This project will produce a management action plan to eliminate the oxygen depletion in the San Joaquin River during the fall.

Many point and non-point sources and physical factors have been attributed to cause of the oxygen depletion in the river, but available data and modeling tools have been inadequate to develop a reliable and efficient management action plan.

The management action plan will be developed over 3 years and will include:

1. development of a database containing new and historical data on source loads of oxygen depleting substances
2. collection of supplemental field data on source loads and controlling mechanisms
3. filling data gaps in the existing dissolved oxygen management model for verification and calibration of controlling factors
4. evaluation of management alternatives
5. development of a management action plan

Dissolved oxygen depletion occurs over a 10 mile reach of the San Joaquin River near Stockton in the fall when concentrations decrease below 6 mg/l; concentrations below 2.5 mg/l are common (USBR 1968-1974; CDWR 1987-1995; Jones and Stokes 1998). Dissolved oxygen concentrations below 6 mg/l are ecologically damaging because they are a barrier to upstream migration of adult fall-run Chinook salmon that spawn in the Merced, Tuolumne and Stanislaus Rivers between September and December (CDFG 1970). The San Joaquin salmon population has severely declined and is considered a "species of concern" by the US FWS and was listed as a threatened species by NMFS. Low dissolved oxygen concentrations can also kill, stress or block migration of other fish and may negatively impact the health of the entire aquatic community (CVRWQCB 1997).

Oxygen depletion in the San Joaquin River is considered a significant water quality problem in the CALFED Estuarine Restoration Program (ERP) and impedes the CALFED goals to:

1. recover at-risk species in order to establish self-sustaining populations and minimize the need for future endangered species listings
2. rehabilitate natural processes that support natural aquatic communities and favor native communities
3. improve and maintain water and sediment quality to eliminate toxic impacts on organisms in the ecosystem. Oxygen depletion in the San Joaquin River is a focused action for this proposal package

This project is directed toward the ERP target species, fall-run Chinook salmon and will assist with CALFED Water Quality Program goals to:

1. eliminate occurrences of dissolved oxygen concentrations below 6 mg/l in the fall
2. eliminate the impairment or blockage of fish migration
3. eliminate stress to fish and other aquatic organisms due to oxygen depletion
4. eliminate fish kills near Stockton.

These goals also interface with Title 34 of the CVPIA and the program for restoring anadromous fish populations outlined in "Restoring Central Valley Streams: A Plan for Action" (CDFG).

The primary objective of the project is to fully evaluate our current conceptual model of the causes of the dissolved oxygen depletion near Stockton in order to design a management action plan to eliminate the problem.

The current conceptual model is that algal biomass from the San Joaquin River upstream of Mossdale, sediment deposits and Stockton treated effluent are major sources of oxygen depleting substances in the San Joaquin River and that these sources become a problem in the fall when water temperature is high and streamflow is low. Current information, however, is inadequate to fully evaluate this conceptual model and allocate the loads among potential sources for management.

We will evaluate the conceptual model by direct field measurements and modeling results. Continuous fluorometry and simple mass balance calculations will directly measure the transport of algal biomass from Mossdale to the oxygen depletion zone. We will verify the relative contribution of both living and dead algal biomass from Mossdale to the oxygen demand in the oxygen depletion zone using biomarkers. The percent contribution of algal biomass to the total load of oxygen depleting substances will be determined from measurements of BOD, COD, chlorophyll a concentration, TOC, nutrients, biomarkers and flow from urban, industrial and agricultural sources throughout the upper and lower San Joaquin River. These surface water loads of oxygen depleting substances will be compared with direct measurements of organic and inorganic oxygen depleting substances in the sediment (sediment oxygen demand). Field sampling will begin at locations known to be important from historical data.

New and historic data on surface and sediment sources of oxygen depleting substances and associated physical and chemical data will be used to fill data gaps in the existing dissolved oxygen management model and enhance calibration and verification of controlling mechanisms. Comparison of new and historical field data with modeling results will provide insight for evaluation of alternatives and best management practices needed for development of a management action plan. Development of an IEP database and CD disk version of the model will make the model and data readily available to Stakeholders.

Field data collection and analyses will be done with the guidance of a statistician and field and laboratory analyses will be done using US EPA QA/QC guidelines.