Hydrology is a critical driver controlling mangrove wetlands structural and functional attributes at different spatial and temporal scales. Yet, human activities have negatively affected hydrology, causing mangrove diebacks and coverage loss worldwide. In fact, the assessment of mangrove water budgets, impacted by natural and human disturbances, is limited due to a lack of long-term data and information that hinders our understanding of how changes in hydroperiod and salinity control mangrove productivity and spatial distribution. In this study, we implemented a mass balance-based hydrological model (RHYMAN) that explicitly considers groundwater discharge in the Shark River estuary (SRE, southwestern Everglades) located in a karstic geomorphic setting and influenced by regional hydrological restoration. We used long-term hydroperiod and porewater salinity (PWS) datasets obtained from 2004 to 2016 for model calibration and validation and to determine spatiotemporal variability in water levels and PWS at three riverine mangrove sites (downstream, SRS-6; midstream, SRS-5; upstream, SRS-4) along SRE. Model results agree with a distinct PWS pattern along the estuarine salinity gradient where the highest PWS occurs at SRS-6 (mean: 25, range: 22–30 ppt), followed by SRS-5 (17, 14–25 ppt) and SRS-4 (5, 3–13 ppt). A commensurate increase in PWS over a thirteen-year period indicates a long-term reduction in freshwater inflow coupled with sea-level rise (SLR). Increasing freshwater scenario simulation results show a significant reduction (17–27%) in PWS along the estuary in contrast with a high SLR scenario when salinity increases up to 1.1 to 2.5 times that of control values. Model results show that freshwater inflow and SLR are key drivers controlling mangrove wetlands PWS in this karstic coastal region. Given its relatively simple structure, this mass balance-based hydrological model could be used in other environmental settings to evaluate potential habitat and regime shifts due to changes in hydrology and PWS under regional hydrological restoration management.