TMDL Projects
San Joaquin River Salt and Boron TMDL and Water Quality Objectives Basin Plan Amendments

Control Program for Salt and Boron Discharges into the Lower San Joaquin River

The Water Quality Control Plan for the Sacramento River Basin and San Joaquin River Basin (Basin Plan), pages 4-61 through 4-71, includes the Control program for Salt and Boron Discharges into the Lower San Joaquin River (LSJR) (Control Program). The purpose of the Control Program is to manage salt and boron discharged from irrigated lands within the LSJR Basin into the LSJR and into the Sacramento-San Joaquin Delta at the Airport Way Bridge near Vernalis. The goal of the Control Program is to achieve compliance with salt and boron water quality objectives at Vernalis, and in the LSJR between the Merced and Stanislaus Rivers, without restricting the ability of dischargers to export salt out of the LSJR Basin.

The Control Program was developed in two phases through Basin Plan Amendments. The first amendment, adopted by the California Regional Water Quality Control Board, Central Valley Region (Central Valley Water Board) in September 2004, established Phase 1. The Central Valley Water Board adopted the second amendment in June 2017, establishing Phase 2. Phase 1 became effective in July 2006 with a phased compliance schedule that began in July 2014 and will be fully implemented by July 2026; Phase 2 was approved by the U.S. Environmental Protection Agency on 17 December 2018 and will become effective in January 2020.

Description of Phase 1

Phase 1 identifies seven geographic subareas of the LSJR drainage basin. It establishes Salt and Boron TMDLs for dischargers within these subareas and for the U.S. Bureau of Reclamation’s (USBR’s) imports of salt through the Delta Mendota Canal (DMC). A map of the subareas with the DMC are available at the following link: LSJR Salt and Boron Control Program Project Area Map

Subareas contributing the most salt per acre, and the DMC are scheduled for earliest implementation of the TMDLs. The Phase 1 compliance schedule table is available at the following link: Phase 1 LSJR Salt and Boron Compliance Schedule. The schedule assigns two implementation dates for each: An earlier date for all water year types, except for Critically Dry water years when a later date applies.

There are two options for compliance with the Phase 1 TMDLs. The first establishes strict salt and boron load limits that are based on the driest water years determined by modeling historical discharges from 1922 through 1995. The second establishes relaxed load limits as long as the salinity water quality objectives (WQOs) at Vernalis, set in the Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (Delta Plan), are not exceeded. To comply with the second option, a discharger must be a participating member of a real-time salinity management program (RTMP) approved by the Central Valley Water Board. Also, for USBR compliance, it must participate with the Central Valley Water Board through a Management Agency Agreement (MAA).

Status of Phase 1 Control Program

Compliance with the Phase 1 TMDLs by dischargers in the priority subareas and USBR in the DMC, shown on the LSJR Salt and Boron Control Program Project Area Map, was not required during the 2014 and 2015 water years because they were Critically Dry years. As is shown by the dates in the LSJR Salt and Boron Compliance Schedule, compliance was required during the 2016, 2017, and 2018 water years because they were not Critically Dry years. The final compliance date for priority subareas during Critically Dry water years has past and compliance is required during all water year types after 2018.

The USBR and Central Valley Water Board signed a MAA in 2008 and a revised MAA in 2014. Also, in 2014 dischargers in the priority subareas and USBR for the DMC developed and proposed a RTMP for approval by the Central Valley Water Board, which approved it in December 2014. The RTMP implemented the program in the 2016 water year and, to date, have maintained compliance with the TMDLs.

Compliance with the Control Program TMDLs is now required of dischargers in the Tuolumne River Subarea during all but Critically Dry water years as shown in the LSJR Salt and Boron Compliance Schedule.

Description of Phase 2

Phase 2 sets salinity WQOs in the LSJR between the Merced and Stanislaus Rivers. In 2010, after initial evaluations and CEQA Scoping in 2005 through 2009, the Central Valley Water Board requested that the Central Valley Salinity Alternatives for Long-Term Sustainability (CV-SALTS) initiative continue the effort on LSJR beneficial use and salt and boron objectives evaluation. The Lower San Joaquin River Committee (LSJRC Committee) which is a stakeholder driven subcommittee of CV-SALTS, developed Phase 2 amendment recommendations for the Central Valley Water Board’s consideration. 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. In 2017, the LSJR Committee submitted its science and policy recommendations to the Central Valley Water Board.

On 9 June 2017 the Central Valley Water Board adopted Resolution R5-2017-0062 amending the Basin Plan to add electrical conductivity (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, and in December 2018 by the US EPA. The amendment will take effect in January 2020 and sets an EC WQO of 1,550 micro Siemens per centimeter (µS/cm) except during extended dry periods when the WQO will be 2,470 µS/cm.

Status of Phase 2 Control Program

Compliance with Phase 2 of the Control Program is required in January 2020.

Contact Us

Central Valley Water Quality Control Board
11020 Sun Center Drive, Suite 200
Rancho Cordova, CA 95670