Storing runoff during the monsoon season in Himalayan hills is crucial to have enough water to cope with the dry season, especially considering that climate change is changing rainfall intensity and patterns. Traditional Nepalese water ponds, called pokharis, are used to store runoff mainly for cattle rearing and rice fields’ supplementary irrigation. Local communities are interested in restoring existing pokharis and building new ones to improve their economical and living conditions. Selecting the most suitable locations for pokharis is of crucial importance; however, scarce information is available for large-scale site selection. A comprehensive analysis of multiple relevant parameters for traditional ponds siting can lead to more efficient rainwater collection and provide a useful water resource management tool. In this work, we propose a methodology for pokharis’ best-siting analysis, based on geographic information system (GIS), multi-criteria decision-making (MCDM), and participatory research. To our knowledge, this is the first large-scale best-siting analysis for traditional ponds in Nepal. An area of 0.423 km2 (3.47% of the study area) is classified as highly suitable, with 100% agreement with existing pokharis. Despite the low data resolution, which requires a further field inspection for the final site selection, our results provide reliable guidance for pokharis large-scale suitability, supporting water-resilience projects in the area.