Reservoirs play an important role in the urban water supply, yet reservoirs receive an influx of large amounts of pollutants from the upper watershed during flood seasons, causing a decline in water quality and threatening the water supply. Identifying major pollution sources and assessing water quality risks are important for the environmental protection of reservoirs. In this paper, the principal component/factor analysis-multiple linear regression (PCA/FA-MLR) model and Bayesian networks (BNs) are integrated to identify water pollution sources and assess the water quality risk in different precipitation conditions, which provides an effective framework for water quality management during flood seasons. The deterioration of the water quality of rivers in the flood season is found to be the main reason for the deterioration in the reservoir water quality. The nonpoint source pollution is the major pollution source of the reservoir, which contributes 53.20%, 48.41%, 72.69%, and 68.06% of the total nitrogen (TN), phosphorus (TP), fecal coliforms (F.coli), and turbidity (TUB), respectively. The risk of the water quality parameters exceeding the surface water standard under different hydrological conditions is assessed. The results show that the probability of the exceedance rate of TN, TP, and F.coli increases from 91.13%, 3.40%, and 3.34%, to 95.75%, 25.77%, and 12.76% as the monthly rainfall increases from ≤68.25 mm to >190.18 mm. The risk to the water quality of the Biliuhe River reservoir is found to increase with the rising rainfall intensity, the water quality risk at the inlet during the flood season is found to be much greater than that at the dam site, and the increasing trend of TP and turbidity is greater than that of TN and F.coli. The risk of five-day biochemical oxygen demand (BOD5) does not increase with increasing precipitation, indicating that it is less affected by nonpoint source pollution. The results of this study can provide a research basis for water environment management during flood seasons.