Balancing wetland conservation with food security is a critical challenge for developing countries. This study compares land use change and its impacts on soil properties in two hydrologically distinct wetlands: the rain-fed Jinchuan Peatland in China and the flood-fed Kilombero Valley Floodplain (KVFP) in Tanzania. Using remote sensing data from 1990 to 2018 and soil physicochemical analysis, we found divergent reclamation trajectories. Wetland conversion has slowed in China but accelerated in Tanzania’s KVFP due to population pressure. Our results reveal a fundamental mechanism: rain-fed wetlands, lacking external nutrient replenishment, experience significantly greater soil degradation after conversion compared to flood-fed wetlands, which benefit from continued alluvial sediment inputs. Both sites showed post-conversion declines in soil moisture, total organic carbon (TOC), and total nitrogen (TN), alongside increased pH and bulk density. However, soil fertility loss was markedly more severe in Jinchuan than in KVFP. This disparity is attributed to the inability of rain-fed systems to replenish nutrients externally, whereas flood-fed KVFP benefits from continued alluvial sediment inputs. Our findings elucidate a key mechanism: flood-fed wetlands possess a natural resilience to agricultural disturbance through hydrological replenishment, making them potentially more suitable for sustainable utilization in food-insecure nations. Consequently, we propose that wetland management policies must be customized based on water source type and national development context, advocating for the targeted, science-based utilization of flood-fed wetlands as a strategic approach to reconcile food production with ecosystem preservation in regions like Tanzania.