The HSPF model was modified to improve the growth-temperature formulation of phytoplankton and used to simulate Chl-a concentrations at the outlet of the Seom River watershed in Korea from 2025 to 2050 under four climate change scenarios: RCP 2.6, RCP 4.5, RCP 6.0, and RCP 8.5. The mean and median Chl-a concentrations increased by 5–10% and 23–29%, respectively, and the number of algal outbreak cases per year (defined as a day with Chl-a concentration ≥100 µg/L) decreased by 31–88% relative to the current values (2011–2015). Among the climate change scenarios, RCP 2.6 (stringent) showed the largest number of algal outbreak cases, mainly because of the largest yearly variability of precipitation and TP load. For each climate change scenario, three nutrient load reduction scenarios were in the HSPF simulation, and their efficiencies in reducing algal blooms were determined. Nonpoint source reduction in TP and TN from urban land, agricultural land, and grassland by 50% (S1) and controlling the effluent TP concentration of wastewater treatment plants (WWTPs) to 0.1 mg/L (S2) decreased algal outbreaks by 20–58% and 44–100%, respectively. The combination of effluent TP control of WWTPs during summer and S1 was the most effective management scenario; it could almost completely prevent algal outbreaks. This study demonstrates the cost effectiveness of using a season-based pollutant management strategy for controlling algal blooms.