Climate change and human interference, notably nutrient input, affect the water quality. Nitrogen (N) and phosphorus (P) are pivotal in managing eutrophication. This study investigated the effects of water dynamics and chemical constituents on water quality in Hongfeng Lake, a typical weakly stratified reservoir suffering from algae blooms in Southwest China, using the Environmental Fluid Dynamics Code. Leveraging climate, hydrological, and water quality data, we constructed, calibrated, and validated the temperature-hydrodynamics-water quality-sediment model. Various scenarios were analyzed, including wind speed, air temperature, solar radiation, rainfall, water discharge, N and P external input, and internal release. The findings revealed that no rain and warming increased trophic state index (TSI) and chlorophyll-a (Chl-a) concentration, and no solar radiation initially elevated nitrate concentration, followed by an increase in ammonium concentration. Besides, no solar radiation and changes in rainfall significantly increased total phosphate concentration. The management scenarios of N and P reduction, halving tributary, and mainstream flow scenarios improved water quality and reduced eutrophication. The wind speed under the N and P reduced scenarios showed that a doubling in wind led to increased concentrations of the particulate organic matter, Chl-a, and dissolved oxygen, alongside decreased ammonium and nitrate, while TSI exhibited minimal change. However, 5- and 10-times wind speed scenarios amplified TSI in shallow water, potentially due to a substantial rise in internal nutrient release. The degradation trend observed in drinking water quality amid climate change (warming and flooding) raises concerns regarding health-related risks. These simulations provided the quantified influence of climate change and environmental management strategies on water quality in the weakly stratified reservoir, notably highlighting the looming threat of exacerbated eutrophication due to warming, necessitating more stringent N and P reduction measures compared to current practices.