The existence of coastal ecosystems depends on their ability to gain sediment and keep pace with sea level rise. Similar to other coastal areas, Northeast Florida (United States) is experiencing rapid population growth, climate change, and shifting wetland communities. Rising seas and more severe storms, coupled with the intensification of human activities, can modify the biophysical environment, thereby increasing coastal exposure to storm-induced erosion and inundation. Using the Guana Tolomato Matanzas National Estuarine Research Reserve as a case study, we analyzed the distribution of coastal protection services–expressly, wave attenuation and sediment control–provided by estuarine habitats inside a dynamic Intracoastal waterway. We explored six coastal variables that contribute to coastal flooding and erosion–(a) relief, (b) geomorphology, (c) estuarine habitats, (d) wind exposure, (e) boat wake energy, and (f) storm surge potential–to assess physical exposure to coastal hazards. The highest levels of coastal exposure were found in the north and south sections of the Reserve (9% and 14%, respectively) compared to only 4% in the central, with exposure in the south driven by low wetland elevation, high surge potential, and shorelines composed of less stable sandy and muddy substrate. The most vulnerable areas of the central Reserve and main channel of the Intracoastal waterway were exposed to boat wakes from larger vessels frequently traveling at medium speeds (10–20 knots) and had shoreline segments oriented towards the prevailing winds (north-northeast). To guide management for the recently expanded Reserve into vulnerable areas near the City of Saint Augustine, we evaluated six sites of concern where the current distribution of estuarine habitats (mangroves, salt marshes, and oyster beds) likely play the greatest role in natural protection. Spatially explicit outputs also identified potential elevation maintenance strategies such as living shorelines, landform modification, and mangrove establishment for providing coastal risk-reduction and other ecosystem-service co-benefits. Salt marshes and mangroves in two sites of the central section (N-312 and S-312) were found to protect more than a one-quarter of their cross-shore length (27% and 73%, respectively) from transitioning to the highest exposure category. Proposed interventions for mangrove establishment and living shorelines could help maintain elevation in these sites of concern. This work sets the stage for additional research, education, and outreach about where mangroves, salt marshes, and oyster beds are most likely to reduce risk to wetland communities in the region.