To investigate the long-term variation of water qualities, we have daily monitored physio-chemical characteristics of surface water in the Geum River estuary from June 1996 to April 2004. We found that the water qualities were determined by three dominant factors : 1. fluvial input from Geum River (), 2. chemical processes such as nitrification and phosphate addition originated from sediment resuspension and domestic sew- age input (), 3. biological processes such as nutrient consumption by primary producers (). The factor 1 (fluvial input) effectively affected the water quality of the estuary particularly during the normal or low river discharge. The factor 2 (chemical processes) and the factor 3 (biological processes) showed distinct seasonal differences due to their relative strengths of biological activities. The factor 3 was a governing parameter during the period of spring algal bloom in 2004. For the spring period, an empirical equation derived from the multi-regression analyses showed that the in-situ chlorophyll-a distributions in the estuarine water were successfully simulated by the phosphate concentrations and N/P ratios. Therefore we suggest that phosphate functions as a limiting factor for the primary productivity in the Geum River estuary for the dry season, especially during spring.