Stream and groundwater qualities of small agricultural watershed in Kangwon Probince, Korea were monitored 1 to 2 years, and the relationships between stream and groundwater qualities and seasonal water quality changes analyzed. Flooded paddy fields influenced groundwater level and quality during rice culture. The differences between groundwater levels during rice culture and non-culture spans were between 0.8 and 2.91 m. Seasonal changes of total nitrogen and nitrate nitrogen concentrations of stream and groundwater were very similar and groundwater quality was thought to have a profound impact on stream quality of the research watersheds. Suspended solids and BOD maintained the first degree stream water quality throughout the monitoring period except for a few and short flooding spans. The concentrations of total phosphorus and total bacteria of both waters showed wide variations and any seasonal trends were not observed. Long-term monitoring studies on small rural watersheds were recommended to understand the pattern of both stream and groundwater quality changes with respect to land use, season and cultural practice, and to apply the results to develop effective water quality management policies for large river and domestic water supply systems.