Purposely introduced in 1879, Pacific coast Striped Bass Morone saxatilis once supported a commercial fishery and currently supports a recreational fishery in the San Francisco Estuary Watershed, CA, USA; however, the population has been in decline for decades. Since little is known about sub-adult behavior on the Pacific coast, we used acoustic telemetry to investigate seasonal movement patterns and habitat use across three regions (bay, delta, and river) and the effects of temperature and salinity on habitat use over a 2-year period. Sub-adult movement and habitat use differed by year and age. In spring, age-I and age-II sub-adults moved within the delta (60%), river (20%), and bay (20%) regions, and by summer, some individuals moved to the bay (36%), while others remained in the delta (42%) and river (22%). Fall and winter showed equal movement between the bay and delta regions. During year 2, age-II and age-III fish inhabited the bay region across all seasons with the exception of spring when a few individuals migrated up river. Generally, sub-adults did not inhabit the river region in fall or winter. Sub-adults were not detected in water temperatures < 10 °C and occurred most often in 20–25 °C. Younger sub-adults inhabited limnetic habitat where older fish inhabited mesohaline and polyhaline habitats. Our findings suggest that sub-adult seasonal movement patterns and habitat use hotspots have important fishery management implications and can be useful to address concerns over how this non-native fish’s predation impacts native and endangered fishes.