Throughout the Caribbean region, coastal areas are of vital importance for national incomes from the tourism industry. However, accelerated coastal development has impacted the coastal ecosystems, including the beaches, and deterioration of the shore results from cumulative impacts on both marine and coastal ecosystems. It is essential to identify the areas that need special attention for targeted management plans and actions, especially in areas with high anthropogenic pressure. This research proposes an integrated assessment of the conservation state of shore and coastal ecosystems in the Puerto Morelos National Reef Park (PNAPM) in the Mexican Caribbean, through the spatial monitoring of key parameters. A Geographic Information System (GIS) was employed to analyze the land use on the shore, foredune condition, morphological characteristics of the beaches, shoreline evolution, and the condition of coral reefs and seagrass meadows. The analysis identified the most critical areas in relation to shore deterioration and priority areas for the preservation of ecosystems. The spatial data obtained for the PNAPM can serve as a basis for ongoing shore monitoring, and targeted management actions through the designation of areas that require either preservation or ecosystem restoration practices. This methodology can be applied to other reef systems in the Caribbean.