The movements and dam passage of individual juvenile Chinook salmon (Oncorhynchus tshawytscha) were studied at Cougar Reservoir and Dam, near Springfield, Oregon, during 2012 and 2013. Cougar Dam is a high-head flood-control reservoir with a temperature control tower as its outlet enabling selective withdrawals of water at various depths to control the temperature of water passed downstream. This report describes the second year of a 2-year study with the goal of providing information to inform decisions about future downstream passage alternatives. Inferences were based on the behavior of yearling-size juvenile Chinook salmon implanted with acoustic transmitters. The fish were released near the head of the reservoir during the spring (March, April, and May) and fall (September, October, and November) of 2012. Most tagged fish were of hatchery origin (468 spring, 449 fall) because of the low number of wild fish captured from within the reservoir (0 spring, 65 fall). Detections at hydrophones placed in several lines across the reservoir and within a collective system used to estimate three-dimensional positions near the temperature control tower were used to determine fish behavior and factors affecting dam passage rates. Most tagged fish made repeated non-random migrations from one end of the reservoir to the other and took a median of 3.7–11.7 days to travel about 7 kilometers from the release site to within about 100 meters of the temperature control tower, depending on season and origin. Reservoir passage efficiency (percentage of tagged fish detected at the head of the forebay) was 97.8 percent for hatchery fish and 74.2 percent for wild fish. Tagged fish commonly were within about 100 meters of the temperature control tower, and often spent considerable time near the entrance to the tower; however, the dam passage efficiency (percentage of dam passage of fish detected at the head of the forebay) was low for fish released during the spring (11.1 percent) and moderate for fish released during the fall (58.1 percent for hatchery fish, 65.2 percent for wild fish) over the 90th percentile of the empirically determined tag life, which was about 90 days. The primary factors affecting the dam passage rate were diel period, dam discharge, and reservoir elevation, and most passage occurred during conditions of night, high dam discharge, and low reservoir elevation. Most fish entering the temperature control tower passed the dam without returning to the reservoir. The common presence of tagged fish near the tower entrance and high proportion of dam passage after tower entry suggests that the primary cause of the poor dam passage rate was the low rate of tower entry. We hypothesize that fish reject the tower entrance because of low water velocities contributing to a small flow field, an abrupt deceleration at the trash rack, or a combination of those two conditions. Results of a controlled test of head differential (the difference between water elevation outside and inside the temperature control tower) indicated weak statistical support (P= 0.0930) for a greater tower entry rate when the differential was 0.65–1.00 foot compared to 0.00–0.30 foot. Results from hatchery and wild fish were similar, with the exception of the reservoir passage efficiency, indicating hatchery fish were suitable surrogates for the wild fish for the purpose of this study.