EPA releases Action Plan for the Delta: Reducing pollution and restoring freshwater flows are key to improving water quality

Following an analysis that determined that existing state and federal water quality standards were not adequately protecting the Delta’s ecosystem, the Environmental Protection Agency (EPA) released an Action Plan in August of 2012 to address water quality challenges in the Bay Delta Estuary. The report identifies seven measures for improving water quality, restoring habitat, and improving the management of the Delta that will be pursued in partnership with the State Water Resources Control Board, the regional water boards for the Central Valley and the San Francisco Bay, as well as other state and federal agencies.

California’s economic security depends on a healthy Bay Delta,” said Jared Blumenthal, EPA’s Regional Administrator for the Pacific Southwest, in an agency press release. “By upholding the goals of the Clean Water Act, we can ensure that our water is fit for drinking, farming, recreation, and for fish and wildlife.

The EPA’s statutory mission is to implement the provisions of the Clean Water Act (CWA). The EPA has determined that even though much has been done, the decline of fish species is evidence that CWA programs are not adequately protecting the Delta. While the Water Boards are making progress on the most significant tasks, some efforts have fallen behind schedule, either due to resource constraints, unforeseen tasks, or lengthy public process. However, the EPA recognizes that “in the face of complex ecological problems, declining budgets, and a high degree of political interest, the Water Boards have accomplished much. They have targeted their efforts at the most crucial tasks and are making steady progress.”

The EPA has concluded that updating and implementing the State Water Board’s Bay-Delta Water Quality Control Plan is critical. The EPA also recommends the State Water Board update the Board’s 2008 Strategic Plan as new scientific knowledge acquired since then may suggest different or additional priorities. The EPA also encourages all Water Boards to more fully and specifically identify impairments when water quality impacts a designated use or a narrative standard is violated.

The EPA is one of the more than 25 state and federal governmental agencies that have responsibilities for some aspect of the Delta. The EPA supports the efforts of these other agencies and organizations to improve conditions in the Delta, including the Delta Stewardship Council’s Delta Plan, the Department of Fish and Game’s Conservation Strategy, and the Central Valley Flood Protection Plan. The EPA also supports development of the Bay Delta Conservation Plan (BDCP) and is participating as a cooperating agency in the environmental review process.

The Action Plan identifies seven actions that are considered the most significant steps the agency can take within their authorities and resources to assist in improving conditions in the Delta. However, the EPA recognizes that even if these seven actions are all successfully implemented, it still would not resolve all of the Delta’s problems. “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,” the report states.

The EPA also recognizes that the next 20 years will bring change to the Bay-Delta. Some of these changes are controllable by humans, such as conveyance, pollution, and land use; other changes are largely beyond control, such as climate change, earthquakes, legacy pollutants, and population growth. While the response to uncontrollable factors may be by necessity adaptive, any plans to restore the Delta must consider all likely threats.



The State Water Board should ‘expeditiously’ finish updating the Bay-Delta Water Quality Control Plan. The EPA concurs with the time frame set by the Delta Stewardship Council of June 2014.

In 1995, the State Water Board established a Delta outflow standard which was adopted as a springtime standard only with no attempt made at the time to define outflow standards for any other times of the year. For the next four years, there was significant recovery of Delta fish populations. However, around the year 2000, many fish species suffered steep declines, coinciding with increases in fall pumping in the south Delta. Since then during the fall, the low salinity zone, the area where fresh water mixes with sea water, moves into the inhospitable channels of the western Delta where habitat is poor. The low salinity zone is where the most favorable aquatic habitat conditions exist for many of the Delta’s fish species, and many species show greater abundance and improved survival when this low salinity zone is located in the shallows of Suisun Bay rather than the rock-lined channels of the Western Delta. In 2009, a periodic review of the 2006 Bay Delta Water Quality Control Plan concluded that a change of Delta outflow objectives may be required.

The last several years, the State Water Board has been working to update the 2006 Bay Delta Water Quality Control Plan, with the initial work focused on Southern Delta salinity and San Joaquin River flow objectives. With this phase of the process well underway, the Board has begun the process of reviewing remaining portions of the Plan with the goal of adopting a revised Plan by June of 2014. The EPA is providing assistance and recommendations to the State Water Board as they work to complete the update.


The EPA supports the establishment of the Regional Water Quality Monitoring and Assessment Programs in the Central Valley, and applauds the Central Valley Regional Water Boards’ commitment to develop a Delta Regional Monitoring Program (RMP).

The lack of an effective system for collecting and assessing water quality data is a significant impediment to improving water quality in the Delta. Some contaminants are monitored regularly while others maybe occasionally or in some cases, not at all. There is little standardization of procedures and the data that is collected is not easily accessed. Most importantly, there aren’t any programs to integrate the data that is collected into meaningful assessments of water quality; this has impeded efforts by scientists to assess the possible stressors responsible for the decline of native species.

The development of a Delta Regional Monitoring Program, which would include data collection and assessment, is incremental and currently underway by the Central Valley Regional Water Board.  The Board is currently developing governance and finance options and has released a draft framework document of the program proposing monitoring questions and design principles. Similar efforts are underway in the San Joaquin River Basin.


EPA will work with the Water Boards to strengthen implementation of Total Maximum Daily Loads (TMDLs).

All waters in the Delta are considered impaired by one or more contaminants. TMDLs provide a technical foundation for identifying pollutant loads and the actions needed to reduce them in order to meet water quality standards. There are 27 adopted TMDLs in the Delta, nine of which address stressors the EPA considers as having the most impact on fish populations. Fifteen additional TMDLs addressing other contaminants are currently under development.

The EPA supports efforts to strengthen TMDL implementation as oversight of implementation can establish accountability and ensure timely achievement of water quality standards. The EPA will assist by working with the Water Boards with assessing progress in TMDL implementation, expanding the use of watershed plans and decision tools, and assisting in developing tools to document and publicly report TMDL progress.


By December 2012, the EPA will draft new site-specific numeric selenium criteria.

The EPA’s multi-decade work on selenium standards continues with the EPA agreeing to develop site-specific selenium criteria, beginning with the Delta. More stringent selenium standards will require actions to decrease selenium in the surface waters of the Delta, thus reducing the chronic exposure of species to selenium. The EPA plans to propose selenium criteria for the Delta by December of 2012 with plans to develop site-specific criteria for other parts of California, including the San Joaquin Valley watershed.


EPA will help ensure that federal regulation of pesticides more fully considers effects on aquatic life, and will work to minimize pesticide pollution in urban runoff.

In California, some pesticides have been found to cause water quality impairments even though they are used in compliance with federal regulations. In order to thoroughly evaluate these impacts during pesticide registration review, data will be essential. The EPA is working with California agencies to be sure the most current data will be available for use in assessing pesticide impacts.

The EPA will also work with Water Boards and other partners to address pesticides in urban runoff. The EPA supports Low Impact Development (LID) and supports the inclusion of LID requirements in all urban stormwater (MS4) permits for new development and redevelopment. With Fresno, Modesto, Stockton and the county of Sacramento all holding expired or soon-to-expire urban stormwater discharge permits, the EPA notes that the Central Valley Regional Water Board will have an opportunity to minimize the effects of pesticide and other stormwater pollutants in the Delta.


The EPA will advance both the restoration of aquatic habitats and implementation of the Delta mercury TMDL by funding research and by collaborating on proposed restoration projects to ensure methylmercury is effectively managed.

Restoration of wetlands is essential to restoring the health of the Delta’s ecosystem; however, nearly all sites proposed for habitat restoration are contaminated with, or are at risk of being contaminated with, mercury. A legacy contaminant from the Gold Rush era, mercury is a particular challenge for wetland restoration as conditions prevalent in wetlands can cause mercury to be transformed into methylmercury, a toxic form capable of bioaccumulation in fish and aquatic-dependent wildlife. Therefore, preventing methylmercury from forming and mobilizing is critical.

The EPA is providing research funds to the USGS to study methods to sequester methylmercury in accreting wetlands and to develop management measures to minimize the formation and transport of methylmercury at the Consumnes River Preserve. The EPA has also awarded funds to the California Coastal Conservancy for the Dutch Slough restoration project in Contra Costa County and to study mercury cycling in South Bay tidal wetlands and salt ponds. The EPA will also collaborate on proposed restoration projects within the Yolo Bypass to ensure methylmercury is effectively managed.


EPA supports development of the Bay Delta Conservation Plan (BDCP).

Since the EPA has an interest in how the implementation of the Bay Delta Conservation Plan (BDCP) will affect water quality standards in the Delta, the EPA has agreed to be a Cooperating Agency for the BDCP EIS. The EPA particularly concerned that that any change in location and operation of water infrastructure will not further impair water quality. The EPA is also concerned with the location and extent of the low-salinity zone, an important habitat area for many fish species, as the location and operation of Delta diversions can significantly impact the location of the low salinity zone.

The EPA is also focused on the impacts of any new diversion facilities might have on the “waters of the U.S.”, especially the Sacramento River and other Delta tributaries. The EPA will work with the Corps to help verify jurisdictional extent of impacts to waters and wetlands, ascertain the least damaging alternatives, and review the proposed mitigation of unavoidable impacts to the waters of the U.S.

The EPA is encouraged by the legislated mandates and the DSC’s Delta Plan policy to reduce reliance on the Delta for water supply and by other developments as well:  “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.’. We are also optimistic that the State Water Board’s upcoming review of the Bay-Delta Water Quality Control Plan will appropriately address this California policy.”

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