This study aimed to derive major pollutants for standard watersheds with relatively high pollution levels and identify their trends. Hence, the water quality index (WQI) and multivariate statistical techniques were used to analyze the water quality evaluation of standard watershed during the total maximum daily load (TMDL) policy period implemented since 2004. The WQI was calculated for 41 standard watersheds, divided into 14 main streams and 27 tributaries. Consequently, in the main stream, WQI decreased as it moved downstream after the MS5 site. In the tributary, WQI values were found to be low at TS11, TS15, TS16, and TS17 sites. However, the Mann–Kendall test results indicated that the overall WQI value was increasing, suggesting that the water quality of the study basin was improving as the TMDL policy phase progressed. Principal component analysis of the group with relatively low WQI among the standard watersheds revealed that water temperature, dissolved oxygen, total phosphorus, chemical oxygen demand, biochemical oxygen demand, and electrical conductivity were the main variables in the main stream cluster. In the tributary stream cluster, total phosphorus, dissolved oxygen, total suspended solids, total nitrogen, and electrical conductivity showed high loading values. This study proposed a series of methods to provide the basic data required for watershed management through detailed water quality assessment methods, statistical techniques for deriving major pollutants, and trend analysis of water quality evaluation.