Workshop Highlights New IEP Science Initiatives and Results

The annual Interagency Ecological Program (IEP) Workshop serves as a focal point for IEP activities in the San Francisco Estuary. The April 2012 workshop featured a three-day program and close coordination with the California Water and Environmental Modeling Forum (CWEMF). Four hundred attendees attended oral and poster sessions offering a full spectrum of current IEP science activities such as the IEP’s new “FLaSH” (Fall Low Salinity Habitat) studies and “MAST” (Management, Analysis, and Synthesis Team) effort.

FLaSH is an integrated set of studies initiated to provide better information regarding Fall Low Salinity Habitat for delta smelt. The salinity gradient from salty ocean water to brackish low salinity water (1-6 psu) and finally fresh river water is one of the defining features of estuaries. This gradient is very dynamic - in very wet winters and springs, fresh water can be found all the way to the Golden Gate, while in very dry summers and falls low salinity water can intrude up the Sacramento River to Rio Vista. The exact position and extent of the low salinity zone depends on the interplay of river flows and the tides.

Estuarine species have evolved to cope with fluctuating salinity and many are associated with specific salinity ranges. Delta smelt live mostly in the freshwater and low salinity zones of the San Francisco estuary. In the fall, the center of their distribution is in the low salinity zone, although some are found year-round in fresh water. Previously published work suggests that delta smelt do better when the fall low salinity zone overlays the large, shallow Suisun Bay region to the west of the Delta than when it is positioned in the deeper river confluence to the east of Chipps Island.

The FLaSH studies explore relationships between salinity fluctuations and other habitat components in the fall and their influence on delta smelt health and survival. The FLaSH studies are part of an adaptive management plan required by the 2008 U.S. Fish and Wildlife Service delta smelt Biological Opinion (BO) for long-term state and federal water project operations.

Due to the very wet conditions in 2011, river inflows to the Delta remained high into the fall. This allowed for record high exports of water from the Delta as well as a westward low salinity zone. Delta smelt abundance improved considerably in 2011 – its fall abundance was the highest since 2001. FLaSH presenters at the IEP workshop presented this and many other observations from the 2011 FLaSH studies. Their preliminary results are summarized in a draft report which will be reviewed by an independent Delta Science Program panel on July 31-August 1, 2012.

The FLaSH report is part of the new IEP Management, Analysis, and Synthesis Team (MAST) effort. MAST provides a new organizational structure and process for IEP data analysis, synthesis, and work planning. Annual deliverables include a work plan for approval by the IEP Agency Directors and annual synthesis reports. The FLaSH report is one such report, but a broader MAST report describing habitat conditions and fish responses covering all 2011 seasons is also in preparation.

In addition to FLaSH and MAST, the 2012 IEP workshop also highlighted salmon and new scientific tools.


“Chinook Salmon spend portions of their lives in rivers, the estuary, and the ocean. Conditions in these systems all matter to their survival and growth, along with the “Four H’s:” hydrology, harvest, hatcheries and habitat.”


Chinook Salmon spend portions of their lives in rivers, the estuary, and the ocean. Conditions in these systems all matter to their survival and growth, along with the “Four H’s:” hydrology, harvest, hatcheries and habitat. In the Delta, survival of outmigrating juveniles has been getting worse: it’s generally best in the North Delta/Sacramento River, poor in the Central Delta, and poorest in the South Delta/San Joaquin River (often less than 10 percent). But even in the Sacramento River survival can be low. Predation may be one of the reasons: rip-rapped banks near the city of Sacramento appear to provide good habitat for predators lying in wait for young salmon and other small fishes.

New scientific tools help scientists gather better data and analyze it in new ways. The IEP workshop included presentations about progress with the SmeltCam (see February 2012 issue of Science News) new genetic methods to assess predation and contaminant effects on native fishes, and cutting-edge life cycle modeling for delta and longfin smelt.

The IEP for the San Francisco Estuary / Sacramento-San Joaquin Delta consists of nine member agencies, three State (Department of Water Resources, Department of Fish and Game, and State Water Resources Control Board) and six Federal (Fish and Wildlife Service, Bureau of Reclamation, Geological Survey, Army Corps of Engineers, NOAA Fisheries, and Environmental Protection Agency). The IEP also partners with the San Francisco Estuary Institute, the Delta Science Program, and many academic and private scientists. The mission of the IEP is, in collaboration with others, to provide ecological information and scientific leadership for use in management of the San Francisco Estuary.

More information about the IEP can be found at