To explore the variations in nutrients concentrations of the Yuqiao Reservoir Basin, we analyzed the spatial and temporal variations of total nitrogen and total phosphorus concentrations and TN/TP (mass ratio of total nitrogen to total phosphorus) in three periods from 1990-2002, 2003-2014 and 2015-2018. Simultaneously, the effect of pollution reduction, water transfer, and retention on nutrient concentrations were elucidated based on the monthly observed data of inlet rivers and reservoirs in the basin from 1990 to 2018. The results showed that the annual average TN concentration of Yuqiao Reservoir from 1990 to 2018 ranged from 1.14-3.74 mg/L and the annual average TP concentration ranged from 0.025-0.131 mg/L. The multi-year average TN/TP of Yuqiao Reservoir from 1990 to 2018 was 45, which was a phosphorus-limited reservoir. Both TN and TP concentrations were higher in the inflow than that were in the reservoir. Additionally, the TP retention rate in the reservoir was slightly higher than that of TN. The TN and TP concentrations in the reservoir decreased in the mid-to-late 2000s, but rebounded thereafter. The water protection project implemented in 2003 effectively reduced the incoming nutrient concentrations, especially the TP concentration. At the end of 2014, when the first-stage of the Middle Route South-to-North Water Diversion Project delivered water, the amount of diversion from Luanhe River was decreased and TP concentration increased. Excessive growth of phytoplankton in summer and autumn led to an increase in TP concentration during the third period in the reservoir. Based on the monthly water quality dataset, TN concentration in the reservoir was the lowest and TP concentration reached its peak in summer. The principal component analysis showed that a significantly positive correlation between Chl.a concentrations and TP concentrations in the reservoir from June to October. In the future, the TN from the Shahe River and the surrounding non-point sources should be controlled, and it should reduce the TP loadings of the whole basin simultaneously. In addition, engineering measures, such as front storage, sewage intercepting ditch, can be used to reduce the incoming nutrient concentrations.