Recent significant flooding events in the Muskoka River Watershed in Ontario, Canada prompted the provincial government to provide funding for research to help reduce the impact of flooding and improve the watershed’s health while considering implications of social, environmental, and economic factors in the decision-making process. This study comprises the development, calibration, and validation of a hydrologic model of the 5,100 square kilometres watershed using the Soil and Water Assessment Tool (SWAT+) to better understand the sensitivity of the watershed to various changes in land use and climate. The model was calibrated at a daily timestep using a five-year period and further validated using a separate five-year period. It was then run for a 30-year period under varying climate scenarios. Multiple climate change scenarios were run including both mid-century and late-century scenarios across Shared Socioeconomic Pathways (SSPs) SSP2-4.5 and SSP5-8.5. The scenario analysis showed that climate change had a significant impact on the flow regime in the watershed. Results indicated that temperature increase was the largest climate change factor impacting the watershed, causing freshet to occur earlier in the year and a reduction in snowpack leading to a reduction in peak spring flows even under late-century “wet” scenarios. Nearly all climate scenarios resulted in a reduction in annual peak flows across the watershed due to temperature increases in the winter. However, cooler winters combined with higher precipitation are still possible. The “cool wet” scenario resulted in a significant increase in flood risk Significant changes to average and peak flows will likely require modifications to the current watershed management and dam operation protocols to maintain target flows and levels and mitigate the risk of flooding in the future. The developed hydrologic model and scenario analysis results can inform future planning and watershed management.