Understanding the effects of freshwater inflow on estuarine fish habitat use is critical to the sustainable management of many coastal fisheries. The Baffin Bay Complex (BBC) of south Texas is typically a reverse estuary (i.e., salinity increases upstream) that has supported many recreational and commercial fisheries. In 2012, a large proportion of black drum (Pogonias cromis) landed by fishers were emaciated, leading to concerns about the health of this estuary. In response to this event and lacking data on black drum spatial dynamics, a 2-year acoustic telemetry study was implemented to monitor individual-based movement and seasonal distribution patterns. Coupled with simultaneous water quality monitoring, the relationship between environmental variables and fish movement was assessed under reverse and “classical” estuary conditions. Acoustic monitoring data suggested that the BBC represents an important habitat for black drum; individuals exhibited site fidelity to the system and were present for much of the year. However, under reverse estuary conditions, fish summertime distribution was constrained to the interior of the BBC, where food resources are limited (based on recent benthic sampling), with little evidence of movement across the system. Out of eight environmental variables used to model fish movement using multiple linear regression, the only significant variable was salinity, which exhibited a negative relationship with movement rate. These findings suggest that prolonged periods of hypersalinity, which are detrimental to other euryhaline species due to increased osmoregulatory costs, reduce black drum distribution patterns and can limit the species’ access to benthic habitats supporting abundant prey resources.