European flounder (Platichthys flesus) is generally considered to be a marine euryhaline species. Most existing studies have focused on the brackish part of its life cycle. This is the first time that acoustic telemetry has been used to study the movements, home range, and habitat use of late-stage juvenile flounders (2 +, 3 +) in a freshwater tidal segment of an estuary. A total of twenty individuals were marked during the summer of 2008. Fish movements were monitored using sixteen fixed receivers, as well as through manual tracking. To allow the combined use of both types of tracking data, a Brownian Bridge movement model was employed. This type of model takes into account the time-ordered nature of position data and calculates the proportion of time spent in certain areas based on movement paths. Summer movements of European flounder in freshwater habitats were restricted to longitudinal ranges of 50 m to 870 m, suggesting a sedentary life phase. Diet analysis and habitat preferences for both shaded and shallow areas of water suggest that the fish were searching for both food and shelter from predators. Small individual home ranges, coupled with the level of overlap between them, suggest that many fish shared small home ranges with conspecifics. In addition, there was a tendency for 3 + flounders to have higher rates of movement and larger home ranges. The results of this study further emphasise the importance of preserving freshwater habitats as foraging areas for European flounder, especially intertidal habitats up to the tidal limit.