San Joaquin River Watershed Surface Water Ambient Monitoring Program

San Joaquin River Basin

The San Joaquin River (SJR) flows northward and drains the portion of the Central Valley south of the Sacramento-San Joaquin Delta and north of the Tulare Lake Basin. The basin covers 15,880 square miles and yields an average annual surface runoff of about 1.6 million acre feet. The lower Basin (below Millerton Reservoir) has had a highly managed hydrology since implementation of the Central Valley Project (CVP) in 1951. Most of the SJR flow is diverted into the Friant-Kern Canal, leaving the river channel upstream of the Mendota Pool dry except during periods of wet weather flow and major snow melt. Flows from the west side of the river basin are dominated by agricultural return flows since west side streams are ephemeral and their downstream channels are used to transport agricultural return flows to the main river channel. Poorer quality (higher salinity) water is imported from the Delta for irrigation along the west side of the river to replace water lost through diversion of the upper SJR flows. The principal streams in the basin are the San Joaquin River and its larger tributaries: the Cosumnes, Mokelumne, Calaveras, Stanislaus, Tuolumne, Merced, Chowchilla, and Fresno Rivers which all drain the east side of the basin. Major reservoirs and lakes include Camanche, Pardee, New Hogan, Millerton, McClure, Don Pedro, and New Melones. Major land use along the San Joaquin Valley floor is agricultural, with over 2.1 million irrigated acres, representing 22% of the irrigated acreage in California. Urban growth is rapidly converting historical agricultural lands leading to an increased potential for storm water and urban impacts to local waterways. Upper watershed areas can be impacted by timber activities, grazing, abandoned mines, rural communities, and recreation.

The proposed SWAMP program for the SJR builds upon a site-specific monitoring framework developed as part of the agricultural subsurface drainage management program that has evolved since 1985.

The monitoring objectives of the SJR SWAMP program are:

1) To evaluate whether the most limiting beneficial uses in a specific water body are being protected and help identify sources of potential impairment.

2) Determine, over time, if implementation efforts are improving water quality.

The most limiting beneficial uses were identified for water bodies in the SJR Basin. Parameters were selected to measure beneficial use impacts: salt, bacteria, TOC (drinking water); trace elements, toxicity, bioassessments (aquatic life); salt, boron, minerals (irrigation water supply); bacteria (recreation); and selenium (waterfowl). To identify potential sources of impairment, a layered monitoring framework was developed. The first layer are sites selected along the main stem of the river downstream of major inflows. The second layer is a series of sites representing inflows from specific sub-watersheds into the main stem of the river. The final layer is a more detailed survey of water quality within each of the sub-watersheds-once every 5-years.

To evaluate implementation efforts, the sites along the main stem of the San Joaquin River and those representing drainage inflows from five sub-basins have been designated as permanent monitoring locations. These sites will also allow evaluation of water quality over time and over water year types that can range from flood to critically dry years. More information about each layer in the overall program follows.

Bioassessment has been conducted in the Basin through a separate effort (more info).

• Summary Table of Current Program (sites, constituents, and frequency) - UNDER DEVELOPMENT
• For information on previous monitoring see Annual Workplans
• Site Descriptions (coming soon)
• Water quality reports

Main-stem San Joaquin River Information Data Grassland Bypass Project Information Data Drainage Basin Inflows to the Lower San Joaquin River Information Data Intensive Rotational Basin Program Information Data Northeast Basin (2002) Information Data Eastside Basin (2003) Information Data Westside Basin (2005) Information Data

Water Quality Reports

• SJR Water Years 1999 & 2000
• SJR WaterYear 1998
• Grasslands Water Years 1999-2000
• Grasslands Water Year 1998
• Grassland Bypass Project Monthly and Annual Reports Index (San Francisco Estuary Institute)
• Grassland Bypass Project 2000-2001 Annual Report (San Francisco Estuary Institute)
• Grassland Bypass Project 2001-2002 Annual Report (San Francisco Estuary Institute)
• Grassland Bypass Project 2002-2003 Annual Report - Water Quality Chapter (San Francisco Estuary Institute)
• Grassland Bypass Project 2004-2005 Annual Report - Water Quality Chapter (Draft)
• Benthic Macroinvertebrate Bioassessment of San Joaquin River Tributaries: Spring and Fall 2002
• Macroinvertebrate Assemblages of the San Joaquin River Watershed, (2001)

Water Quality Reports in progress

• Water Quality in the San Joaquin River Basin: Water Year 2001 and 2002
• Water Quality in the Northeast Sub basin of the San Joaquin River Basin: Cosumnes, Mokelumne, Calaveras, Lone Tree, and Littlejohns Watersheds (January 2001-December 2002)
• Water Quality in the Eastside Sub basin of the San Joaquin River Basin: Stanislaus, Tuolumne, and Merced River Watersheds (January 2003 - March 2004)

Program and Contact Information:

• San Joaquin River - Water Year Reports. For more information, please contact Jeanne Chilcott at (916) 464-4788 or email: jchilcott@waterboards.ca.gov.
• Surface Water Ambient Monitoring Program. For more information, please contact Jeanne Chilcott at (916) 464-4788 or email: jchilcott@waterboards.ca.gov.
• Grasslands Bypass Project. For more information, please contact Jeanne Chilcott at (916) 464-4788 or email: jchilcott@waterboards.ca.gov.
• Intensive Rotational Basin Program. For more information, please contact Catherine Graham at (916) 464-4714 or email: CGraham@waterboards.ca.gov.
• Bioassessment Program. For more information, please contact Jeanne Chilcott at (916) 464-4788 or email: jchilcott@waterboards.ca.gov.