Abandoned mines remain a social, environmental, and health-risk problem for the Philippines. These abandoned sites are generally characterized by water-filled pit lakes surrounded with disturbed and exposed soils and sediments containing elevated values of heavy metals and other environmental contaminants. Previous studies with abandoned mines in the Philippines have initiated the use of integrated methods for the assessment of existing abandoned mine site conditions as a tool for decision-making. To further provide a numerical basis for rehabilitation prioritization, this paper aimed to utilize the modified Historic Mine Site Scoring System (HMS-SS) for physical and environmental hazard assessment of the abandoned mercury mine located in Barangay Sta. Lourdes, Puerto Princesa City, Philippines and to produce hazard classification maps based on the generated scores. Results identified the pit lake to be extremely hazardous physically, however, the liquid material (rainfall accumulation in the pit) yielded very low environmental hazard scores with only a few identified points that exceed the regulatory limit. Moreover, the two (2) identified mine tailings sites were found to be physically moderately hazardous but are categorized as extremely hazardous for the environmental aspect. The hazard scoring, coupled with the integrated environmental methods for characterization and development of hazard maps, is recommended as a scientific and quantitative basis for providing decisions in priority of actions to be taken with regards to abandoned mine sites.