The objective of this study was to determine whether fisheries-related stressors differently influence two populations of adult sockeye salmon (Oncorhynchus nerka) with shared migration timing and location but where one population (i.e., Harrison) spawns 1 mo after the other (i.e., Weaver). Four stressor treatments were used following beach seine capture: (1) immediate release, (2) release after 10-15 min in the beach seine, (3) an additional 3-min gill net entanglement and 1-min air exposure, and (4) an additional 3-min tangle net simulation and 1-min air exposure. A comprehensive acoustic telemetry array and manual tracking revealed that survival was low overall, with more Weaver fish (34.2% of 38 tagged) reaching spawning areas compared to Harrison fish (17.8% of 78 tagged). For the Harrison population but not the Weaver, the gill net treatment influenced immediate (i.e., survived treatment) and short-term (i.e., 5-d postrelease) survival as well as survival to reach spawning areas. Harrison fish were more likely to be injured by the treatment, and reflex impairment predicted their short-term and long-term survival. Physiological condition did not differ between populations at the time of release, although both populations showed signs of severe physiological disturbances from the gill and tangle net simulations. These results suggest that even short durations of gill or tangle net entanglement can result in profound population-specific physiological disturbances and mortality. The notion that there can be population-specific variation in response to fisheries encounters adds complexity to management and provides further evidence for intraspecific differences in migration success.