Excessive anthropogenic nutrient input has resulted in eutrophication and algal blooms which have severely impacted the function and sustainability of aquatic ecosystems, underscoring the need to implement nutrient management strategies. It was assumed that the increasing rainfall during flood season would affect the stoichiometric ratio of total nitrogen (TN): total phosphorus (TP), driving the nutrient limitation of algal growth. In order to test this concept and explore corresponding nutrient management strategies, nutrient addition bioassays were carried out in Xiangxi Bay, one of the largest tributaries of the Three Gorges Reservoir (TGR), China. Results indicated that nutrient limitation on algal growth fluctuated from nitrogen (N) to phosphorus (P) limitation. N limitation dominated in the early flood season. However, the reduction of dissolved P, accompanied with an increase of TN: TP caused by an increase in extreme rainfall events intensified P limitation throughout the bay. Then P limitation was alleviated due to the reduction of rainfall and the process of impoundment after the flood season. The variation of TN: TP caused by the increasing of rainfall and flooding could be the main driving factor of the nutrient limitation shift in aquatic ecosystems mainly affected by external nutrient inputs. Nutrient dilution and enrichment bioassays showed that TN and TP concentration thresholds should be targeted at below 0.55 mg/L and 0.057 ∼ 0.064 mg/L respectively, to limit the growth of algae and maintain chlorophyll a below 30 μg/L. Dual nutrient (N & P) reductions were required for long-term bloom mitigation in the entire basin. This study provided a scientific basis for a nutrient management strategy to combat eutrophication and reduce algal bloom potentials in the tributaries of the TGR. We recommend that long-term determinations of nutrient limitation and nutrient threshold will be needed to control algal growth, considering future anticipated changes in land use, population density and the impacts of climate change.