Riverine input is essential for the sustainability of the estuaries, wetlands, and swamps into which they flow. An existing coastal ecosystem model was used with forested wetland and fish habitat indicators to evaluate current environmental conditions as well as future restoration projects via 50-year simulations of riverine flow with sea level rise and subsidence. The objective of this study was to utilize the Integrated Compartment Model developed for the Louisiana Coastal Protection and Restoration Authority’s 2017 Coastal Master Plan to understand how alternations of riverine flow from existing rivers and future restoration projects may influence the spatial and temporal distribution of wetland habitats and suitability of fish habitats. The model was applied to the Lake Maurepas ecosystem where the Amite River flows into the lake and supports vital fisheries for surrounding communities, as well as a unique and valuable recreational resource. Additionally, the Amite River nourishes the marshes and swamps around Lake Maurepas that are essential for storm surge protection for the broader region. Modeling results suggest that the major contributing factor to the freshwater conditions to the Lake Maurepas area is the challenge of relative sea level rise − the combination of rising seas and subsidence. Fresh forested areas comprised of bald cypress (Taxodium distichum) and tupelo gum (Nyssa aquatica) in Maurepas Swamp decrease significantly under all future climate and relative sea level rise simulations except when future restoration projects are utilized. An estimated ∼1000 km2 of fresh forested wetland could be maintained over a 50-year period when considering certain restoration projects that increase freshwater flow and under climate change-related rainfall patterns, sea level rise and subsidence. However, modeled results indicate that more than 100% of the current riverine flows into the Maurepas Swamp region are still not sufficient to fully counteract the impacts of the assumed future sea level rise scenario and maintain the current forested wetlands surrounding Lake Maurepas. The higher salinities and more estuarine open water areas provide additional habitat in the future that will likely be more suitable for spotted seatrout (Cynoscion nebulosus), and adult bay anchovy (Anchoa mitchilli) than largemouth bass (Micropterus salmoides). Modeled future conditions of this ecosystem can inform restoration agencies and organizations by helping to prioritize and plan for future decades by incorporating critical factors such as sea level rise, subsidence and precipitation patterns, including the possible need to plan and prepare for changes in the fish communities and consider how that might influence the well-being of local communities.