In this study, water quality data of eight main sites in the Geumho River watershed were collected and analyzed for long-term changes in water quality over the period from 2005 to 2015. The results showed that BOD concentration was gradually improved by the Total Maximum Daily Load (TMDL), stages 1 and 2. Recently, a tendency of increasing BOD concentration was observed in the downstream section of the river. The concentration of COD was analyzed to be contaminated throughout the water system regardless of the water quality improvement project, and the TN concentration tended to increase in the midstream of the river from 2013. The TP concentration has clearly decreased from 2012 after the second stage of TMDL. For the statistical analysis of PCA ordination, monthly water qualities (pH, DO, Electrical Conductivity (EC), Water Temperature (WT), BOD, COD, TN, TP, TOC, and SS) and flow rate data for 5 years from 2012 to 2016 were used. Seasonally the Geumho River showed an increase in the TN concentration at point sources during the dry season (December to February). TP showed the effect of non-point sources in the summer, because rainfall has caused a rise in flow rate in the upstream. Besides, the origin of pollution source was changed from non-point sources with BOD, COD, and TOC.