Identifying the potential pollution sources of surface water pollutants is essential for the management and protection of regional water environments in drinking water source areas. In this study, absolute principal component score-multiple linear regression (APCS-MLR) and positive matrix factorization (PMF) models were applied to assess water quality and identify the potential pollution sources affecting the surface water quality of Xin’an River Basin. For this purpose, a 10-year (2011–2020) dataset of eight water quality indicators (including pH, EC, DO, COD, NH3-N, TN, TP, and FC) covering eight monitoring stations and 7248 monthly observations was used. The results indicated that Pukou section had the worst water quality among the eight monitoring stations, and TN was the most serious water quality index. Both the APCS-MLR and PMF models identified agricultural nonpoint source pollution, urban nonpoint source pollution and rural domestic pollution, and meteorological factors. The sum of these three sources was very close, accounting for 60% and 58%, respectively. The APCS-MLR results demonstrated that for EC, COD, and NH3-N, the major pollution sources were urban nonpoint sources and rural domestic pollution. The major contamination source of TN was agricultural nonpoint source pollution (30.4%). Meanwhile, the major pollution sources of pH, DO, TP, and FC were unidentified factors. The PMF model identified five potential sources, and pH and DO were affected by meteorological factors. NH3-N and TP were influenced mainly by agricultural nonpoint source pollution. Atmospheric deposition was the major pollution source (87.9%) of TN. FC was mostly derived from livestock and poultry breeding (88.3%). EC and COD were mostly affected by urban nonpoint sources and rural domestic pollution. Therefore, receptor models can help managers identify the major sources of pollution in watersheds, but the major factors affecting different pollutants need to be supplemented by other methods.