Habitat use of juvenile southern flounder Paralichthys lethostigma was examined within a shallow estuarine seascape during June and July 2011 using acoustic telemetry. Fine-scale movement and habitat use of P. lethostigma was investigated with an acoustic positioning system placed in a seascape that varied in habitat type, physicochemical conditions and bathymetry. The use of different habitat types was examined with Euclidean distance-based analyses, and generalized additive models were used to determine the relative importance of habitat type relative to physicochemical conditions and bathymetry. Tracks of P. lethostigma ranged in distance between 1477 and 8582 m and speed was 4·2 ± 1·1 m min−1 (mean ± s.e.) for all P. lethostigma combined. Depth, slope and habitat type had the most influence on P. lethostigma occurrence and deep sandy areas with shallow slopes were used most frequently. In addition, depth use by P. lethostigma was influenced by tidal cycles, indicating habitat use varies temporally and is dynamic. Finally, temperatures <30·5° C were used more than warmer waters within the study area. The results successfully identify movements by juvenile P. lethostigma, and indicate that definitions of essential habitats need to account for dynamics in habitat use.