Controls on the entrainment of juvenile Chinook Salmon (Oncorhynchus tshawytscha) into large water diversions and estimates of population-level loss.

Diversion of freshwater can cause significant changes in hydrologic dynamics and this can have negative consequences for fish populations. Additionally, fishes can be directly entrained into diversion infrastructure (e.g. canals, reservoirs, pumps) where they may become lost to the population. However, the effect of diversion losses on fish population dynamics remains unclear. We used 15 years of release and recovery data from coded-wire-tagged juvenile Chinook Salmon (Oncorhynchus tshawytscha) to model the physical, hydrological and biological predictors of salvage at two large water diversions in the San Francisco Estuary. Additionally, entrainment rates were combined with estimates of mortality during migration to quantify the proportion of total mortality that could be attributed to diversions. Statistical modeling revealed a strong positive relationship between diversion rate and fish entrainment at both diversions and all release locations. Other significant relationships were specific to the rivers where the fish were released, and the specific diversion facility. Although significant relationships were identified in statistical models, entrainment loss and the mean contribution of entrainment to total migration mortality were low. The greatest entrainment mortality occurred for fish released along routes that passed closest to the diversions and certain runs of Chinook Salmon released in the Sacramento River suffered greater mortality but only at the highest diversion rates observed during the study. These results suggest losses at diversions should be put into a population context in order to best inform effective management of Chinook Salmon populations

Estimates of the % of total migration mortality accounted for by loss at each diversion (relative loss) for releases in the Sacramento and San Joaquin Rivers.

<p>Estimates were generated for Sacramento River fish released at Coleman National Fish Hatchery (CNFH) and directly into the tidal Delta. San Joaquin River estimates were only made for fish released into the tidal Delta.</p

Plot of the percentage of migration mortality accounted for by loss at the two diversions (relative loss) as a function of diversion rate for three runs of Chinook Salmon released from the Coleman National Fish Hatchery (CNFH) or directly into the Delta.

<p>Open circles in the Delta late-fall run plot represent a set of releases that occurred within days of each other in 2007 and experienced unusually high loss. Note that the range of the y-axis changes among release locations.</p

Predicted relationships between independent variables and salvage (count model) and independent variables and zero salvage (zero-inflation model).

<p>Predicted relationships between independent variables and salvage (count model) and independent variables and zero salvage (zero-inflation model).</p

Parameter estimates for zero-inflated negative binomial regression describing salvage of coded wire tagged juvenile salmon at the Central Valley Project and State Water project facilities.

<p>The count model describes the salvage process whereas the zero-inflated model describes the process resulting in zero salvage. All releases were in the San Joaquin River.</p

Map depicting the location of the study region within California and relevant locations within the study region.

<p>Release locations in the Sacramento River are indicated by closed circles and release locations in the San Joaquin River are indicated by closed triangles. The number of releases that occurred at each that location appears next to the marker. Abbreviations: SWP  =  State Water Project, CVP  =  Central Valley Project.</p

Percent of migration mortality accounted for by loss at the diversions (relative loss) with and without accounting for salvage.

<p>Percent of migration mortality accounted for by loss at the diversions (relative loss) with and without accounting for salvage.</p

Means and coefficients of variation for variables used in models of salvage.

<p>Variables were separated by run for Sacramento releases. Currently the San Joaquin only supports fall run Chinook Salmon.</p