Route Use and Survival of Juvenile Chinook Salmon through the San Joaquin River Delta

Abstract The survival of juvenile Chinook Salmon through the lower San Joaquin River and Sacramento–San Joaquin River Delta in California was estimated using acoustic tags in the spring of 2009 and 2010. The focus was on route use and survival within two major routes through the Delta: the San Joaquin River, which skirts most of the interior Delta to the east, and the Old River, a distributary of the San Joaquin River leading to federal and state water export facilities that pump water out of the Delta. The estimated probability of using the Old River route was 0.47 in both 2009 and 2010. Survival through the southern (i.e., upstream) portion of the Delta was very low in 2009, estimated at 0.06, and there was no significant difference between the Old River and San Joaquin River routes. Estimated survival through the Southern Delta was considerably higher in 2010 (0.56), being higher in the Old River route than in the San Joaquin route. Total estimated survival through the entire Delta (estimated only in 2010) was low (0.05); again, survival was higher through the Old River. Most fish in the Old River that survived to the end of the Delta had been salvaged from the federal water export facility on the Old River and trucked around the remainder of the Delta. The very low survival estimates reported here are considerably lower than observed salmon survival through comparable reaches of other large West Coast river systems and are unlikely to be sustainable for this salmon population. More research into mortality factors in the Delta and new management actions will be necessary to recover this population. Received March 28, 2012; accepted September 5, 2012