The principal indicators contributing to water qualities was screened by factor analyses, based on the monitored chemical parameters of water quality for various water resources from 1995 to 1999 in the small agricultural catchments of the Han River Basin. Water samples of streams, groundwaters, and reservoirs were taken four times a year from upper (Daegwanryong), middle (Dunnae and Chunchon) and lower (Guri) reaches of Han River Basin. In these areas, the respective type of farming practiced was alpine agriculture and livestocks raising, typical upland and paddy cultivation, and intensive cropping in the plastic film house. Water quality was monitored for twenty-one water quality parameters, including pH, EC, SS, T-N, T-P, COD, cations, anions, and heavy metals. pH, EC and COD of the stream waters were suitable for the Korea irrigation water quality guidelines. However, T-N and T-P concentrations of water samples in four catchments far exceeded the irrigation water guideline. Concentrations of canons and heavy metals in Wangsuk stream in Guri area were higher than those in streams in other areas. Factor analysis revealed that significant correlation was observed for 81 pairs out of 231 water quality indicators of stream water among the $21\;{\times}\;21$ cross correlation matrix of stream water quality indicators. The first factor accounted for 27.01% of the total variation in stream water quality indicators, and high positive factor loadings were shown on EC, K, Na, $NH_4\;^+-N$, $PO_4\;^{3-}$, $SO_4\;^{2-}$, and COD. Fifty-three water quality indicator pairs were significant out of 190 ground water quality parameters. The first factor accounted for 28.54% of the total variation in ground water quality indicators, and high loadings were revealed on EC, Ca, Mg, K, Na, $NH_4\;^+-N$, and $SO_4$. Twenty-nine pairs of reservoir water quality indicators were significant out of 66 pairs. The first factor accounted for 37.06% of the total variation in reservoir water quality indicators, and high loadings were shown on EC, Mg, K, Na, SS, T-P, Cl, and COD. These results demonstrate that EC was the first factor contributing to water quality.