Section 303 of the Clean Water Act (CWA) requires States to adopt and implement water quality standards to restore and maintain the chemical, physical, and biological integrity of the Nation’s waters. Water quality standards consist of beneficial uses designated for specific water bodies and water quality criteria necessary to protect those beneficial uses.
To comply with Section 303 of the CWA, the California State Water Resources Control Board (SWRCB) adopted water quality plans for Enclosed Bays and Estuaries (EBEP) and Inland Surface Water (ISWP) in the early 1990s. The plans established statewide water quality objectives for many toxic pollutants in California. However, various polluters filed suit against the State and won, resulting in the SWRCB rescinding the two water quality control plans in September of 1994. As a result, USEPA took over by promulgating federal water quality criteria with what is now called the California Toxics Rule.
Consultation under the federal Endangered Species Act was required for the California Toxics Rule because many listed species were affected. NMFS and USFWS issued a joint Biological Conference Opinion on March 24, 2000.  A remaining unresolved issue for California was the establishment of water quality criteria/objectives for selenium that takes into account bioaccumulation. The current State water quality objectives for selenium (2 µg/l monthly mean for lentic (still) waters of the Grasslands marshes; and 5 µg/l 4 day average for lotic/flowing waters of sloughs and rivers) do not consider bioaccumulation and are generally considered inadequate.
The California Toxics Rule Biological Opinion (p 9-10) required that USEPA perform the following actions:
1. EPA will revise its recommended 304(a) acute and chronic aquatic life criteria for selenium by January 2002.
2. EPA will propose revised acute and chronic aquatic life criteria for selenium in California by January of 2003.
Neither of these requirements of the CA Toxics Rule Biological Opinion has yet to be implemented. However, USEPA has released a report by the US Geological Survey upon which to base revision of San Francisco/Sacramento/San Joaquin Bay-Delta selenium water quality criteria and is now accepting comments on the report. Go here to see the USEPA’s California Toxics Rule page with studies and information.
The new selenium water quality criteria will be based on consideration of bioaccumulation using the Presser/Luoma (USGS) selenium model and the study by USGS funded by USEPA that has undergone peer review. The recently released USGS report shows that the Bay-Delta standard should be lowered from 5 µg/l to 1 µg/l or less, depending on residence time of selenium.
However, the study and subsequent water quality criteria do not go as far as establishing a new selenium water quality objective for all of California and particularly the San Joaquin River, a portion of which has received a 9-plus-year time extension by the Central Valley Regional Water Quality Control Board as a basin plan amendment to continue waiving the 5 µg/l objective after 14 years of existing waivers. C-WIN intends to take a key role in pressuring and supporting USEPA to fund the necessary studies that will establish new selenium water quality criteria/objectives for the San Joaquin River.
 In general, federal water quality standards are described as “criteria”. State water quality standards are described as “objectives.” State water quality objectives are then implemented through water quality proceedings, water rights, waste discharge requirements, NPDES permits, etc. by the Regional and State Boards. In most cases, USEPA has delegated its Clean Water Act Authority to California.
 USFWS/NMFS Biological Opinion on California Toxics Rule; letter to Felicia Marcus, Region IX USEPA Administrator, March 24, 2000. See https://www.c-win.org/webfm_send/40, accessed 5/19/210
 http://www.waterboards.ca.gov/centralvalley/water_issues/grassland_bypass/usepa_com.pdf accessed 5/11/2010
 Tom Stokely Personal Communication with Diane Fleck, U.S. Environmental Protection Agency, Region IX, 4/7/2010. E-mail dated 5/10/2010.
 http://www.waterboards.ca.gov/centralvalley/water_issues/grassland_bypass/ . For monitoring reports on the Grasslands Bypass Project area see http://www.sfei.org/grassland/reports/gbppdfs.htm