Abstract: As the water source for the Middle Route of the South-to-North Water Diversion Project, the water quality and ecological security of the Danjiangkou Reservoir are of critical importance.However, comprehensive studies integrating nitrogen and phosphorus reference conditions, hydrological factors, the impact of flood intensity, and seasonal perspectives on algal proliferation and eutrophication assessment are currently scarce.Consequently, there remains significant room for improvement in the effectiveness of management support for the reservoir.To address this, an analysis was conducted on the spatiotemporal characteristics of key water quality and trophic level indicators in the Danjiangkou Reservoir from 2021 to 2023 and historical trends since 1989—namely chlorophyll-a, total phosphorus (TP), total nitrogen (TN), and the permanganate index (COD_Mn).The quantile method was employed to investigate the nitrogen and phosphorus reference conditions for the reservoir.The results indicated that: ① Over the past two decades, TP and TN in the Danjiangkou Reservoir have generally fluctuated within a certain range without significant increasing or decreasing trends.From 2021 to 2023, the annual water quality of the reservoir was mainly Class Ⅰ~Ⅱ, but the monthly water quality could not consistently meet the Class Ⅱ standard (management target).Most areas of the reservoir experienced Class Ⅲ~Ⅳ water quality in certain months, with total phosphorus and total nitrogen being the main pollutants exceeding the standards.The average concentrations of TP and TN from 2021 to 2023 were 0.020 mg/L and 1.34 mg/L, respectively, while the average chlorophyll-a concentration was 2.84 μg/L.The concentrations of nitrogen, phosphorus, and chlorophyll-a in the Hanjiang section of the reservoir were higher than those in the Danjiang section, and the levels in Hanjiang Zone Ⅰ (upstream of Yuanhe Bay) were higher than those in Hanjiang Zone Ⅱ (from Yuanhe Bay to the dam).② The reservoir as a whole was at a mesotrophic level, but Hanjiang Zone Ⅰ reached a mildly eutrophic state, with a relatively higher risk of algal blooms.Algal blooms were particularly prominent in some tributary backwater areas, with sensitive periods occurring from August to October, followed by March to April.The TP concentration in the reservoir was significantly higher during the autumn flood season than in other seasons, most notably in Hanjiang Zone Ⅰ, followed by the area upstream of Baidu Beach in the Danjiang section.TN concentrations were slightly higher during the dry season than during the wet season, with the lowest TN concentrations generally observed in July and August.The reference value for TP in the Danjiangkou Reservoir was approximately 0.012 mg/L.Preventing abnormal algal proliferation in localized areas of the reservoir, especially in tributary bays, remains the primary task for water ecological protection in the Danjiangkou Reservoir in the coming period.Water pollution prevention and control should continue to be strengthened, and while controlling TP, the control of TN should also be emphasized.