<p>Numerous species face redistribution and compression of habitat due to climate change. Compounded with anthropogenic stressors, coastal systems are among those experiencing the largest shifts in distribution and degradation of habitats. We coupled long-term movement and environmental data to assess how a freshwater species responds to changes in a coastal refuge habitat to quantify distributional changes, identify key environmental variables, and provide restoration targets. Salinity, variation in salinity, and stage of surrounding marsh habitat were the most important variables driving Florida bass (<i>Micropterus salmoides</i>) occurrence in the estuary. Salinity below 8.7 ppt had the largest positive effect on Florida bass occurrence, while low levels of daily variation in salinity (&lt; 1.3 SD) and marsh stages between 11.4 and 27.7&#xa0;cm were associated with an increased probability of Florida bass occurrence. Years with above average freshwater inputs that shifted mesohaline boundaries downstream generated 15.3 km² of both core and conditional habitat for Florida bass, average conditions generated 4.4 km² of core and conditional habitat, whereas dry conditions compressed Florida bass habitat to 1.7 km². These results suggest that varying environmental scenarios can shift the amount of suitable habitat available for freshwater species using conditional coastal habitats. Our study provides salinity and marsh depth thresholds that offer actionable management targets to maximize the presence of Florida bass in coastal rivers, with population and fishing quality benefits. Climate change will likely result in large-scale reductions of critical dry season habitat for these species, while restoration efforts and adaptive management can bolster the resiliency of these habitats.</p>