Understanding Juvenile Salmon Entrainment and Survival in the South Sacramento/San Joaquin Delta Through the Use of Acoustic Telemetry and Hydrodynamic Measurements

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This study will use the release-recapture information derived from the 2012 receiver array to populate a mark-recapture model based on a Cormack-Jolly-Seber model in combination with a route-specific survival model of Skalski et al. (2002) to derive maximum likelihood estimates and standard errors of reach specific survival and entrainment rates at important junctions, similar to what was used in the 2011 steelhead survival study and 2010 VAMP study (SJRGA 2011).

Summary of the The Six-Year Acoustic Telemetry Study

Map of the Sacramento/San Joaquin Delta.

Map of the Sacramento/San Joaquin Delta. (Public domain.)

The Sacramento-San Joaquin Delta (delta) is the hub of the California’s water delivery system. Surface water supplies are in the north, demand in the south. Thus, water supply reliability in California critically depends on the amount of water that can be transferred from the north to the southern part of the state through the delta. For the past four decades, environmental regulations designed to protect endangered species, including salmon, and downstream estuarine habitats have constrained water supplies south of the delta.

The central conservation objective for salmon, the subject of this proposal, is to improve outmigrant survival through the delta. Salmon emigrate through the delta from three watersheds: (1) The Sacramento, (2) the San Joaquin and (3) the Mokelumne River systems. The outmigrants from each of these regions are in jeopardy and thus each controls water project operations to varying degrees by location, time of year and water year type. The major exporters of water from the delta – the US Bureau of Reclamation (USBR), California Department of Water Resources (DWR), and East Bay Municipal Water District (EBMUD) - are required, as a condition of their permits to remove water from the delta and various biological opinions, to conduct salmon outmigration studies to quantify the impacts of their operations and to develop management strategies that mitigate those impacts.

San Joaquin River outmigrants, the focus of this study, have a particularly challenging migratory pathway involving channels in the delta that are functionally canals and they must traverse a series of junctions whose channels lead directly to the export facilities. Salmonids in the San Joaquin River basin were once abundant and widely distributed, but currently face numerous limiting factors. The National Marine Fisheries Service (NMFS) Public Draft Central Valley Recovery Plan identified ‘Very High’ stressors for juvenile steelhead outmigration on the San Joaquin River including habitat availability, changes in hydrology, water temperature, reverse flow conditions, contaminants, habitat degradation, and entrainment. Many of these stressors can be studied using acoustic telemetry. For example, recent advances in acoustic technology have allowed investigators to evaluate the influence of behavior, species interactions, and physiology on reach-specific survival of salmonids in the Sacramento-San Joaquin river basins (Perry et al. 2010, Vogel et al. 2010).

This study will use the release-recapture information derived from the 2012 receiver array to populate a mark-recapture model based on a Cormack-Jolly-Seber model in combination with a route-specific survival model of Skalski et al. (2002) to derive maximum likelihood estimates and standard errors of reach specific survival and entrainment rates at important junctions, similar to what was used in the 2011 steelhead survival study and 2010 VAMP study (SJRGA 2011).

In addition to the purely scientific objectives, we are experimenting with a variety of new field techniques and technologies. The overall goal of these hardware specific investigations is to expand the acoustic telemetry network in 2012, which is mostly focused on the South Delta, and is mostly autonomous, and will be deployed for a short duration (2 months), to a network that covers the entire delta, is run year-round and the data is telemetered in real-time. The implementation of past studies and our proposed 2012 study plan is incredibly man-power intensive, and, thus unduly expensive. The goal of the equipment development aspect of this investigation is develop the technologies that will allow us to reduce the manpower associated with these experiments by telemetering all of the acoustic receiver data from a delta-wide network in real-time. Telemetry of the data will save on manpower, increase the data return rate and quality of the data and will, most importantly, allow us to use acoustic telemetry data as a real-time management tool. Moreover, year-round, delta-wide operations will allow for the study of predators and other large fish, such as sturgeon, etc. with large tags that last multiple years. Finally, a delta-wide network will allow us to study all of the outmigrant groups – San Joaquin, Sacramento and Mokelumne river fish.

This study is an interdisciplinary, interagency endeavor involving USBR, California Water Resources (DWR), US Fish and Wildlife Service (FWS) and the USGS. USBR is providing funding, the linkage to regulatory requirements, assistance on study design and coordination. DWR is adding receivers to the overall network and the FWS is participating in the fish handling and tagging efforts. Initially, the USGS will be involved in two study elements as part of this overall investigation: (1) operation and maintenance of the acoustic telemetry array and (2) fish acoustic tagging and a tag shedding study. However, as the telemetry network is expanded to include the north delta and the Mokelumne system, we expect our analytical and reporting role in this 6-year study to increase.