A two-dimensional physical based hydrodynamic watershed model, HydroSed2D, was used to estimate the impact of climate change on flood magnitude and frequency in the Upper Santa Cruz River Watershed (USCRW) in the Southern Arizona. Hourly precipitation data from a Regional Climate Model (RCM), Weather Research and Forecasting model (WRF), for three periods, 1990-2000, 2031-2040 and 2071-2079, were used to quantify the impact of climate change on flood. Precipitation outputs from RCM-WRF model were bias-corrected using observed gridded precipitation data for three periods before directly used in the watershed model. The calibrated watershed model was applied to USCRW for simulating surface flow routing for the selected three periods. Simulated discharges are analyzed to obtain future flood magnitude and frequency curves. Results indicate that flood discharges for different return periods are increased: the discharges of 100-year and 200-year return period are increased by 3,000 and 4,000 cfs, respectively.