The prairie waterbodies face a future of warming temperatures and growing water demands. There are increasing concerns about how water quality will be affected. Water quality models are an effective tool for examining scenarios of future conditions that cannot be measured directly. This study combined WASP and CE-QUAL-W2 to investigate the potential impacts of changing flow management and climate change in the Canadian Prairies. The two models were loosely coupled to simulate a strategically managed river-reservoir network. Climate data from the Coupled Model Intercomparison Project Phase 6 (CMIP6) model ensemble were used to create future climate scenarios. Interbasin water transfers were then simulated through the coupled models to determine if any negative impacts from climate change on water quality could be offset through flow management. Climate change impacts in the river stretch were minimised due to the rapid flow travel time along the channel. The interbasin water transfers had a greater influence on water quality concentrations in the river. This result was limited by the uncertain hydro-climatic future of the contributing watershed. Climate change impacts in the downstream reservoir were far more apparent. Evaporative losses increased approximately 150% from the base model by the 2080–2100 period. Chlorophyll-a concentrations increased an average of 53% in this same period based on monthly mean percentage change. Reservoir water quality was improved after adding the interbasin water transfers. Results indicated that flow management would have a positive impact on water quality in the reservoir in the face of future climate change.