To acquire 3-D tracking data on juvenile salmonids, Juvenile Salmon Acoustic Telemetry System (JSATS) cabled hydrophone arrays were deployed in the forebays of two dams on the Snake River and at a mid-reach reservoir between the dams. The depth distributions of fish were estimated by statistical analyses performed on large 3-D tracking data sets from ~33,500 individual acoustic tagged yearling and subyearling Chinook salmon and juvenile steelhead at the two dams in 2012 and subyearling Chinook salmon at the two dams and the mid-reach reservoir in 2013. This research investigated the correlation between vertical migration behavior and passage routes. The depth distributions of fish within the forebays of the dams were significantly different from fish passing the mid-reach reservoir. Fish residing deeper in the forebay tended to pass the dam using deeper powerhouse routes. This difference in depth distributions indicated that the depth distribution of fish at the mid-reach reservoir was not related to behaviors of fish passing through certain routes of the adjacent dams. For fish that were detected deeper than 17.5 m in the forebays, the probability of powerhouse passage (i.e., turbine) increased significantly. Another important finding was the variation in depth distributions during dam passage associated with the diel period, especially the crepuscular periods.