Controversial Permit Jeopardizes Efforts to Secure Water Supplies for Californians

Action by a state department to dictate when and how much water can be pumped out of the Sacramento-San Joaquin Delta, the hub of the state’s water delivery system, threatens the collaborative approach to keeping water flowing for Californians.

The California Department of Fish and Wildlife issued a controversial Incidental Take Permit (ITP) to the California Department of Water Resources for the long-term operations of the State Water Project on March 31, as the COVID-19 pandemic was dominating the news. The 143-page ITP lays out when and how much water the State Water Project can pump out of the Delta.

Six California congressional representatives sent a letter to Governor Gavin Newsom, expressing their concern with the ITP and the negative impact it would have on coordination between the State Water Project and the federal Central Valley Project.

Immediately, agricultural and water agency stakeholders working on the voluntary agreement framework with the Newsom administration said the ITP jeopardized the process. Without the voluntary agreements, the concern is the State Water Resources Control Board will require that 40% to 70% of water flows be reserved for endangered fish and their habitat, severely reducing the amount of water available for human and agricultural needs.

The environmental community also issued statements arguing that the ITP didn’t go far enough to ensure protection of endangered fish species.

Voluntary Agreement Interface

The State Water Board adopted new flow requirements in its Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary in December 2018. The most controversial piece of this plan was the potential 40%–70% reduction in flow to rivers, which reduces water to all water rights holders, including the State Water Project, and therefore reduces water to landowners, water agencies and, ultimately, customers.

Governor Edmund G. Brown Jr. and Governor Newsom asked the State Water Board to slow finalizing the process of reducing flow requirements, in order to allow stakeholders to work out voluntary agreements based on recent and updated biological opinions (biops) regarding how to use less water and protect more species.

The ITP interferes with the voluntary agreements process, as it dictates a specific level of water for fish and the environment, rather than allowing the stakeholders to determine the appropriate level through negotiated compromise, the method preferred by both Governor Brown and Governor Newsom.

What Is in the ITP?

The ITP is a permit to take (kill or harm) a species listed under the California Endangered Species Act, and requires State Water Project operations to minimize, avoid and fully mitigate impacts to listed species. This ITP covers four species: delta smelt, longfin smelt, winter-run Chinook salmon and spring-run Chinook salmon.

The state agencies contend that the permit balances fish protections with human needs. It allows for real-time flow flexibility when excess flows occur rather than strict adherence to calendar times for water releases. Water can be released earlier or later depending on climate. Excess flows in wet years can be stored for use during drier times for fish or human needs. The ITP also includes interagency coordination for conservation, hatchery approaches and controlling predatory fish.

Water agencies disagree that the ITP is balanced. They are concerned the ITP adds additional requirements that reduce the amount of water available to their customers, who are businesses, developers, landowners, industrial and institutional users, and agricultural operations, as well as residential properties. The ITP mitigation measures are costly and unjustified, in the water agencies’ opinion.

The water agencies also are concerned with the amount of authority the ITP provides to the Fish and Wildlife Department director to make real-time decisions about water flow reductions and the impact the ITP will have on the voluntary agreements process.

State and Federal Water Projects

Each year, the State Water Project delivers more than 3 million acre-feet of drinking water to about 27 million people and irrigates an estimated 750,000 acres of farmland. Roughly 30% of State Water Project water is delivered for agricultural uses, mostly in the San Joaquin Valley, and about 70% goes to residential, municipal and industrial uses, mainly in Southern California but also in the San Francisco Bay Area.

The federally operated Central Valley Project supplies an average of 5 million acre-feet of water each year for Central Valley farms and 600,000 acre-feet of water for municipal and industrial uses.

The state and federal water projects share many water facilities, such as the federal San Luis Canal and the California Aqueduct. Both projects use the canal to ship water from north to south. Water can be interchanged between the two projects to meet peak water demands.

During the Obama administration, the state Fish and Wildlife Department deemed State Water Project operations to be consistent with federal biops and the federal Endangered Species Act, so no further authorization or approval was needed under the California Endangered Species Act.

In 2018, however, the Trump administration withdrew the biops developed by the Obama administration and directed federal agencies to expedite a new set of biops, based on the belief that the Obama-era biops were not based on the best and most current scientific criteria. The President also indicated that he was in favor of sending more water to Central Valley farmers through the Central Valley Project.

California responded by initiating, for the first time, a separate take permit from the Fish and Wildlife Department to ensure State Water Project operations met California Endangered Species Act requirements.

This inconsistency between state and federal permits issued has affected both the state and federal water projects. The State Water Project will have to operate under the ITP criteria, but the federal Central Valley Project does not. Many are concerned that if the federal project releases too much water too soon, the State Water Project will have to make up the supply shortfall even though the state project has less capacity.


The ITP is another chapter in a long history of water wars among the various stakeholders. Although there appeared to be promise of compromise through the voluntary agreements framework, the ITP jeopardizes the opportunity. The surface water available is limited, meaning water allocated for one purpose comes at the expense of other uses, be it flows to protect endangered species, voluntary agreements or a take permit.

Several water agencies and other stakeholders are already considering legal action, which would further polarize the stakeholders in this arena.

In the final analysis, the discord means all stakeholders will have to pay more money for less water.

Staff Contact: Valerie Nera