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In Fall 2011, a large-scale investigation (FLaSH, fall low salinity habitat investigation) was implemented by the Bureau of Reclamation (Reclamation) in cooperation with the Interagency Ecological Program (IEP) to explore hypotheses about the ecological role of low salinity habitat (LSH) in the San Francisco Estuary (SFE), and specifically the importance of fall low salinity habitat to the biology of delta smelt Hypomesus transpacificus, a federal and state listed species endemic to the SFE. This investigation constitutes one of the actions stipulated in the Reasonable and Prudent Alternative (RPA) issued with the 2008 Biological Opinion (BiOp), which called for adaptive management of fall Delta outflow following “wet” and “above normal” water years to alleviate jeopardy to delta smelt and adverse modification of delta smelt critical habitat. The basic hypothesis at the foundation of the RPA is that greater outflows move the low salinity zone (LSZ, salinity 1-6), an important component of delta smelt habitat, westward and that moving the LSZ westward of its position in the Fall of recent years will benefit delta smelt, although the specific mechanisms providing such benefit are uncertain. An adaptive PRELIMINARY, PREDECISIONAL, AND SUBJECT TO REVISION DO NOT RELEASE OR CITE 2 management plan (AMP) was prepared to guide implementation of the RPA (Reclamation 2011) and reduce uncertainty. This report has 3 major objectives: • Provide a summary of the results from the first year of coordinated FLaSH studies and monitoring. • Provide an integrated assessment of whether the results of the FLaSH studies and other ongoing research and monitoring support the hypotheses behind the RPA as set forth in the AMP (Reclamation 2011. • Begin to put the results from the FLaSH studies into context within the larger body of knowledge regarding the San Francisco Estuary (SFE) and in particular the upper SFE, including the Sacramento-San Joaquin Delta (Delta) and Suisun Bay and associated embayments. Our basic approach was to evaluate predictions derived from the conceptual model developed aa part of the AMP. We considered all available data from studies and monitoring conducted in fall 2011 and similar data from fall 2006, which was the most recent wet year preceding 2011. We also considered 2005 and 2010 to include conditions antecedent to each of those years. Many of the predictions either could not be evaluated with the data available or the needed data are not being collected. Most of the predictions that could be addressed involved either the abiotic habitat components (i.e., the physical environment) or delta smelt responses. In general, the FLaSH investigation has been largely inconclusive as of the writing of this report. That should not be unexpected in the first year of what is intended to be a multi-year adaptive management effort. This report should be viewed as the first chapter of a “living document” that should be continually updated as part of the adaptive management cycle. The results of this report, especially predictions with insufficient data for evaluation, suggest a number of science-based recommendations for improving the FLaSH investigations: PRELIMINARY, PREDECISIONAL, AND SUBJECT TO REVISION DO NOT RELEASE OR CITE 3 • Develop a method of measuring “hydrodynamic complexity”. This concept is central to a number of the predictions that could not be evaluated. • Determine if wind speed warrants a stand-alone prediction. The wind speed prediction is directly related to the turbidity predictions and wind is only one of several factors important in determining turbidity. • Determine the correct spatial and temporal scale or scales for monitoring and other studies. Many of the assessments in this report were based on monthly sampling of dynamic habitat components such as phytoplankton and zooplankton populations that can change on daily scales. • Address the nutrient predictions as part of developing a phytoplankton production model if feasible. At a minimum develop a mechanistic conceptual model to support more processed-based interpretations of data or design of new studies rather than making simple predictions of increase or decrease. • Determine if studies of predation rates are feasible in areas where delta smelt occur.

Synthesis of studies in the fall low-salinity zone of the San Francisco Estuary, September-December 2011