Recently, the provision of food and water resources of two of the world's largest river basins, the Murray and the Yangtze, has been significantly altered through widespread landscape modification. Long-term sedimentary archives, dating back for some centuries from wetlands of these river basins, reveal that rapid, basin-wide development has reduced the resilience of biological communities, resulting in considerable decline in ecosystem services, including water quality. 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 modification of aquatic biological communities. Changes to cladoceran zooplankton (water fleas) were used to assess the historical 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), showed strong responses to hydrological changes in the river after the mid-20th century. In particular, river regulation caused by construction of dams and weirs together with river channel modifications, has led to significant hydrological alterations. These hydrological disturbances were either (1) a prolonged inundation of wetlands or (2) reduced river flow, both of which caused variability in wetland depth. Inevitably, these phenomena have subsequently transformed the natural wetland habitats, leading to a switch in cladoceran assemblages to species preferring poor water quality, and in some cases to eutrophication. The quantitative and qualitative decline of wetland water conditions is indicative of reduced ecosystem services, and requires effective restoration measures for both river basins which have been impacted by recent socioeconomic development and climate change. © 2016 Author(s).