degradation. 

The Water Boards prioritize development of TMDLs based on the severity of impairments. There 

are nine adopted TMDLs in the San Francisco Bay Delta Estuary addressing stressors that EPA 

identified in the ANPR as having the most significant impact on fish populations. see Table 1 on 

page 23. These TMDLs are designed to eliminate selenium and pesticide-caused aquatic toxicity 

and to remove low dissolved oxygen (DO) conditions that kill fish and block fish migration. 

Selenium, pesticides, and poor habitat conditions, like low dissolved oxygen, are linked to declining 

resident and migratory fish populations. There are also five EPA-approved mercury TMDLs in the 

Bay Delta Estuary. see Table 2 on page 27. 

Mercury and methylmercury pose unique water management challenges in the Bay Delta Estuary. 

Mercury contamination affects public health, aquatic-dependent wildlife, and subsistence,

recreational, and commercial fishing. Some elemental mercury is transformed to toxic 

methylmercury in the low-oxygen conditions present in some wetlands. Large-scale tidal and 

freshwater wetland restoration is proposed for mercury-contaminated sites in the Delta to provide 

habitat needed for protecting and increasing populations of resident and migratory fish. (See action 

#6 for information on activities to minimize the formation and mobilization of methylmercury).

Although TMDLs in the Bay Delta Estuary have succeeded in reducing pollutant loads, they also 

illustrate challenges to fully attaining water quality standards, as shown in Table 1. DO levels in the 

Stockton Deepwater Ship Channel violate the standard despite improvement in DO values as a

result of upgrading the Stockton wastewater treatment plant to 

tertiary treatment and installing an aerator in the ship channel. 

Water quality standards have been achieved in Salt Slough and 

the Grasslands Marsh by reducing selenium loads by twothirds (from 1996 to 2007) through water management 

improvements and redirecting contaminated flow to Mud 

Slough. Nevertheless, the

selenium load reductions needed to attain water quality 

standards in Mud Slough have not yet been met. Diazinon and 

chlorpyrifos TMDL implementation activities, along with 

FIFRA label changes and cancelation of registrations for most 

non-agricultural uses, resulted in meeting diazinon water quality standards in Bay Area and 

Sacramento urban streams and on 79-river miles in the Sacramento and Feather River systems. 

To read more about how a 

watershed approach has led to 

water quality improvements in 

the Grasslands Marsh and the 

Sacramento and Feather 

Rivers, visit EPA’s website at: 

www.epa.gov/sfbaydelta/improvement.htm 
16

However, the majority of river miles identified as impaired by these pesticides in the Bay Delta 

Estuary still have levels which exceed water quality standards, and many now have pyrethroid 

pesticides that cause aquatic toxicity. 

EPA is supporting efforts to strengthen TMDL implementation. TMDL implementation refers to 

completing required TMDL actions, achieving load limits, and removing water quality impairments. 

EPA will continue to work with the Regional Water Boards to implement TMDLs through the 

CWA nonpoint source program and the NPDES regulatory program. For example, incorporating 

TMDL Waste Load Allocations (WLAs) into Municipal Separate Storm Sewer System (MS4) 

permits is critical to addressing urban runoff, which significantly contributes to water quality 

impairments in the Bay Delta Estuary. There are four MS4 permits in the Bay Delta Estuary that 

are either expired or will expire by the fall of 2013. The updates of these MS4 permits need to 

include urban runoff WLAs as clear, measurable, and enforceable permit provisions. EPA also 

encourages the Water Boards to fully use their broad authorities to address water quality 

impairments, including the Irrigated Lands Regulatory Program and, where appropriate, the water 

rights program. 

EPA and Water Board oversight of TMDL implementation can improve accountability and help 

align grant and program activities to ensure timely achievement of load limits and removal of 

impairments. EPA has identified several additional actions to address TMDL implementation 

challenges in the Bay Delta Estuary. 

First, EPA will work with the Water Boards to assess progress in implementing approved TMDLs. 

This will begin with the TMDLs (identified in Table 1) for the contaminants EPA believes are of 

most importance to aquatic species in the Bay Delta Estuary. California began reporting TMDL 

implementation progress in the California Water Boards’ 2010-2011 Annual Performance Report.34 

EPA will build on this effort with the Water Boards to identify complete, incomplete and overdue 

actions for TMDLs listed in Tables 1 and 2; evaluate overdue actions to achieve load limits; create a 

list of priority TMDL actions; identify methods for completing these actions; and confirm target 

dates for achieving TMDL load limits. This is the beginning of an EPA sustained effort to oversee 

progress towards achieving water quality restoration goals specified in the Bay Delta Estuary 

TMDLs.

Second, EPA will expand the use of watershed plans and decision tools to improve the efficiency 

and effectiveness of management practices necessary to achieve TMDL pollutant load reductions. 

Decision tools can identify cost-effective, individual TMDL actions focused on achieving water 

quality goals. For example, EPA worked with DWR and other partners to develop a pesticide risk 

assessment model, the “Spatial and Temporal Quantification of Pesticide Loadings to the 

Sacramento River, San Joaquin River, and Bay-Delta”, that identifies the best locations and times 

 

34 STATE WATER RES.CONTROL BD. , THE CALIFORNIA WATER BOARDS' ANNUAL PERFORMANCE REPORT - FISCAL 

YEAR 2010-11, available at http://www.waterboards.ca.gov/about_us/performance_report_1011/ (last visited 

06/27/12).
17

for BMP installation based on the presence of sensitive aquatic life and pesticide use.35 This 

information can minimize aquatic life exposure to land-applied pesticides by informing choices 

about the type, location, and timing of BMPs. EPA will help make this tool widely available and 

encourage its use. This model could be used to inform choices about priority implementation areas 

for programs such as the California Nonpoint Source Program (CWA Section 319 funds) and the 

new Natural Resources Conservation Service’ Bay-Delta Initiative. Decision-makers will have 

better information to make cost-effective implementation decisions to improve water quality and 

aquatic habitats by developing watershed plans and decision tools based on TMDLs.

Third, EPA will assist the Water Boards in developing tracking and accounting tools to document 

and publicly report TMDL progress. Reliable tracking and accounting of pollutant reduction efforts 

are essential for program managers and policy makers to determine if current strategies are 

sufficient or if new strategies are necessary to meet TMDL milestones and goals. In addition, 

accurate and transparent tracking and accounting are critical to maintaining public confidence that 

water quality restoration funds are being wisely invested and that watershed partners are fulfilling 

their commitments to reduce loads and enhance aquatic habitat.

4. Selenium water quality standards 

By December 2012, EPA will draft new site-specific numeric selenium criteria to protect 

aquatic and terrestrial species dependent on the aquatic habitats of the Bay Delta Estuary. 

EPA’s selenium work continues a multi-decade effort responding to scientific evidence that the 

current selenium water quality standards do not adequately protect sensitive species. In 2000, FWS

and NMFS drafted a Biological Opinion finding jeopardy under ESA for the selenium criteria 

which EPA proposed in the California Toxics Rule. To avoid a final jeopardy opinion, EPA agreed 

to develop site-specific water quality criteria for selenium, beginning in the Bay Delta Estuary. 

EPA is using an ecosystem-based model created by the U.S. Geological Survey (USGS) 36 with 

advice from the FWS and NMFS. The model reflects the food web in the Bay Delta Estuary, the 

diet of sensitive species and their use of habitats, and hydrological conditions. Certain threatened 

and endangered species, including sturgeon and certain birds, feed on clams. The Corbula 

amurensis clam species, which is the Estuary’s dominant bivalve, bioaccumulates selenium very 

efficiently. More stringent selenium water quality criteria will require actions that decrease 

allowable concentrations of selenium in surface waters of the Bay Delta Estuary and may set 

allowable levels of selenium in the tissue of fish and wildlife. The new criteria would reduce the 

chronic (long-term) exposure of sensitive species to selenium. 

 

35 Hoogeweg, C.G., W.M. Williams, R. Breuer, D. Denton, B. Rook and C. Watry. 2011. Spatial and Temporal 

Quantification of Pesticide Loadings to the Sacramento River, San Joaquin River, and Bay-Delta to Guide Risk 

Assessment for Sensitive Species. CALFED Science Grant #1055. November 2, 2011. available at

http://gis.waterborne-env.com/downloads/CALFED_Final_Report_2011-Nov_2_FINAL.pdf (last visited 07/23/12).

36 Theresa Presser & Samuel N. Luoma, A Methodology for Ecosystem-Scale Modeling of Selenium , 6 Integrated 

Environmental Assessment and Management 685 (October 2010), available at 

http://onlinelibrary.wiley.com/doi/10.1002/ieam.101/full (last visited 06/27/12). 
18

Following the development of the Bay Delta selenium criteria, site-specific criteria will be 

developed for other parts of California, including the San 

Joaquin Valley watershed. 

EPA is engaged in other efforts to minimize selenium 

discharges to the San Joaquin River and the Bay Delta Estuary, 

including the Grasslands Bypass Project and the North San 

Francisco Bay TMDL. These are described in Appendix I

beginning at page 2.

5. Pesticide pollution prevention

EPA will help ensure that federal regulation of pesticides under FIFRA more fully considers 

effects on aquatic life. EPA will also work with our partners to minimize pesticide pollution in 

urban runoff. 

EPA is committed to using its authority under FIFRA to minimize aquatic toxicity related to the use 

of pesticides. In California, pesticides registered by EPA under FIFRA have been found to cause 

aquatic toxicity and water quality impairments, even though they are applied in full compliance 

with FIFRA requirements. Data regarding these impacts is essential to a more thorough evaluation 

during the pesticide registration review process which is done every 15 years by EPA’s Office of 

Pesticide Programs (OPP) in Washington D.C. EPA Region 9 is working with California agencies

and OPP to ensure OPP has the most currently available pesticide water quality data for use in 

pesticide aquatic exposure assessments. California data will help OPP assess potential risk to 

aquatic organisms and develop the necessary use restrictions to prevent pesticide water quality 

problems in the future. OPP and EPA’s Office of Water are also developing a “Common Effects 

Methodology” to establish a common approach under FIFRA and CWA for estimating effects of 

pesticides on aquatic life.

In addition, EPA will work with the Water Boards and other partners to mitigate pesticide pollution 

in urban runoff.37 EPA supports the inclusion of measurable and enforceable Low Impact 

Development (LID) requirements in all MS4 permits for new development and redevelopment to 

minimize pollution in urban runoff. The Central Valley Regional Water Board has the opportunity 

to foster LID to minimize pollutants in urban runoff when they update MS4 permits for the cities of 

Fresno, Modesto, and Stockton and the county of Sacramento (all of which have expired or will 

expire within the next two years.)

EPA also recommends including LID requirements in CWA Section 401 Water Quality 

Certifications. CWA Section 401 applies to development projects that require a CWA Section 404 

 

37 EPA notes that recent research has shown a significant reduction in diazinon and chlorpyrifos in urban settings after 

EPA’s phase out of those pesticides. See K.R. RYBERG, ET AL., U.S. GEOLOGICAL SURVEY, TRENDS IN PESTICIDE 

CONCENTRATIONS IN URBAN STREAMS IN THE UNITED STATES, 1992-2008 (2010), available at

http://pubs.usgs.gov/sir/2010/5139/pdf/sir2010-5139.pdf (last visited 06/26/12).

To learn more about EPA’s 

Strategic Plan for the San 

Joaquin Valley, go to:

www.epa.gov/region9/strateg

icplan/sanjoaquin
19

permit from the Corps. These projects include many new residential and commercial developments. 

EPA recommends the Central Valley Regional Water Board consider EPA’s June 5, 2012, guidance 

on integrated municipal stormwater and wastewater planning.

38

 If aquatic toxicity from urban 

runoff persists in the Bay Delta Estuary and its tributaries, EPA recommends the Central Valley 

Regional Water Board evaluate the use of residual designation authority to establish a Delta Region 

Municipal MS4 permit. 

EPA is funding pesticide pollution prevention efforts by the San Francisco Estuary Partnership 

(SFEP). SFEP’s Pesticide Reduction Campaign will promote less toxic pesticide options through 

educating retail employees and Bay Area residents. 

EPA has identified several other actions to support California’s groundbreaking work to minimize 

pesticide discharges and accelerate the restoration of water quality in the Bay Delta Estuary. These 

are outlined in Appendix I beginning at page 9. 

6. Restore aquatic habitats while managing methylmercury 

EPA will advance both the restoration of aquatic habitats and the implementation of the Delta 

methylmercury (MeHg) TMDL. EPA will fund research by USGS to study whether 

treatment technology used for carbon capture in the Delta can also be used to sequester MeHg 

in accreting wetlands. EPA will also collaborate on proposed restoration projects to ensure 

MeHg is effectively managed. 

Restoring wetlands in and near the Delta is an essential component of reviving the Estuary’s health. 

However, nearly all the locations targeted for habitat restoration in the Delta have been, or are at 

risk of being, contaminated with mercury from historical mining sources and ongoing air deposition 

from industry. This mercury can be transformed into MeHg by the anaerobic (low oxygen) 

conditions prevalent in wetlands. This toxic form of mercury can accumulate in fish and people 

who eat them.

39 Health advisories have been issued for the Delta and several upstream rivers.40

Given the long-term benefits of restoring aquatic habitats in the Delta (as well as the health benefits 

of eating fish), preventing the formation and mobilization of methylmercury in wetlands is critical. 

Scientific methods are being explored to prevent MeHg formation.

 

38 U.S. ENVTL. PROT.AGENCY, MEMORANDUM FROM NANCY STONER AND CYNTHIA GILES RE: INTEGRATED MUNICIPAL 

STORMWATER AND WASTEWATER PLANNING APPROACH FRAMEWORK (JUNE 5, 2012), available at

http://www.epa.gov/npdes/pubs/integrated_planning_framework.pdf (last visited 06/27/12). 

39 See generally STATE WATER RES. CONTROL BD., SWAMP –SURFACE WATER AMBIENT MONITORING PROGRAM 

COASTAL STUDY – BIOACCUMULATION IN SPORT FISH, available at

http://www.waterboards.ca.gov/water_issues/programs/swamp/coast_study.shtml. (last visited 06/27/12).

40 The Central Valley Regional Water Board is developing an exposure reduction program, pursuant to the Delta 

Mercury TMDL adopted in 2010 and approved by EPA in 2011. See page 14 of the TMDL, available at:

http://www.swrcb.ca.gov/rwqcb5/water_issues/tmdl/central_valley_projects/delta_hg/2011oct20/bpa_20oct2011_final.p

df (last visited 06/27/12).
20

USGS has demonstrated on Twitchell Island that growing tules can rebuild peat soils, reverse 

subsidence, and sequester carbon dioxide. With DWR support, USGS is now studying the methane 

emissions from the restored wetlands and the treatment options for dissolved organic carbon (DOC) 

to safeguard water quality. EPA research funds will augment this work by enabling USGS to study 

whether the treatment technology used for DOC could also be used to sequester MeHg in the 

accreting wetlands. This work is consistent with the DSC’s draft Delta Plan which calls for the 

linking of restoration projects with efforts to reverse subsidence on sunken Delta islands, sequester 

carbon, and address the effects of MeHg on food webs and the estuarine ecosystem. 

In the Cosumnes River Preserve, using CWA Section 319 funds, the Central Valley Regional Water 

Board awarded the U.S. Bureau of Land Management and USGS $832,000 to develop management 

measures for ricelands to minimize the formation and transport of MeHg, including the control of 

irrigation water and the harvesting of organic matter specifically.

EPA will also collaborate on proposed restoration projects within the Yolo Bypass to ensure MeHg 

is effectively managed during both the near-term restoration phase and the long-term stewardship 

phase. The 59,000-acre Yolo Bypass was constructed as a flood control feature and retains some of 

its pre-settlement floodplain functions as it supports 42 species of fish, 200 species of birds, and an 

abundance of phytoplankton and zooplankton. Proposed restoration projects include increasing the 

areal extent of aquatic habitat beyond that already contained in the Yolo Wildlife Area and 

renovating weirs that have proved harmful to fish. However, sediments within the Bypass are 

contaminated with mercury and could provide the substrate necessary for the formation of 

methylmercury. In addition, Cache Creek transports mercury from abandoned mercury mines in the 

Coast Range to the Cache Creek Settling Basin and eastward to the Bypass, and accounts for 60% 

of all the mercury discharged within the Central Valley. EPA’s Superfund Program (and 

responsible parties) have already substantially controlled mercury releases from the Abott/Turkey 

Run Mine and the Sulphur Bank Mercury Mine at Clear Lake, upstream of Cache Creek. EPA will 

build on these efforts to further reduce the environmental threats posed by methylmercury.

In addition, EPA has awarded $1.5 million to the California Coastal Conservancy to help restore 

tidal marsh and related habitats on the 1,166-acre Dutch Slough property in Contra Costa County, 

where Marsh Creek enters the Delta at Big Break. Marsh 

Creek receives acid mine drainage from the abandoned Mount 

Diablo Mercury Mine situated 30 miles upstream from Dutch 

Slough, and mercury-laden sediment occupies space within the 

Marsh Creek Reservoir upstream from Dutch Slough. EPA 

will work with stakeholders to ensure MeHg is effectively 

managed at Dutch Slough. The Dutch Slough Restoration 

Project presents a rare opportunity to restore tidal marsh and a 

floodplain on the delta of a creek and to do so in a way that 

prevents the formation and transport of MeHg as anaerobic 

processes take hold on a newly restored tidal marsh. 

EPA is also funding the Coastal Conservancy to study mercury 

cycling in South Bay tidal wetlands and salt ponds in order to adaptively manage future restoration 

activities. 

EPA recently awarded 

Friends of Marsh Creek 

$60,000 to help the local 

community improve water 

quality through pollution 

prevention, best management 

practices for agricultural 

discharges, and appropriate 

creekside land uses.

www.fomcw.org/
21

These projects will provide lessons learned that may be applicable to other restoration projects in 

the Estuary. EPA will assist with this information transfer. Additional activities are described in 

Appendix I beginning at page 29.

7. Bay Delta Conservation Plan

EPA is supporting development of the Bay Delta Conservation Plan (BDCP) as one of the 

means of meeting the co-equal goals established by the California legislature – a more reliable 

water supply and a restored Delta ecosystem. 

As the BDCP is an ESA mechanism, EPA does not have a direct regulatory role. However, under 

Clean Air Act Section 309, EPA will review and comment on NEPA documents for the BDCP. In 

addition, EPA shares permitting responsibilities under CWA Section 404 with the Corps, and 

several BDCP projects will require CWA 404 permits. EPA also has an interest in how changes in 

Delta hydrology caused by BDCP implementation might affect attainment of water quality 

standards in the Delta. 

Given these interests, EPA has agreed to be a Cooperating Agency for the BDCP EIS to provide 

early input to the lead agencies (DWR, DFG, USBR, FWS and NMFS)) on the draft EIR/EIS.41 We 

are also working with the Corps and the lead agencies to integrate CWA requirements into the 

process of NEPA and ESA compliance so that CWA permitting of BDCP projects can proceed 

efficiently.

In both these capacities (NEPA and CWA 404), EPA will focus on three issues. The first is 

antidegradation. Any change in the location and operations of Delta water diversions must not 

further impair water quality in the Estuary. The Central Valley watershed is the source of many 

pollutants of concern in the Delta, including pesticides, nutrients (including ammonia), selenium, 

and mercury. All of the water bodies in the Bay Delta Estuary have been identified as “impaired” 

(i.e. not meeting water quality standards) for one or more parameters. Existing concentrations and 

loads of contaminants entering the Delta from upstream harm the health of the Delta ecosystem, as 

well as the upstream waters. In particular, large storm pulses can flush contaminants into the Delta. 

Changes in the location, timing, and amount of Delta diversions could exacerbate this problem. As 

Sacramento River inflow is reduced and/or San Joaquin River inflow increases, water quality will 

be affected. 

In addition to contaminants, EPA is concerned with the location and areal extent of the low salinity 

zone (LSZ), the area of the Estuary where sea water mixes with fresh river water creating important 

habitat. Many estuarine organisms show greater abundance or improved survival when the LSZ is 

 

41 Letter from Kathleen Goforth and Karen Schwinn, USEPA, to John Engbring, USFWS (November 12, 2008), 2 pp. 

available at http://www.epa.gov/sfbay-delta/pdfs/EPA_CooperatingAgencyStatus_BDCP_111208.pdf (last visited 

06/27/12).
22

located in the broad, complex shallows of Suisun Bay rather than in the less hospitable, rock-lined 

channels of the Western Delta. The location and operation of Delta diversions can significantly

affect the location of the LSZ. This is of particular concern given the record low levels of some 

pelagic fish species over the last decade.

Secondly, any new Delta diversion and conveyance facilities will have substantial impacts (direct 

and indirect) to “waters of the U.S.”, including the Sacramento River and other Delta tributaries, 

sloughs and wetlands, depending on their location. Pursuant to EPA’s shared responsibilities with 

the Corps, EPA will assist the Corps during the CWA 404 permitting process by: helping to verify 

the jurisdictional determination of the extent of impact to waters and wetlands; assessing the CWA 

Alternatives Analysis to ascertain the “Least Environmentally Damaging Practicable Alternative”; 

and reviewing the compensatory mitigation proposed for any unavoidable impacts to waters of the 

U.S. 

Lastly, the California legislature and the Delta Stewardship Council (as well as many scientists) 

have identified a need to reduce reliance on the Delta for water supply. We are encouraged by the 

position of the lead federal agencies for the BDCP that the Purpose and Need Statement of the 

BDCP “is not intended to imply that increased quantities of water will be delivered under the 

BDCP.”42 We are also optimistic that the State Water Board’s upcoming review of the Bay-Delta 

WQCP will appropriately address this California policy. Completion of the Board’s work is 

essential for fully informed decisions on the BDCP.

 

42 Letter from Ren Lohoefener, et al. to Jared Blumenfeld, et al. (October 26, 2010), 3 pp. available at

http://www.epa.gov/sfbay-delta/pdfs/LeadFedAgncysBdcpPurpose-NeedLtrOct262010.pdf (last visited 06/27/12).
23

Table 1: 

TMDLs in the San Francisco Bay Delta Estuary Addressing Aquatic Resource Impairments Identified in the ANPR

TMDL 

Pollutant/Stressor

and water body

(EPA Approval Date)

Primary Pollutant Sources & Allocations

Target 

Compliance 

Date

Load Limits/TMDL Targets Achieved 

Load Reduction/TMDL Progress 

Selenium

Salt Slough

(1999)

Major: Shallow ground water drainage (agricultural tile 

drainage) from the 97,000-acre Drainage Project Area 

of the Grassland Watershed (88% of total load)

Minor: Distributed inputs throughout the San Joaquin 

River Basin

100% load allocation for non point source

October 20101

Selenium loads reduced by two-thirds (1996-2007) through 

water & crop management.

Selenium contaminated shallow ground water drainage is 

routed away from Salt Slough to achieve load limits 

(balance)

Selenium removed as impairment from Salt Slough on 

303(d) List

Selenium

Grasslands 

Marshes

(2000)

Major: Shallow ground water drainage (agricultural tile 

drainage) from the 97,000-acre Drainage Project Area 

of the Grassland Watershed (88% of total load) 

Minor: Distributed inputs throughout the San Joaquin 

River Basin

100% load allocation for non point source

October 20101

Selenium loads reduced by two-thirds (1996-2007) through 

water & crop management.

Selenium contaminated shallow ground water drainage is 

rerouted away from Grasslands Marsh to achieve load 

limits

Selenium removed as impairment from Grasslands 

Marshes on 303(d) List

Selenium

Lower San Joaquin 

River2

(2003)

Major: Subsurface agricultural return flows (tile 

drainage) from the 97,000-acre Drainage Project Area 

of the Grassland Watershed (88% of total load) 

Minor: Distributed inputs throughout the San Joaquin 

River Basin

100% load allocation for non point source

December 

2019

Selenium removed as impairment downstream of the 

confluence with the Merced River on 303(d) list

Selenium loads reduced by two-thirds (1996-2007) through 

water & crop management.

Standards not yet achieved for Mud Slough North, from the 

end of the San Luis Drain to the San Joaquin River and in 

the San Joaquin River from Mud Slough, North, to the 

Merced River.
Table 1: TMDLs in the San Francisco Bay Delta Estuary Addressing Aquatic Resource Impairments Identified in the ANPR

24

TMDL 

Pollutant/Stressor

and water body

(EPA Approval Date)

Primary Pollutant Sources & Allocations

Target 

Compliance 

Date

Load Limits/TMDL Targets Achieved 

Load Reduction/TMDL Progress 

Diazinon & 

Chlorpyrifos 

Sacramento County 

Urban Streams3

(2004)

Urban runoff from applications of pesticide in nonagricultural areas

September 

2013

Elk Grove Creek impairment removed from 303(d) List

Central Valley RWQCB anticipates delisting most of these 

streams in the next 303(d)/305(b) Report.

FIFRA registrations cancelled for most non-agricultural 

uses.

Water quality improving. 

Low Dissolved 

Oxygen (DO)

Stockton Deep 

Water Ship Channel

(2007)

WWTP, urban and rural runoff sources of oxygen 

demanding substances5(e.g., organic nutrients).

Ship channel geometry.6

Reduced flow.7

TMDL assigns equal responsibility of impairment to all 

three factors.

December 31, 

2011

Substantial reduction in organic nutrient discharges from 

Stockton WWTP.

Installation of aerator.

DO levels improving, but are still too often below the 

objective.

Diazinon & 

Chlorpyrifos

Lower San Joaquin 

River4

(2006)

Primarily agricultural applications.

Load and wasteload allocations are equal to the Delta 

Loading Capacity. 

2011

Approximately 46 miles of San Joaquin River de-listed for 

diazinon 

85 miles remain on the 303(d) list for diazinon..

130 miles remain on 303(d) list for chlorpyrifos.
Table 1: TMDLs in the San Francisco Bay Delta Estuary Addressing Aquatic Resource Impairments Identified in the ANPR

25

TMDL 

Pollutant/Stressor

and water body

(EPA Approval Date)

Primary Pollutant Sources & Allocations

Target 

Compliance 

Date

Load Limits/TMDL Targets Achieved 

Load Reduction/TMDL Progress 

Diazinon & 

Pesticide-Related 

Toxicity

Bay Area Urban 

Creeks

(2007)

Urban runoff that contains pesticides as a result of 

pesticide application for structural pest control, 

landscape maintenance, agricultural, and other pest 

management purposes.

100% of the TMDL is allocated to urban runoff as a 

“wasteload allocation” to stormwater point sources

Adjusts to 

changes in 

pesticides 

causing 

toxicity

Diazinon and chlorpyrifos registrations cancelled for most 

non-agricultural uses are is no longer the source of aquatic 

toxicity.

Aquatic toxicity in urban streams is caused by pyrethroid 

pesticides

Pesticide-related toxicity load limits are not met. Load limits 

are met for diazinon.

Diazinon & 

Chlopryifos

Sacramento-San 

Joaquin River Delta

(2007)

Primarily agricultural applications.

Load and wasteload allocations are equal to the Delta 

Loading Capacity.

December 1, 

2011

2011 monitoring shows diazinon concentrations below 

objective in some Delta waterways.

2011 monitoring shows chlorpyrifos concentrations 

exceeding objectives in some Delta waterways.

All waters in Delta remain on 303(d) List in for diazinon & 

chlorpyrifos.

Diazinon & 

Chlorpyrifos

Lower Feather River 

and Lower 

Sacramento River8

(2008)

Primarily agricultural applications.

Load and wasteload allocations are equal to the Delta 

Loading Capacity objectives.

2010

Diazinon impairment removed from 79-river miles of Lower 

Sacramento and Feather Rivers.

Load limits & objectives met for chlorpyrifos on Lower 

Sacramento.

Chlorpyrifos impairment remains on Lower Feather River.

1. The 5 μg/L four-day average water quality objective for the SJR below the Merced River must be met in above normal and wet years starting in water year 2006. The 5 μg/L four-day average 

objective must be met for critically dry, dry and below normal years starting in water year 2011. The 5 μg/L four-day average water quality objective must also be met for all year types in Mud 

Slough and the SJR from Sack Dam to the Merced River starting in water year 2011.

2. 50 miles of Lower San Joaquin River between Salt Slough (upstream border) and Vernalis at Airport Way Bridge (downstream border). 

3. Arcade Creek, Elder Creek, Elk Grove Creek, Morrison Creek, Chicken Ranch Slough, and Strong Ranch Slough. 

4. 130 miles of Lower San Joaquin River from Mendota Dam to Vernalis at Airport Way bridge. 

5. Stockton WWTP, algae loads from the watershed, and urban and agricultural runoff. 
Table 1: TMDLs in the San Francisco Bay Delta Estuary Addressing Aquatic Resource Impairments Identified in the ANPR

26

6. Channel geometry reduces the assimilation capacity of oxygen demanding substances in three ways: 1) the deep wide channel reduces water velocity, increasing water residence time, 

concentration of organic material, and consumption of available oxygen; 2) the small water surface area to depth ratio reduces the proportion of water that is naturally aerated at the water air 

surface; and 3) poor light penetration, the result of increasing the concentration of organic material, encourages algal death and consumption of oxygen through decay process. 

7. Reduced flows from San Joaquin River water diversions to the State and Federal water projects, water transfers, and in basin diversions reduce reduces the assimilation capacity of oxygen 

demanding substances by reduces water velocity, increasing water residence time, and concentration of organic material which consumes available oxygen. 

8. Sacramento River below Shasta Dam, Feather River below Oroville Dam. 
27

Table 2: Mercury and Methylmercury TMDLs in San Francisco Bay Delta Estuary Watershed

TMDL Pollutant/Stressor

and water body

(EPA Approval Date)

Primary Pollutant Sources & Allocations

Target 

Compliance 

Date

Implementation Progress

Mercury

Clear Lake

(2003)

100% Load Allocation = nonpoint sources, 

Sulphur Bank mercury mine, atmospheric 

deposition, tributaries,

2023

Implementation activities at Sulphur Bank mine are 

occurring.1 

Water quality monitoring is done for special studies and 

associated with individual actions.

Monitoring data is not easily available and a periodic 

monitoring program has not been established.

Mercury Cache, Bear, & 

Sulphur Creeks & Harley 

Gulch 

(2007)

100% Load Allocation = nonpoint sources, 

mercury mines 20272

Water quality monitoring is done for special studies and 

associated with individual actions.

Monitoring data is not easily available and a periodic 

monitoring program has not been established.

Mercury

San Francisco Bay

(2008)

Load Allocation = 85% to bed erosion, upstream 

watersheds, atmospheric deposition, non-urban 

and stormwater runoff.

Waste Load Allocation is ~ 15% of sources 

including NPDES facilities and MS4 outfalls.

2030

Mercury & Methylmercury 

Guadalupe River 

Watershed

(2010)

~85% Load Allocation. Nonpoint sources = 

mining waste, impoundments (tributary lakes 

and reservoirs), and atmospheric deposition.

~ 15% Waste Load Allocation to urban storm 

water point sources (MS4s).

2030

Mercury & Methylmercury 

Sacramento-San Joaquin 

Delta 

(2011)

Load Allocation = 96% to Nonpoint sources 

including: Agricultural drainage, Atmospheric 

wet deposition, Open water, Tributary Inputs, 

Inputs from Upstream Subareas, Urban 

(nonpoint source), Wetlands.

Waste Load Allocation is ~ 4% of sources 

including NPDES facilities and MS4 outfalls. 

2030

Workplans for phase I control studies are being 

created.

Water quality monitoring will be part of control studies 

and other implementation actions.

Developing exposure reduction strategy

Monitoring data will be made available after it is 

generated.

1. Clear Lake Mercury TMDL 2010 Update http://www.swrcb.ca.gov/centralvalley/water_issues/tmdl/central_valley_projects/clear_lake_hg/cl_final_tmdl_5yr_update.pdf

2. Target date for load reduction achievement – 15 – 20 years after implementation of mercury control program; 5 – 10 additional years after water column objectives are met to 

reduce fish tissue concentrations to objective concentrations.