A Scientific Assessment of Alternatives for Reducing Water Management Effects on Threatened and Endangered Fishes in California’s Bay Delta (2010)

The California Bay-Delta region receives fresh water from the Sacramento and San Joaquin rivers and their tributaries, and some of that water is diverted for agriculture and southern California metropolitan areas. However, the region’s growing population and engineered water-control systems have substantially altered the delta ecosystem and have changed the composition of fish species; while some native species have declined, some introduced species have increased. This report provides a scientific evaluation of two “biological opinions” issued by the U.S. Fish and Wildlife Service and the National Marine Fisheries Service in 2008 and 2009, respectively, that require actions to reduce adverse effects of water diversions on delta smelt, Chinook salmon, Central Valley steelhead, and green sturgeon, such as restricting water diversions during certain periods.

The report concludes that most of the actions are scientifically justified, but many need clarification concerning details. For example, the Fish and Wildlife Service and the National Marine Fisheries Service actions to reduce risks to delta smelt and juvenile salmon and steelhead by limiting how much water is pumped from the delta in winter have a sound conceptual basis. However, the data do not permit a confident identification of when to limit pumping or the benefits fish receive. Thus careful monitoring, adaptive management, and additional analyses are needed. The report further concludes that our understanding of the risks to the fishes and the benefits likely to accrue from the actions requires an integrated, quantitative analytical framework that ties the various actions together within the species, between smelt and salmonids and sturgeon, and across the watershed. The lack of such an integrated analytic framework hampers both the agencies’ and the committee’s ability to thoroughly evaluate the effects of the RPAs on the fishes, on water quality and quantity in the delta, and on water operations.

Key Messages

• A proposed U.S. Fish and Wildlife Service action to create or restore 8,000 acres of intertidal and subtidal habitat in the delta is weakly justified, because the relationship between tidal habitats and food availability for smelt is poorly understood.
• A proposed U.S. Fish and Wildlife Service action to manage the contour line of 2 parts per thousand salinity, called X2, is beneficial to smelt needs further clarification.
• A proposed U.S. Fish and Wildlife Service action to protect delta smelt by limiting how much water is pumped from the delta to reduce reverse flows in the Old and Middle rivers, two branches of the San Joaquin River is scientifically justified; however, the data do not permit confident identification of when to limit reverse flows or of the benefits fish receive, so careful monitoring, adaptive management, and additional analyses is needed.
• Adverse effects of all other stressors on the listed fish — such as contaminants in the delta and structures on rivers that block fishes from access to their spawning habitat — are potentially large.
• Regarding a Nation Marine Fisheries Service biological opinion, which applies to the Chinook salmon, steelhead, and green sturgeon in the delta and farther upstream, the committee concluded that on balance the actions are scientifically justified; however, specific environmental triggers, thresholds, and flows should receive additional evaluation that is integrated with the analyses of similar actions for delta smelt.
• Reversing or even slowing the declines of the listed fish species cannot be accomplished immediately.
• The effects of an increasing population and the operation of the engineered water-control system have substantially altered the delta ecosystem, including its fish species.