Comprehensive flood risk assessment is often constrained by a lack of appropriate data in high-altitude watersheds, particularly in developing countries like Nepal, where institutional capacities are limited for mapping and monitoring flood-prone communities. This study, one of the first of its kind, produced spatial multi-criteria-based flood susceptibility, vulnerability, and risk index maps for the Kathmandu Valley (KV) watershed in Nepal using an Analytical Hierarchy Process (AHP) approach and Geographical Information System (GIS). The result shows that most parts of the KV (around 80%) have moderate to low flood susceptibility around the watershed but susceptibility is prominent in southern areas. Highly flood-susceptible regions (about 14%) are found mainly along the riverbanks. Flood vulnerability, primarily influenced by population density and literacy rate, is moderate to low in most areas of the watershed (around 86%), predominantly higher in the central urban areas, and gradually lower towards the edge of the watershed. Flood risks in the major portion of the watershed (around 72%), mainly in the southern and eastern parts, are estimated as moderate to low risk, whereas higher risk zones are found in the central urban areas. The high contrast in flood vulnerability scores across the watershed has mainly contributed to the variation of flood risk zones, as flood susceptibility scores are fairly distributed over the watershed. The study findings will help policymakers develop location-specific sustainable flood risk management strategies for the flood-vulnerable communities in the KV watershed.