Characterizing water quality and identifying potential pollution sources could greatly improve our knowledge about human impacts on the river ecosystem. In this study, fuzzy comprehensive assessment (FCA), pollution index (PI), principal component analysis (PCA), and absolute principal component score-multiple linear regression (APCS-MLR) were combined to obtain a deeper understanding of temporal-spatial characterization and sources of water pollution with a case study of the Jinjiang River, China. Measurement data were obtained with 17 water quality variables from 20 sampling sites in the December 2010 (withered water period) and June 2011 (high flow period). FCA and PI were used to comprehensively estimate the water quality variables and compare temporal-spatial variations, respectively. Rotated PCA and receptor model (APCS-MLR) revealed potential pollution sources and their corresponding contributions. Application results showed that comprehensive application of various multivariate methods were effective for water quality assessment and management. In the withered water period, most sampling sites were assessed as low or moderate pollution with characteristics pollutants of permanganate index and total nitrogen (TN), whereas 90% sites were classified as high pollution in the high flow period with higher TN and total phosphorus. Agricultural non-point sources, industrial wastewater discharge, and domestic sewage were identified as major pollution sources. Apportionment results revealed that most variables were complicatedly influenced by industrial wastewater discharge and agricultural activities in withered water period and primarily dominated by agricultural runoff in high flow period.