This study aims to identify spatially water quality distribution of groundwater and surface water in reservoirs, and comprehensively to address possible influencing factors. The concentration of NO3 in the reservoirs along the main stream of the Geum River was generally lower than that in groundwater. The pollution level of the reservoir, especially the particulate pollutant SS, clearly showed seasonal variations and increased significantly downstream. The H-3 concentration of the groundwater was high in the plains and low in the mountain areas, indicating a difference in residence time between the two regions. The hydrochemical properties and factor loading values of the principal components indicated that the major factors were water‒rock interactions and residence time, but a positive correlation of K-NO3 and Mg-Cl showed the influence of agricultural activities. The main groundwater pollutants were likely to be contributed by agricultural activities at upstream and seawater infiltration at downstream. The sensitive redox species uranium in the groundwater of this region existed as the uranyl ion, and it showed a positive correlation with HCO3, pH, and Ca. The results emphasize the importance of monitoring both tributaries and groundwater together in order to effectively manage the water quality of the Geum River basin.