When Will the State Protect the Lower San Joaquin River?

Twenty years ago, the State Water Resources Control Board approved water quality standards establishing minimum flows in the lower San Joaquin River and its tributaries (the Stanislaus, Tuolumne, and Merced Rivers, each of which begins in the southern Sierra Nevada Mountains and flows westward to join the lower San Joaquin River before flowing into the San Francisco Bay-Delta Estuary). At the time, fishermen, conservation groups, and state biologists warned that those flows were inadequate to protect the health of these rivers, their salmon runs, and the health of the Bay-Delta estuary. With the benefit of hindsight, it’s clear that these flows were inadequate—salmon populations in these three rivers have declined even further, the estuary and its native fish species are in even worse shape, and we’ve seen worsening water quality problems including microcystis and other harmful algal blooms that threaten human health and water hyacinth and other invasive plants choking marinas and waterways.  

In recent years, more than half of all the water that would naturally flow in these rivers has been diverted. In the Tuolumne and Merced rivers, nearly three quarters of the unimpaired flow (the water that would naturally flow down the river in the absence of dams or diversions) has been diverted. These unsustainable water diversions by agricultural water districts and cities (including San Francisco) have had devastating effects on salmon, steelhead and the health of these rivers.

And in recent drought years, as the graphic below shows, even greater percentages of the unimpaired flow have been diverted, leaving a tiny fraction of the unimpaired flow actually flowing downstream and into the Bay-Delta estuary. 

Increasing instream flows in these rivers during the February to June period is critical to restoring their health.  In 2013, the California Department of Fish and Wildlife submitted written comments stating that “approximately 50% - 60% unimpaired flow is the minimum necessary to reestablish and sustain fish and wildlife beneficial uses.”

State and federal law require the Board to periodically review and update these standards, generally every three years.  However, these twenty-year old, inadequate flow standards are still in place today, and over the past several years the Board has repeatedly delayed updating the standards:

  • In 2008, the Board began the process of updating these standards, scheduling completion of this phase of the process in 2012. 
  • In 2012, the Board released an updated schedule, planning to complete the process in 2014.
  • In 2015, the Board released an updated schedule, planning to complete the process in 2016.
  • Currently, the Board’s current schedule states that they will release a revised environmental document that analyzes the potential environmental benefits and impacts of new flow and water quality standards in the Spring of 2016 and complete the process of setting new flow standards for the Lower San Joaquin River and its tributaries in the Fall of 2016.

The State Board has an opportunity and obligation to adopt water quality standards that will protect these rivers, their native salmon and steelhead populations, and the health of the Bay-Delta estuary.  The need to do so is more urgent than ever. This action is Phase I of the Board’s update of the Bay-Delta Water Quality Control Plan, with Phase II setting new flow and water quality standards for the Sacramento River and the Bay-Delta estuary.  

NRDC prepared a fact sheet (online here) that explains the importance of instream flows, the inadequacy of existing instream flows in these rivers, and solutions to help sustain healthy rivers and a healthy economy. If you care about California’s rivers, salmon, or the Bay-Delta estuary, now is the time to get involved in the State Water Resources Control Board’s process and urge the Board to adopt stronger flow standards.   

About the Authors

Doug Obegi

Director, California River Restoration, Water Division, Nature Program

Join Us

When you sign up you'll become a member of NRDC's Activist Network. We will keep you informed with the latest alerts and progress reports.