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Climate change is predicted to impact river systems in the southeastern United States through alterations of temperature, patterns of precipitation and hydrology. Future climate scenarios for the southeastern United States predict (1) surface water temperatures will warm in concert with air temperature, (2) storm flows will increase and base flows will decrease, and (3) the annual pattern of synchronization between hydroperiod and water temperature will be altered. These alterations are expected to disturb floodplain plant communities, making them more vulnerable to establishment of invasive species. The primary objective of this study is to evaluate whether native and invasive riparian plant assemblages respond differently to alterations of climate and land use. To study the response of riparian wetlands to watershed and climate alterations, we utilized an existing natural experiment imbedded in gradients of temperature and hydrology-found among dammed and undammed rivers. We evaluated a suite of environmental variables related to water temperature, hydrology, watershed disturbance, and edaphic conditions to identify the strongest predictors of native and invasive species abundances. We found that native species abundance is strongly influenced by climate-driven variables such as temperature and hydrology, while invasive species abundance is more strongly influenced by site-specific factors such as land use and soil nutrient availability. The patterns of synchronization between plant phenology, annual hydrographs, and annual water temperature cycles may be key factors sustaining the viability of native riparian plant communities. Our results demonstrate the need to understand the interactions between climate, land use, and nutrient management in maintaining the species diversity of riparian plant communities. Future climate change is likely to result in diminished competitiveness of native plant species, while the competitiveness of invasive species will increase due to anthropogenic watershed disturbance and accelerated nutrient and sediment export.