Shallow, highly managed coastal lagoons are increasingly affected by interacting pressures from hydrological alteration, nutrient enrichment, and climate variability, creating a need for hydrodynamic models that can resolve management-relevant spatial heterogeneity without prohibitive computational cost. Biscayne Bay, a shallow subtropical lagoon in southeast Florida, USA, exemplifies these challenges, with anthropogenic hydrological modifications contributing to nutrient enrichment, seagrass die-offs, and recurrent fish kills. In this study, we configured and evaluated the Biscayne Bay Operational Model (BBOM) using RiverFlow2D, a GPU-accelerated, two-dimensional (2D) flexible-mesh hydrodynamic model. Hydrodynamic evaluation used January 2021 water-level and current observations from ten FIU stations reserved for performance assessment, with the previously calibrated bed-roughness distribution retained without adjustment; additional comparisons included stations whose water-level observations supplied tidal boundary conditions. The 2019 salinity and water-level comparisons used SFWMD records that also contributed to boundary specification and salinity calibration, without a documented subset withheld from both activities. The evaluated framework showed pronounced spatial heterogeneity in hydrodynamic conditions. In North Biscayne Bay, relatively rapid exchange at external boundaries coexisted with substantially slower residence times in interior zones, demonstrating that whole-bay exchange metrics can obscure localized retention environments relevant to pollutants exposure. In the central and southern basins, freshwater-plume distributions were shaped by the interaction of continental inflows with tidal intrusion and marine exchange, illustrating that freshwater influence cannot be inferred from watershed discharge magnitude alone. These applications demonstrate the importance of resolving internal connectivity and spatial variability when evaluating freshwater and water-quality management strategies. Beyond Biscayne Bay, the BBOM provides a computationally efficient, high-resolution framework for investigating transport, residence times, and freshwater connectivity in comparable shallow, highly managed coastal systems facing increasing anthropogenic and climatic pressures.