CV-SALTS
San Joaquin River Upstream of Vernalis

June 2017 Salt & Boron Basin Plan Amendment - Phase 2

This web page contains information on a Basin Plan Amendment for the Control of Salt and Boron Discharges into the San Joaquin River upstream of Vernalis. This Basin Plan Amendment project fulfills a Phase 2 requirement of the 2004 Lower San Joaquin River Salt and Boron Control Program and was developed in coordination with the CV-SALTS Lower San Joaquin River Committee. Information on the Basin Plan Amendment that established Phase 1 of the Salt and Boron Control Program and its associated Vernalis TMDL requirement can be found on the San Joaquin River at Vernalis Salt and Boron TMDL and Basin Plan Amendment page.

Overview of the Salt and Boron Basin Plan Amendment

In Revised Water Right Decision 1641, the California State Water Resources Control Board (State Water Board) directed the Central Valley Regional Water Quality Control Board (Central Valley Water Board) to develop and adopt salinity objectives and a program of implementation for the main stem of the San Joaquin River upstream of Vernalis. In 2004, the Central Valley Water Board adopted the Control Program for Salt and Boron Discharges into the Lower San Joaquin River (Control Program) that included a Total Maximum Daily Load (TMDL) to address electrical conductivity (EC) in the LSJR and meet the water quality objectives (WQOs) in the Bay-Delta Plan at the Airport Way Bridge near Vernalis. The Control Program and TMDL were subsequently approved by the United States Environmental Protection Agency (US EPA) in 2006. The TMDL is implemented through waivers of waste discharge requirements (WDRs) or WDRs that apportion load allocations to different geographic subareas in the valley. As an alternative to the load allocations, the TMDL allows discharger participation in a Central Valley Water Board approved real-time management program as a means to attain salinity WQOs, while maximizing the export of salts out the watershed to help protect the region's agricultural production and long-term sustainability. The Control Program also required a second phase to establish and implement new salinity and boron objectives for the San Joaquin River upstream of Vernalis.

Concurrently, the Board requested that the Central Valley Salinity Alternatives for Long-Term Sustainability (CV-SALTS) initiative continue the effort on the upstream San Joaquin River beneficial use and salt and boron objectives evaluation. The development of amendments was stakeholder driven and led by the LSJR Committee, which is a subcommittee of CV-SALTS. The committee includes members of irrigation, water, and resource conservation districts, city, county, state and federal agencies, producers, growers, irrigators, water quality and watershed coalitions, managed wetlands, drainage authorities, clean water and wastewater associations, consultants of various organizations and other interested parties.

On June 9, 2017, the Central Valley Water Board adopted Resolution R5-2017-0062 amending the Water Quality Control Plan for the Sacramento River and San Joaquin River Basins to add EC water quality objectives in the San Joaquin River between the mouth of the Merced River and the Airport Way Bridge near Vernalis. The amendment was approved by the State Water Board and Office of Administrative Law in early 2018. The amendment is currently going through the US EPA adoption process.

Amendment Approval Processes

United States Environmental Protection Agency (U.S. EPA)


Office of Administrative Law (OAL)


State Water Board Action


Central Valley Water Board Action




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