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Coastal environments around the globe are subject to anthropogenic stresses due to dense coastal populations. The response of development activities on dynamic estuarine ecosystems, influenced by tidal forces, freshwater flows, salinity variations, and intricate coastal land morphology, is often uncertain. This case study evaluates how connectivity and coastal geomorphology influence flow patterns by modeling the effects of a proposed hydraulic reconnection project on water movement between the Manchester Waterway, a coastal residential community, and Charlotte Harbor, a large open water estuary in the Gulf of Mexico. An unstructured grid, 2D model was developed utilizing Delft3D Flexible Mesh to simulate estuary hydrodynamics under proposed conditions for four different weather conditions, including recorded 2021–2022 weather, future sea level rise, an extreme weather event, and a combination of extreme weather and sea level rise. Simulated flow results for proposed conditions were compared to present day flow patterns for analysis of the predicted changes in water levels and velocity magnitudes in the waterway. The results show that increased connectivity between the Manchester Waterway and Charlotte Harbor is expected to increase tidal amplitudes largely due to a lowering of minimum water levels in the waterway. During storm events, water elevations are predicted to drop to lower elevations following peak storm surge due to proposed conditions, which may provide flooding relief. Model simulation results will aid hydraulic reconnection and guide a more comprehensive ecological restoration plan. This case study will also improve understanding of the major influencing forces in intricate estuarine environments and how ecosystems may respond to land development, sea level rise, and increasing magnitude and frequency of tropical storms.