Recently, the provision of food and water resources of two of the world's large river basins, the Murray and the Yangtze, has been significantly altered through widespread landscape modification. Long-term sedimentary archives, dating back to past centuries, from wetlands of these river basins reveal that rapid, basin-wide development has reduced resilience of biological communities, resulting in considerable decline in ecosystem services, including water quality. In particular, large-scale human disturbance to river systems, due to river regulation during the mid-20th century, has transformed the hydrology of rivers and wetlands, causing widespread disturbance to aquatic biological communities. Historical changes of cladoceran zooplankton (water fleas) were used to assess the hydrology and ecology of three Murray and Yangtze River wetlands over the past century. Subfossil assemblages of cladocerans retrieved from sediment cores (94, 45 and 65 cm) of three wetlands: Kings Billabong (Murray), Zhangdu and Liangzi Lakes (Yangtze) strongly responded to hydrological changes of the river after the mid-20th century. River regulation caused by construction of dams and weirs, and river channel modifications has led to hydrological alterations. The hydrological disturbances were either: (1) a prolonged inundation of wetlands, or (2) reduced river flow, which caused variability in wetland depth. These phenomena subsequently transformed the natural wetland habitats, leading to a switch in cladoceran assemblages preferring poor water quality and eutrophication. An adaptive water resource management framework for both of these river basins has been proposed to restore or optimize the conditions of wetland ecosystems impacted by 20th century human disturbance and climate change.