Rural water supply systems (RWSS) in developing countries typically have deficiencies that threaten their sustainability. This research used Multi-Criteria Analysis and the Analytical Hierarchy Process to identify indicators that can be used to assess the sustainability of RWSS. The assessment tool developed is composed of 17 attributes with 95 quantifiable indicators. The tool enables the assessment of the sustainability of RWSS, using data collected through semi-structured interviews, social cartography, technical inspection, household surveys, and water monitoring. The tool was applied in a case study of a RWSS in the Andean region of Colombia, illustrating a participatory, holistic, and structured assessment that provided a single sustainability measure for the system (3.0/5.0). The tool?s completeness is represented by its extensive attributes and indicators that deliver a robust baseline on the state of a system, help identify improvement strategies, and monitor system performance over time that can assists rural community organizations with RWSS management.