To comprehensively understand the water quality status and evolution trend in the water source area since the operation of the eastern route of the South-to-North Water Diversion Project (SNWDP-ER), the water quality index (WQI) assessment method, the Mann-Kendall trend test, and principal component analysis were employed to analyze the evolution trend of water quality and major pollutants in six monitoring sections of the water source area along SNWDP-ER from 2012 to 2023. Based on the stepwise multiple linear regression analysis method, the key indicators affecting the WQI values of the water source area were identified, and a minimum water quality index model was constructed. The application feasibility of this model was evaluated using the WQI data of 2023. The results indicate that the annual average value of WQI shows an overall increasing trend. From 2012 to 2017, the average value of WQI is 38.0, indicating a poor water quality assessment status. The average value of WQI from 2018 to 2023 is 67.4, and the water quality has significantly improved and remained at a good level continuously. The types of water pollutants in the water source area are mainly organic substances and nitrogen and phosphorus nutrients. Agricultural non-point source pollution generated by agricultural planting, industrial wastewater, and point source pollution caused by the direct discharge of untreated domestic sewage are the main sources of pollutants. Strengthening the prevention and control of point source and non-point source pollution is the fundamental way to improve water environment problems in water source areas. The minimum water quality index model has better performance in water quality assessment, which is helpful in saving monitoring costs and improving assessment efficiency.