One thousand late-fall run Chinook salmon (Oncorhynchus tshawytscha) hatchery reared smolts were fitted with ultrasonic coded tags over a two-year period (in 2009 and 2010) and released in the Sacramento River. We tracked their outmigration movements from Benicia Bridge to the Golden Gate. Smolts transited the Bay rapidly in 2 to 4 days, yet also made repeated upstream movements, coinciding with incoming tidal flows. Most smolts were detected in deep, channelized portions of the Bay. Some smolts were detected at nearshore, shallow sites such as marinas, or up tributaries, yet these fish generally returned to the main channel and continued their outmigration. The results suggest that the smolts perceive little benefit to remaining in estuarine waters, and therefore actively attempt to reach the ocean in as short a time as possible, rather than being transported passively by flows.