Precise, up-to-date survival estimates for salmonids that migrate through reservoirs, hydroelectric dams, and free-flowing sections of the Snake and Columbia rivers are essential to develop effective strategies for recovering depressed stocks. To provide this information, survival was estimated for yearling chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss with passive integrated transponder (PIT) tags that migrated through Snake River dams and reservoirs from 1993 through 1998. A multiple-recapture model for single release groups was used to estimate survival from detections of PIT-tagged fish at dams. The stretch of river over which survival was estimated varied between years, depending on the release site, the number of dams with the capability to detect and rerelease PIT-tagged fish back to the river, the total number of fish marked, and the efficiency of detecting PIT-tagged fish at each dam. Precision of survival estimates varied with the number of fish PIT-tagged and released and the amount of spill at dams with PIT-tag detectors. When spill levels were high, detection probabilities were lower, as was precision. Mortality at bypass outfall sites was not significant at any Snake River dam investigated. Estimated annual average per-project (combined reservoir and dam passage) survival ranged from 86% to 94% for yearling chinook salmon and from 88% to 92% for steelhead. Survival estimates were higher for both species in years when spill was used specifically to pass fish through nonturbine routes. Over the same stretches of river in years with similar flow conditions from 1970 through 1975, per-project survival estimates typically averaged 57-71% for yearling chinook salmon and 77-90% for steelhead. From 1993 to 1998, survival estimates for fish released from Snake River basin hatcheries to the Lower Granite Dam tailrace indicated that substantial smolt mortality occurred before fish entered the hydropower system. For each hatchery, estimated survival varied each year, and estimates from different hatcheries to Lower Granite Dam varied inversely with the distance fish traveled.

Using yearling chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss tagged with passive integrated transponders (PITs), we estimated passage survival through bypass systems, turbines, and spill bays with and without flow deflectors at Snake River dams relative to survival of fish released into the tailrace below the dam. Actively migrating fish were collected and marked with PIT tags at Snake River dam smolt collection facilities. Groups of tagged fish were then released through hoses into different passage routes; releases were coincident with a tailrace release approximately 1–2 km below the dam. Relative survival was estimated by the use of tag–recapture models for paired releases from detections of individual PIT‐tagged fish at juvenile collection or detection facilities at downstream dams. Detection sites included Little Goose, Lower Monumental, McNary, John Day, and Bonneville dams, depending on the release location and year. Standard errors of relative survival probability estimates were generally less than 3.0% through all potential passage routes. The estimated relative survival was highest through spill bays without flow deflectors (98.4–100%), followed by spill bays with flow deflectors (92.7–100%), bypass systems (95.3–99.4%), and turbines (86.5–93.4%). These estimates of relative survival, which include both the direct and indirect effects of passage, are generally higher than past estimates but similar to other recent estimates determined with modern techniques under present dam configurations and operating conditions.