Predicted increased variability in rainfall together with the effects of fast-growing population centers, hydropower development, and irrigated agriculture will likely continue to alter landscape and biotic diversity of freshwater ecosystems in the Apalachicola-Chattahoochee-Flint (ACF) River Basin in Alabama, Georgia and Florida. Adaptations to these climatic changes among water users provide examples of how water can be spatially distributed to protect in-channel habitats and biodiversity as well as to supply predictable water for socio-economic needs during periods of highly variable precipitation. Within the ACF and other regions, individuals rely on combinations of groundwater and surface water storage to sustain for ecosystem services in differently sized sub-basins with distinct land uses. Exponential increases in numbers of farm ponds and reservoirs constructed over the last 50 years provide basin-wide adaptations that are valuable during periods of both high and low precipitation. The cumulative and linked effects of these storage systems are likely to go undetected if large and small reservoirs are studied as independent units within a drainage network. Governmental efforts, such as the Flint River Drought Protection Act and other incentives, provide examples of additional adaptive responses to extreme variations in precipitation that sustain flows in rivers with high biodiversity and essential ecosystem services. Comparative studies among regions with different precipitation regimes improve our understanding of how socio-economic adaptations such as constructed ponds and lakes have transformed the landscape and altered the biodiversity essential for sustaining freshwater ecosystem services.