The temporal variations of water quality in rivers reflect the changes in the pollutant load of a basin to a certain extent. The temporal variations of pollution source structures reflect the changes in the contribution rates of different pollution sources. The temporal variations of water quality and pollution source structures were combined in this study to investigate and analyze the water pollution control effects on different pollution sources over 15 years in the upper Tuojiang River Basin (UTRB). The seasonal trend decomposition using loess (STL), principal component analysis (PCA), factor analysis (FA), absolute principal component score (APCS), and multiple linear regression (MLR) were employed in the analysis. According to the results, except for TN, the concentrations of BOD, AN, and TP showed a downward trend. The precipitation had a strong influence on the pollution seasonal patterns. BOD and AN were primarily influenced by urban and rural living sources, while the primary sources for TN and TP were agricultural NPS and phosphate chemical industry sources, respectively. The systematic and comprehensive pollution control strategies in the third stage (2016–2020) have become more effective. In particular, the reduction of TP was successfully achieved by strengthening the pollution abatement on phosphate chemical industry sources. In contrast, the reduction in agricultural NPS emissions was not significant during the study period.