Governments, development banks, corporations, and nonprofits are increasingly considering the potential contribution of watershed conservation activities to secure clean water for cities and to reduce flood risk. These organizations, however, often lack decision-relevant, initial screening information across multiple cities to identify which specific city-watershed combinations present not only water-related risks but also potentially attractive opportunities for mitigation via natural infrastructure approaches. To address this need, this paper presents a novel methodology for a continental assessment of the potential for watershed conservation activities to improve surface drinking water quality and mitigate riverine and stormwater flood risks in 70 major cities across Latin America. We used publicly available geospatial data to analyze 887 associated watersheds. Water quality metrics assessed the potential for agricultural practices, afforestation, riparian buffers, and forest conservation to mitigate sediment and phosphorus loads. Flood reduction metrics analyzed the role of increasing infiltration, restoring riparian wetlands, and reducing connected impervious surface to mitigate riverine and stormwater floods for exposed urban populations. Cities were then categorized based on relative opportunity potential to reduce identified risks through watershed conservation activities. We find high opportunities for watershed activities to mitigate at least one of the risks in 42 cities, potentially benefiting 96 million people or around 60% of the urbanites living in the 70 largest cities in Latin America. We estimate water quality could be improved for 72 million people in 27 cities, riverine flood risk mitigated for 5 million people in 13 cities, and stormwater flooding mitigated for 44 million people in 14 cities. We identified five cities with the potential to simultaneously enhance water quality and mitigate flood risks, and in contrast, six cities where conservation efforts are unlikely to meaningfully mitigate either risk. Institutions investing in natural infrastructure to improve water security in Latin America can maximize their impact by focusing on specific watershed conservation activities either for cleaner drinking water or flood mitigation in cities identified in our analysis where these interventions are most likely to reduce risk.