The frequency of freshwater cyanobacterial blooms is increasing globally due to climate change and eutrophication, particularly in reservoirs. Reservoir ecosystems exhibit unique characteristics, and there is a complex relationship between factors such as light, temperature, nutrient salts, hydrology, and algal growth. The impact of the other factors on algal growth varies significantly among different reservoirs. Thus, it is crucial to assess the effectiveness of various algal control measures implemented in different reservoirs. This study conducted a comprehensive assessment by establishing a eutrophication model for the Shanzi Reservoir in Fuzhou City. The model incorporated meteorology, hydrology, carbon dynamics, nutrient cycling, and biological communities. The effectiveness of diverse management measures was systematically evaluated. The findings demonstrate that increasing the water level, reducing nutrient salts in sediments, and implementing ecological fish stocking effectively suppressed algal growth to varying degrees and improved nitrogen and phosphorus levels. Lower water levels and ecological fish stocking had a significant impact on algal reproduction, while sediment reduction had a minimal effect. Conversely, lower water levels and ecological fish stocking did not significantly improve nitrogen and phosphorus concentrations in the reservoir, whereas sediment reduction had a noticeable effect. Consequently, the management strategies for the Shanzi Reservoir should prioritize external control measures and the implementation of ecological fish stocking.