Farm ponds, which are sometimes numerous and widely distributed in agricultural regions, have faced widespread degradation in recent decades. Although conservation strategies for these biodiversity hotspots have gradually increased, appropriate approaches for developing country contexts are lacking. Farm ponds provided hydrologic, biogeochemical, and socioeconomic benefits to southern China for thousands of years, but they are facing contemporary threats and management challenges, including (1) inadequate planning in terms of construction and conservation regulations; (2) rural nonpoint source and mini-point source pollution; (3) climate change induced abnormalities in the hydroperiod and disturbance to wildlife; (4) invasive species; and (5) inadequate social and political capacity to consider ecological conservation. Because farm ponds function as wetland complexes that are embedded within or integral to larger ecosystems, their conservation requires collaborative efforts over scales ranging from within-pond to regional. We highlight approaches that build public awareness and involve inventory maps as a basis. Policies that integrate top-down regulation and bottom-up engagement and emphasize sustainable management and utilization are recommended to ensure the effectiveness and continuous improvement of conservation programs. Techniques that involve interconnected smart sensors, volunteering and citizen science, and integrated process-based modeling are preferred when conducting comprehensive descriptions of the pond landscape, numerical assessments on their ecosystem services, and associated conservation cost analyses. Nature-based solutions are increasingly recognized as an important opportunity for coping with water-related crises. This paper presents the first synthetic perspective on the ecological roles of farm ponds in agriculturally dominated developing countries. The analytical framework and conservation suggestions are referential to sustainable rural development and the management of other small, scattered wetlands.