This report describes a spatial characterization conducted to support the development of an integrated management plan for Puerto Rico’s Northeast Marine Corridor. The Northeast Marine Corridor is a large, landsea reserve network, making it unique in the region for both its size and the integrated land-sea geographical scope. Here we map and model ecological priorities and threats to support managers with risk assessment and prioritization of management actions. The best available data, including local expert knowledge of special ecological places and threats, were compiled to map key marine features, important habitat types and marine species of concern. Ecological priority areas were identified and ranked based on the number of ecologically important attributes across the region and analyzed relative to the distribution of threats and stressors to help managers identify and prioritize areas of concern. The methods and data used for spatial prioritization are described in this report and resultant maps showing ecological priorities and potential stressors are provided. The approach was implemented through a partnership between NOAA National Centers for Coastal Ocean Science and Puerto Rico’s Department of Natural and Environmental Resources, or Departamento de Recursos Naturales y Ambientales, with funding from NOAA’s Coral Reef Conservation Program.