Juvenile Chinook salmon (Oncorhynchus tshawytscha) emigrating from natal tributaries of the Sacramento River may use a number of migration routes to navigate the Sacramento-San Joaquin River Delta (hereafter called “the Delta”), each of which may influence their probability of surviving. We applied a mark-recapture model to data from acoustically tagged juvenile late fall-run Chinook salmon that migrated through the Delta during the winter of 2008–09 to estimate route entrainment, survival, and migration times through the Delta. A tag-life study was conducted to determine the potential for premature tag failure. Tag failure began after 12 days and continued until the 45th day. Travel times of tagged fish exceeded minimum tag-failure times, indicating that survival estimates obtained from this study were negatively biased due to tag failure prior to fish exiting the Delta. Survival estimates were not adjusted and represent the joint probability of tag survival and fish survival. However, relative comparisons of survival among Chinook salmon choosing different routes appeared to be robust to tag failure, and migration-routing parameters were unaffected by tag failure. Migration-routing patterns were consistent among release groups. The Sacramento River was the primary migration route for all release groups except one. The percentage of fish entering the Sacramento River ranged from 33 to 55 percent. Sutter and Steamboat Sloughs were the secondary migration route for 9 of the 10 releases. The percentage of fish migrating through this route ranged from 10 to 35 percent. Entrainment into the interior Delta ranged from 15 to 33 percent. The Delta Cross Channel gates were open for 7 of the 10 releases. Entrainment into the interior Delta through the cross channel ranged from 1 to 27 percent. We estimated route-specific survival for 10 release groups that were released between November 14, 2008, and January 19, 2009. Population-level survival through the Delta (S_Delta) ranged from 0.019 (standard error of 0.012) to 0.277 (standard error of 0.041) among releases, which represent the probability of a fish surviving from Sacramento to Chipps Island with an operational transmitter. Sacramento River flows throughout the study period were approximately 8,000–15,000 cubic feet per second at Freeport, suggesting that variability in flow contributed little to differences in survival between releases. Fish migrating through the Sacramento River had the highest survival for most releases. Survival in Sutter and Steamboat Sloughs was slightly lower than survival in the Sacramento River for 7 of the 10 releases, but higher than survival in the Sacramento River for 3 releases. Survival in the interior Delta was lowest for all release groups except for one release in November. With the exception of this November release, survival patterns across release groups were similar to those of previous studies.