Background

The U.S. Department of the Interior, Bureau of Reclamation, Mid-Pacific Region (Reclamation) is implementing a program to provide greater flexibility in meeting existing water quality standards and objectives by reducing reliance on New Melones Reservoir releases for those purposes. Implementing this program is consistent with direction given by Congress in the Water Supply, Reliability, and Environmental Improvement Act (Public Law 108-361) to develop and initiate a Program to Meet Standards (PTMS). A February 2006 report, Program to Meet Standards, Response to CALFED Bay-Delta Authorization Act (Public Law 108-361) CALFED Bay-Delta Program, California, summarizes the scope, activities, and management approach Reclamation is pursuing for the program.

Reclamation delivers water to the San Joaquin Valley via the Delta Mendota Canal (DMC). Reclamation and other nonpoint source dischargers, such as Federal and State wildlife refuges, and agriculture and irrigation dischargers are subject to the Central Valley Regional Water Quality Control Board (CV Water Board) requirements for managing salt discharges to the Lower San Joaquin River (LSJR). The Control Program for Salt and Boron Discharges into the LSJR (Control Program) was established in a 2004 amendment to the Water Quality Control Plan for the Sacramento and San Joaquin River Basins (Basin Plan), and further amended in 2017 to include salinity water quality objectives for the reach of the LSJR between the confluence of the Merced River and Airport Way Bridge near Vernalis. According to the 2004 Basin Plan amendment, Reclamation is responsible for 47 percent of the salt load discharged to the LSJR via the DMC. The Control Program requires Reclamation to meet DMC salt load allocations or provide dilution flows to create additional assimilative capacity for salt in the LSJR equivalent to DMC salt loads in excess of their allocation. The Control Program states that “Participation in a Regional Board approved real-time management program (RTMP) and attainment of salinity and boron water quality objectives will constitute compliance with this control program.”

In 2008 (amended in 2014), Reclamation entered into a Management Agency Agreement (MAA) with the CV Water Board. The MAA requires Reclamation to facilitate participation in a RTMP by dischargers of return flows to the LSJR from wildlife refuges and irrigated lands while meeting the following requirements:

  • Continue to implement projects to offset a minimum of 25% of the excess DMC salt load as defined in the Basin Plan, lead efforts to reduce overall salt load in the river and improve scheduling of discharges, and take other actions as appropriate and authorized to provide assimilative capacity in the LSJR;
  • Provide annual work plans and annual reports that incorporate specific activities to be conducted in support of the RTMP;
  • Implement the Annual Work Plan, subject to appropriations;
  • Pursue funding, including but not limited to grant funding, for salinity control efforts in the LSJR watershed;
  • Continue to provide mitigation and dilution flows as needed while the RTMP is being fully developed and implemented (and as required by Revised Water Right Decision 1641, revised March 15, 2000); and
  • Participate in Central Valley Salinity Alternatives for Long-term Sustainability (CV-SALTS)
Last Updated: 9/29/20