Is Ecosystem-Based Management Legal for the Sacramento-San Joaquin Delta?

by Brian Gray (PPIC Water Policy Center), William Stelle (former NOAA Fisheries West Coast Administrator), and Leon Szeptycki (Stanford University, Water in the West)*

The Sacramento-San Joaquin Delta. (Photo credit: Carson Jeffres)


In a recent three-part series posted on this website, a group of independent experts (including one of the authors here) proposed new ways to manage the Sacramento-San Joaquin Delta ecosystem. The purpose of the recommendations is to inform negotiations on the revised Bay-Delta Water Quality Control Plan, which will set new water quality and flow requirements for the Delta and its tributaries.

These experts urged the State Water Board and negotiating parties to: (1) take an integrated approach to the Delta to improve food web productivity and habitat, while reducing harmful algal blooms; (2) coordinate management of freshwater flows, tidal energy, and landscape changes in the North Delta and Suisun Marsh to improve ecosystem function; and (3) develop a robust, well-funded independent science program to guide implementation and assessment of the water quality plan.

The experts note that populations of native fish species listed under the state and federal endangered species acts are so low that they are no longer reliable indicators of Delta conditions. They recommend shifting away from an emphasis on managing the Delta for these listed species. And they outline an ecosystem-based approach that would improve conditions for a wide range of terrestrial, wetland, and aquatic plants and animals—including listed fish species—as well as for human uses of the Delta’s water and lands.

These recommendations are intriguing, especially in light of growing consensus that the current approach to water quality and species protection in the Delta is failing to meet legal and policy objectives. But would management based on the proposed policies be legal?

Ecosystem-Based Management

An ecosystem-based approach to the Delta would differ in several important respects from the existing regulatory regime. Current regulations rely heavily on minimum flow and water quality standards, which are often met by releases from upstream reservoirs. These regulations also impose a variety of constraints on Central Valley Project (CVP) and State Water Project (SWP) operations—including seasonal restrictions on water exports from the south Delta—to minimize reverse flows and prevent dislocation and entrainment of fish.

The proposed approach calls for more flexible deployment of releases from upstream reservoirs to improve aquatic habitat, along with landscape changes to enhance habitat benefits from managed freshwater and tidal flows. The proposal also advocates focusing conservation and recovery actions on an arc of habitat from the Yolo Bypass through the North Delta and into Suisun Marsh (the “North Delta Arc”), which has been less altered by human interventions and is linked by the Sacramento River.  This area has a greater likelihood of producing significant, near-term ecological improvements compared with conservation actions elsewhere in the Delta. The proposal also would alter the current strategy of using large volumes of freshwater outflow to manage salinity in the Delta and Suisun Bay, choosing instead a geographically targeted approach to the application of freshwater flows.

Although it would represent a marked change from existing regulatory policy, an ecosystem-based strategy would be consistent with the water quality laws and the endangered species acts.

The Water Quality Laws

California’s Porter-Cologne Act implements the federal Clean Water Act and establishes independent state standards for water quality. It requires the State Water Board to set water quality standards that provide “reasonable protection” for an array of beneficial uses of the waters of the Delta ecosystem, including fish and wildlife and water supply. The courts have held that the Board has broad authority to determine what water quality criteria are reasonable and appropriate in light of competing demands on the resource, as long as its decision is supported by substantial evidence in the administrative record.

The Porter-Cologne Act thus grants the Board significant discretion to choose how best to deploy the freshwater available in the Delta. For example, if the Board concludes that the North Delta Arc is the most productive habitat for conserving and recovering protected species, then it would have authority to set water quality standards (including targeted flow requirements) that make this a priority region. If the Board is also persuaded that the central and south Delta are now unproductive and inhospitable habitat for native fish species, it could adjust salinity and flow standards accordingly.

In short, because of the multifaceted and flexible authority vested in it by the water quality laws, there is no significant legal impediment for the State Water Board to follow an ecosystem-based approach in revising its water quality standards for today’s Delta.

The Endangered Species Acts

The federal and state endangered species acts pose more difficult questions because they contain more rigid directives than do the water quality laws. Rather than setting standards to accommodate a variety of beneficial uses, these laws categorically prohibit the unauthorized “taking” of any protected fish. The federal statute also requires all federal agencies to ensure that their actions are not likely to jeopardize the continued existence of any listed species or adversely modify their critical habitat. Takings that are “incidental” to otherwise lawful activities—including water diversions and other water project operations—may be authorized by incidental take statements in biological opinions or by incidental take permits for non-federal activities. Both laws require the impacts of authorized takings to be “minimized,” and the state statute requires that they also be “fully mitigated.”

These laws govern water management in the Delta ecosystem principally as applied to the coordinated operations of the CVP and SWP, which must comply with a series of conditions set forth in biological opinions issued by the U.S. Fish and Wildlife Service (USFWS) for Delta smelt and by the National Marine Fisheries Service (NMFS) for anadromous species (salmonids and green sturgeon). The California Department of Fish and Wildlife (CDFW) plays a complementary role. Its principal regulatory authority in the Delta is through the longfin smelt incidental take permit issued to the SWP.

Legal Questions

The proposed ecosystem management approach raises several key legal questions to which we provide brief answers:

  • Is an ecosystem-based approach to water quality and species protection consistent with the federal and state endangered species acts?

Yes. Although the focus of the endangered species acts is on individual species and their critical habitat, there is nothing in the statutes that would preclude the fish agencies from adopting a more holistic and integrated approach—if the best scientific evidence supports the decision that the ecosystem objectives would be an effective means of fulfilling the no jeopardy/adverse habitat modification standards, as well as the mitigation requirements associated with the incidental take of each listed species.

Indeed, this legal question can be framed in a relatively simple way: What are good scientific metrics for predicting and assessing ecosystem functions (e.g., food web productivity) on which each species relies for its survival and recovery, and are these better expressed as ecological system metrics, rather than through the salinity, flow, and temperature metrics that are currently employed? If the ecosystem approach would be a better way to protect and enhance the biological requirements of each listed species, the fish agencies could approve it under the conventional consultation and incidental take regulatory processes.

  • Could the federal fish agencies revise the biological opinions for CVP/SWP operations to recognize the proposed focus on a North Delta Arc of critical habitat?

Yes. If the agencies conclude that creation of a North Delta Arc of habitat would promote the applicable conservation standards for each of the federally listed species, they would have authority to incorporate this strategy into the biological opinions. As noted above, these could include changes in upstream storage and release requirements to provide targeted flows into the Sutter and Yolo Bypasses, as well as other tidal sloughs and channels, to improve food webs and aquatic habitat.

  • Could the federal agencies revise the biological opinions to recognize a geographically specialized Delta ecosystem that reduces the emphasis on the central and south Delta as critical habitat for some species?

Yes. The federal endangered species act does not require conservation and recovery of listed species throughout their entire range of existing or potential habitat. It also affords the fish agencies considerable flexibility in setting priorities for habitat types and locations—if these conservation strategies would satisfy the no jeopardy/critical habitat directives for each listed species.

Therefore, if the best scientific evidence supports the conclusion that the central and south portions of the Delta are irreparably degraded and that the North Delta Arc is now the most promising habitat for the Delta smelt, the USFWS could adopt geographic specialization as a conservation strategy. This would be accompanied by changes in the critical habitat designation for the smelt, as well as adjustments in the incidental take limitations for the CVP and SWP south Delta pumps to account for this change in focus.

Similarly, NMFS could conclude (also based on the best available science) that the most promising habitat for Sacramento River salmonids is the North Delta Arc. Based on this determination, it too could shift the focus of its conservation and recovery directives to that region. The salmonid biological opinion also would have to include measures to promote passage of salmon and steelhead in the central and south Delta and lower San Joaquin River. As there is no scientific consensus on this subject, we recommend that NMFS—in cooperation with CDFW and the State Water Board—convene a small independent panel of creative scientists and engineers to evaluate the options.

  • Could the California Department of Fish and Wildlife revise the State Water Project’s incidental take permit for longfin smelt to recognize a specialized Delta ecosystem?

Yes. Although the longfin smelt once inhabited much of the Delta, its current population exists primarily in San Francisco Bay. As with federal law, the California Endangered Species Act does not require conservation and recovery of listed species throughout the full extent of their habitat, and it grants CDFW discretion to create priority habitat characteristics and locations. The department therefore would have authority to make the North Delta Arc (which once was important spawning habitat for the smelt) the focus of its conservation and recovery efforts.

Longfin smelt are anadromous and depend on freshwater and tidal flows in the Delta and Carquinez Strait. CDFW would have to ensure that the North Delta Arc conservation and recovery strategy would provide conditions that enable the fish to migrate between their freshwater and more saline habitats.

In addition, in revising the SWP’s incidental take permit, the department must determine that the North Delta habitat improvements would “fully mitigate” any adverse effects of the change in policy. Restoration and long-term enhancement of intertidal and sub-tidal wetlands in the North Delta is already part of the mitigation requirements of the SWP’s incidental take permit. If necessary to offset any risks posed to the smelt from the new habitat strategy, CDFW could require the acquisition and management of additional mitigation acreage.

Concluding Thoughts

Ecosystem-based management in the Delta may be a more efficient and effective means of implementing the water quality laws and endangered species acts than the current regulatory regime. Whether this is true will depend on the responses of the ecosystem and the fishes that inhabit it to the combination of targeted freshwater flows, tidal energy management, and landscape changes that would be concentrated along the North Delta Arc.

To test this new strategy, regulators, water managers, and environmental advocates must be willing to assume the risk of moving away from entrenched policies that have largely failed to achieve their objectives. The judgment whether the new approach is the “best available science”—and therefore may serve as the foundation for a revised water quality control plan and new biological opinions—rests with the regulators. We can simply say that there is nothing in state or federal law that would preclude such a decision.

More importantly, the strategy proposed in the earlier blog posts illustrates a foundational—but often neglected—principle of aquatic ecosystem management: Protection of water quality and conservation of species are one in the same, and neither can be achieved without the other. Perhaps the greatest contribution of the new Delta science will be to encourage the State Water Board and the fish agencies to work together to devise truly integrated standards for today’s novel Delta ecosystem.

* With contributions and insights on the intersections between law and science from Peter Moyle and Jay Lund (UC Davis) and Jeff Mount and Ellen Hanak (PPIC Water Policy Center).

 Further Reading

Gartrell, Greg, and Brian Gray. 2017. A Brief Review of Regulatory Assignment of Water in the Sacramento–San Joaquin Delta. Public Policy Institute of California.

Gore, James, Brian Kennedy, Ronald Kneib, Nancy Monsen, John Van Sickle, Desiree Tullos. 2018Independent Review Panel (IRP) Report for the 2017 Long-term Operations Biological Opinions (LOBO) Biennial Science Review: Report to the Delta Science Program. Delta Stewardship Council and Delta Independent Science Program.

Mount, Jeffrey. 2018a. “Advice on Voluntary Settlements for California’s Bay-Delta Water Quality Control Plan Part 1: Addressing a Manageable Suite of Ecosystem Problems.California WaterBlog, Feb. 13.

Mount, Jeffrey. 2018b. “Advice on Voluntary Settlements for California’s Bay-Delta Water Quality Control Plan Part 2: Recommended Actions to Improve Ecological Function in the Delta.” California WaterBlog, Feb. 21.

Mount, Jeffrey. 2018c. “Advice on Voluntary Settlements for California’s Bay-Delta Water Quality Control Plan Part 3: Science for Ecosystem Management.” California WaterBlog, Feb. 27.

Moyle, Peter, William Bennett, John Durand, William Fleenor, Brian Gray, Ellen Hanak, Jay Lund, and Jeffrey Mount. 2012. Where the Wild Things Aren’t: Making the Delta a Better Place for Native Species. Public Policy Institute of California.

Wondolleck, Julia, and Steven Yaffe. 2017. Marine Ecosystem-Based Management in Practice: Different Pathways, Common Lessons. Island Press.

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5 Responses to Is Ecosystem-Based Management Legal for the Sacramento-San Joaquin Delta?

  1. J Rizzi says:

    Outlaw killing of any and all fish for exported water. CVP and SWP do not have to KILL any fish if the West Channel levee is converted into a 1.5 mile fish screen. Filling Clifton Court Forebay only at night while pumping 24/7, allows for normal flows during the day. Let us fix the problem instead of more and more studies. Contact me for more details at

  2. Mike says:

    Ecosystem approach has merit, but there will never be an ecological based solution as long as water is allocated by politics and the hardening of demand, because of permanent crops in the Central Valley, with limited water resources drives policy and the board consists of political appointees.

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