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Great Plains watersheds contribute to the diminishing North American unpolluted surface water supply as well as provide habitat for a number of threatened or endangered species. The number and size of these important systems has been greatly reduced by agriculture and urbanization. Climate change could pose an even greater threat to these endangered systems. There are many climate change scenarios that predict varying changes in future temperature and precipitation amounts for the Great Plains Region. In this study, two Global Climate Model (GCM) scenarios were analyzed to determine monthly rainfall and precipitation trends from 2000 to 2100. The trends were applied to the actual monthly precipitation and temperature distributions in a Northeast Kansas watershed. Daily weather data were simulated for 100 years using the WINDS weather generator. These simulations were input into the Soil and Water Assessment Tool (SWAT) hydrologic model. The streamflow output from these simulations was input into the Indicators of Hydrologic Alteration (IHA) software, which calculated multiple hydrologic indices that were compared back to a baseline scenario. The analysis showed that these climate change scenarios caused a varying increase in mean monthly streamflow patterns as well as a reduction in low flow occurrences and durations. Flood frequency and duration showed varying changes based on the individual scenario. This analysis shows that climate change scenarios have an effect on terrestrial and aquatic ecosystems in the Great Plains Region.