This study evaluated the risk posed by nonpoint-source (NPS) pollution to the 266 community-based water systems (CBWS) in Eastern Visayas, Philippines. Geographic Information System (GIS) techniques, together with Multi-Criteria Decision Analysis (MCDA) was used to develop a Nonpoint-Source Pollution Potential Index (NSPPI) to identify and classify the potential locations of water systems that are at risk from NPS. In developing the NSPPI, this study used three features that contribute to NPS pollution (taken from the original Agricultural Pollution Potential Index (APPI) model) as follows: Runoff Potential Index, Sediment Yield Potential Index, and Nutrient Yield Potential Index. Results showed that 22% (n=59) of the CBWS is at high risk of NPS pollution, 42% (n=111) is categorized as moderate, and 36% (n=96) as low. Using NSPPI as a primary risk evaluation of CBWS from NPS pollution is a cost-effective screening tool in identifying priority sites for environmental management intervention.