Briefing Report: The "Best Available" Science Could Be A Lot Better

Wednesday, April 7, 2010


The 2009 water package established guidelines for finalizing a Bay Delta Conservation Plan (BDCP) to re-engineer water deliveries in the Delta system, including a new conveyance system, and restore Delta ecosystems. Until that plan is implemented years from now, the State Water Project (SWP) and Central Valley Project (CVP) are governed by a pair of Biological Opinions pursuant to the federal Endangered Species Act ( ESA). The opinions are particularly controversial for the severity of their mandates and the resulting reductions in water exports. Since January, when the heaviest rain and snow began to fall, the two projects have lost nearly 500,000 acre-feet of water that could otherwise have been stored or used, with the SWP losing about one-quarter of its average annual deliveries.

A recent report by a committee of the National Academy of Sciences (NAS) has now called into question the scientific bases for some of the actions required by the Biological Opinions. While environmental groups and many in the news media initially lauded the report as a reinforcement of existing requirements, the report points to considerable uncertainty, inadequacy, variance, and conflict in the science upon which regulators rely. It also vindicates a request by Governor Schwarzenegger’s administration to the federal government to improve the coordination of the two opinions, each drafted by different agencies – a request scorned at the time by the Obama Administration. The report is preliminary and begins a two-year study process which, in time, could significantly affect water supplies for farmers and nearly two-thirds of all Californians.


For a third consecutive year, SWP and CVP exporters face a harsh regime of cutbacks on water that can be pumped from the Delta. In 2008 and 2009, a federal judge ordered cutbacks resulting in a combined loss of about 1.2 million acre-feet that otherwise could have been used or stored – enough water to serve ten million people for a year. This year, pumping restrictions are based on two newly-adopted Biological Opinions, one from the National Fish and Wildlife Service (FWS) for the Delta smelt, and one from the National Oceanic and Atmospheric Association (NOAA) for the Chinook salmon, steelhead, and green sturgeon.

Earlier this year, at the behest of Congress and the Department of the Interior (DOI), the NAS began an inquiry into the scientific foundation for these actions. The NAS review will focus on whether other actions could be taken that have less of a water supply impact, the extent to which conflicting rules of the two regulating agencies could be coordinated, and to what extent other “stressors” that may share in the responsibility for declining fish counts.

NAS Preliminary Report

The NAS committee looked specifically at six recommended actions contained in the FWS and NOAA Biological Opinions. NAS found that the concepts may have sound scientific basis but there were significant scientific shortcomings in the specific recommendations, all of which adversely affected water supply. Among them:

Negative flows. Operating the SWP and CVP pumps can reverse the flows of key rivers in the Delta, which draws fish, including endangered species, into the pumps. Both Biological Opinions recommend reductions in exports to reduce those negative flows. For the Delta smelt, the committee found the practice of restricting the pumps is justified, but that current studies “do not permit confident identification of when to limit reverse flows of the rivers or a confident assessment of the benefits fish receive by reducing reverse flows….” For salmon and steelhead, the report concluded that, “the threshold levels needed to protect fish is not definitively established…Uncertainty in the effect of the flow triggers needs to be reduced, and more flexible triggers that require less water should be evaluated (emphasis added).”

Salinity. The FWS Biological Opinion recommended the additional use of freshwater supplies to push saline water out of the Delta (a line known as “X2” which refers to two parts per thousand) and create more freshwater habitat for the Delta smelt. The NAS wrote, “The controversy about the action arises from the poor and sometimes confounding relationship between indirect measures of delta smelt populations and X2. The weak statistical relationship between the location of X2 and the size of the smelt population makes the justification for this action difficult to understand…The X2 action is conceptually sound… [but] the derivation of the details of this action lacks rigor. The action is based on a series of linked statistical analyses with each step being uncertain. The relationships are correlative with substantial variance being left unexplained at each step.”

Wetlands Habitat. The NAS had even harsher criticism for an FWS recommendation of an additional 8,000 acres of tidal habitat as part of the mitigation for take of Delta smelt. They found that, “although the concept of increasing and improving habitat to help offset other risks to smelt is conceptually sound, the scientific justification provided in the biological opinion is weak, because the relationship between tidal habitats and food availability for smelt is poorly understood, and it is inadequate to support the details of the implementation of this action (emphasis added).”

San Joaquin River inflow/outflow. To protect juvenile salmon and steelhead from entrainment in the pumps, NOAA recommended that San Joaquin River flows be increased and that its diversions for water exports be decreased. NAS found a “weak influence of exports in all survival relationships” for steelhead and that regulators may consider easing the export limits “without great risk to salmon” and that the rationale for increasing San Joaquin River flows has a “stronger foundation” than for reducing exports.

Crosscutting Issues

The NAS report found that the lack of coordination between FWS and NOAA created considerable conflict between the smelt and salmon Biological Opinions. In perhaps its toughest criticism of the agencies, the report states that increasing flows in the Yolo Bypass for salmon were scientifically justified but the “implications for routing of flows through the system as a whole were not transparently evaluated.…This exemplifies a general tendency throughout the discussion of actions to focus on the biologically beneficial aspects but not to fully present how any conflicting consequences or potential for such consequences were considered.” That includes specific actions benefiting one species to the detriment of others, and flow management actions that included “no quantitative analysis …to systematically evaluate their aggregate effects on both salmonids and smelt.”

Importantly for SWP and CVP users, the report found that other “stressors” on the Delta environment may have a “potentially large” impact on the survival of fish species. These potential stressors include: 1) pyrethroid pesticides; 2) ammonia; 3) non-native predator fish; 4) impediments to fish passage; 5) diseases; and 6) climate change.

Water users have long argued that regulators have had a myopic focus on water operations because it is the simplest available lever. The extent to which other stressors impact the system will be explored in the final report due sometime in late 2011.


The NAS report underscores the dramatic level of scientific uncertainty that still guides Delta management, provides a useful roadmap for addressing deficiencies, and demonstrates how overlapping regulatory jurisdictions have created unnecessary and harmful impacts to water deliveries.

The outcome of the NAS process is relevant for state policymakers for several reasons. Most obvious is the economic impact of reliable water deliveries. The NAS will not eliminate restrictions but its findings may lead to greater flexibility for water operations. To some it may look like the choice between a greater or lesser deficiency, but that difference can be particularly vital to agriculture, where a 20% or 40% allocation can make the difference for banks to extend credit to farms.

Second, the Biological Opinions guide the enforcement of both state and federal ESA in the Delta. That is because the SWP has chosen to use the federal Biological Opinions as its basis for compliance with state ESA rules (known as a “consistency determination”). Of the two projects only the SWP is subject to the state ESA. Because of the dual enforcement, the SWP does not benefit from successful court challenges by CVP exporters. And SWP users face added risk if the longfin smelt, a state-listed species, should appear near its pumps, a prospect that could completely shutdown its operations.

Finally, it is worth noting the SWP has taken the brunt of pumping restrictions this year, notwithstanding the media focus on impacts to the CVP. As of March 14, the two projects had lost approximately 478,000 acre-feet with over 80% of that, more than 400,000 acre-feet, coming out of the SWP. That is enough water to serve over three million people for a year, and had it been available would have ensured a full San Luis Reservoir this year. These are only the immediate impacts. Accumulated losses over time to storage will prove very harmful in future dry years.


For more information on this report or other Natural Resources & Water issues , contact Steve McCarthy, Senate Republican Office of Policy at 916/651-1501.