October 1998

BACKGROUND
The San Joaquin River Real-time Water Quality Management Program (Real-time) uses telemetered stream stage and salinity data (click to view map) and computer models to simulate and forecast water quality conditions along the lower San Joaquin River (SJR). Its primary goal is to increase the frequency of meeting SJR water quality objectives for salinity, thereby reducing the number and/or magnitude of high quality releases made specifically for meeting SJR salinity objectives. The SJR water quality issues that are directly addressed by the Program include:

• State Water Resources Control Board (SWRCB), water quality objectives for SJR salinity near Vernalis, just upstream from the SJR's entrance into the South Delta. Current SJR salinity management involves releasing water stored in New Melones Reservoir when EC objectives are exceeded to lower the Vernalis EC and maintain compliance.
• Operation of wetlands that discharge brackish water into Mud and Salt sloughs from the periodic drawdown of specially-managed ponds.
• Operation of the USBR's Grassland Bypass Channel Project that regulates agricultural drainage discharge into Mud Slough near its confluence with the SJR. This project, which began in September 1996, has a compliance monitoring program that establishes monthly load limits for selenium.
• Release of Spring and Fall pulse flows resulting from Anadromous Fish Restoration Program (AFRP) and Spring Vernalis Adaptive Management Plan (VAMP) implementation. These seasonal pulse flows temporarily enhance the SJR's assimilative capacity for salt, thereby increasing the amount of brackish wetland and/or agricultural drainage that can be discharged into SJR tributaries without exceeding Vernalis salinity objectives.
• The potential application of real-time water quality management techniques to address water quality problems in the SJR was demonstrated by the SJRMP Water Quality Subcommittee and described in a June 1997 final report fulfilling the Committee's obligations under a $250,000 USBR Challenge Grant. The project showed the feasibility of monitoring and modeling the salinity of the lower SJR on a daily basis. A series of workshops were held and technical papers were written to describe the results of 18 months of flow and water quality forecasting on the San Joaquin River.

The demonstration project successfully provided a forum for information exchange among entities with an interest in managing SJR water quality. The demonstration project also established a trained interagency staff and an operational system featuring a custom GUI with Internet upload and download capabilities. Funding for continued water quality modeling and management activities ended in July 1997 with the termination of the demonstration project's USBR Challenge Grant.

In 1999, funding from a CALFED Ecosystem Restoration Program grant was used to restart the flow and water quality forecasting program on the San Joaquin River, upgrade and reestablish the monitoring network, install and maintain sensors at key monitoring sites (including new west-side tributary locations and the San Luis Drain) and increase utilization of the results of these activities by CALFED organizations and beneficiaries.

OBJECTIVES AND BENEFITS OF PROJECT
The primary stressor addressed by the Program is contaminants entering the lower SJR. The main objective of the project is to facilitate the control and timing of wetland and agricultural drainage to coincide with periods when dilution flow is sufficient to meet Vernalis salinity objectives. By increasing the frequency of meeting Vernalis EC objectives, the project may reduce the number and/or magnitude of high quality releases (e.g, releases of Stanislaus River flows from New Melones Reservoir) made specifically for meeting Vernalis EC objectives. The water saved can be used later to increase SJR basin streamflow during critical periods for anadromous fish restoration efforts. Other specific objectives and benefits include:

1. Reduction in conflicts between reservoir operators, wetlands managers, and agricultural drainers in meeting Vernalis salinity objectives.
2. Improved SJR and Bay-Delta water quality for agricultural, drinking water, industrial, and recreational beneficial uses.
3. Expanded and improved monitoring stations with telemetered streamflow, temperature and EC sensors capable of delivering real-time information. Streamflow temperature data from these stations will be instrumental in the development of river temperature models. Species benefitting from such adaptive stream temperature management as possible modifications to reservoir facilities and stream channels, include white and green sturgeon, chinook salmon, steelhead trout, and American shad. Additionally, EC data may be employed in monitoring adaptive management strategies that deal with use of the lower SJR by splittail.
4. Increased understanding and management of activities that affect SJR water quality. The model may qualify as a tool to assess the impact of other management practices that attempt to reduce the pollutant load into the lower SJR and Bay-Delta. The project will enhance existing water quality programs to monitor aquatic contaminants (e.g., selenium and agricultural chemicals) that may cause acute toxicity and mortality or long-term toxicity and associated detrimental physiological responses.

COOPERATING AGENCIES
DWR - San Joaquin District: The San Joaquin District operates and maintains several surface water monitoring stations in the San Joaquin Valley. The SJR Real-time project utilizes flow, electrical conductivity and temperature data from 8 DWR stations. Some of the installation and equipment costs attributed to these 8 stations were funded by the CalFed grant. Monthly operation and maintenance costs are funded out of District funding sources.

USBR - SJVD: Since the 1996 Challenge Grant, Reclamation has continued to make significant commitments through staff-time and funding to operate and maintain water quality monitoring stations associated with the SJR Real-time program. The SJR Real-time program compliments directly Reclamation's Grasslands Bypass Channel Project, the Refuge Water Supply Acquisition Program, the Cooperative Streamflow Program, and CVP operations in the Delta.

USGS - The Geologic Survey operates and maintains several of the monitoring stations used by the Real-time program. The program could not operate without these stations, which are either funded directly by USGS or from other sources.