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Abstract: Changes in coastal habitats brought about by climate change have the potential to cause population decline of shoreline dependent organisms. In particular, sea level rise associated with climate change can drastically affect wetlands and beaches which are important foraging and nesting areas of these organisms. SLAMM 5 (Sea Level Affecting Marshes Model) is widely used to simulate wetland conversion and shoreline modification for the purpose of habitat vulnerability assessment and decision making, but concerns regarding the suitability of the model due to the uncertainty involved in selecting many of the model’s empirical input parameters have been expressed. This paper applies a generic evaluation framework consisting of a state-of-the-art screening and variance-based global sensitivity and uncertainty analyses to simulate changes in the coastal habitats of the barrier island in Eglin Air Force Base, Florida in order to: (1) identify the important input factors and processes that control SLAMM 5’s output uncertainty; (2) quantify SLAMM 5’s global output uncertainty and apportion it to the direct contributions and interactions of the important input factors; and (3) evaluate this new methodology to explore the potential fate of the coastal habitats of the study area. Results showed that four input factors (DEM vertical error for the lower elevation range, historic trend of sea level rise, accretion, and sedimentation rates) controlled 88–91% of SLAMM 5’s output variance in predicting changes in the beach habitat of Eglin Air Force Base. The most dominant processes governing the fate of the coastline of the study area were inundation (i.e. reduction in elevation due to sea level rise) and accretion/sedimentation. Interestingly, for lower elevation habitats (salt marsh, tidal flat, and beach), results showed possible gain or loss of these habitats depending on the relative strength of these processes resulting from the combination of input factors within their proposed uncertainty ranges. Higher-elevation habitats (swamps and inland fresh marsh) showed decrease in area over 100 years of simulation. These findings are important to implement managerial schemes in the area to protect threatened Plover birds (Charadrius sp.) communities. This generic model evaluation framework is model-independent and can be used to evaluate a wide range of environmental models. [Copyright &y& Elsevier]