The purpose of this study is to investigate the characteristics of water quality in Jeju harbor and to estimate pollutant loadings discharged into Jeju Harbor. To know characteristics of water quality in Jeju harbor, and pollutant loadings of Sanzi river, we have investigated from August, 2000 to May, 2001. The results showed that the concentrations of COD, DIN and DIP were in the range of 1.00∼4.85 mg/L (mean 2.15 mg/L), 2.14∼74.0 $mu extrm{g}$-at/L(mean 12.20 $mu extrm{g}$-at/L) and 0.52∼4.00 $mu extrm{g}$-at/L(mean 1.18 $mu extrm{g}$-at/L), respectively. These values were under III class of seawater quality criteria. The ratio of nitrogen to phosphorus was lower than 16 except for Station 1 in Jeju harbor. Therefore, nitrogen was playing an important role in phytoplankton growth as limiting factor in Jeju harbor. The mean values of eutrophication index were exceeding 1, which was the eutrophication criteria. The results of estimating pollutant loadings at Sanzi river are 0.30 ton/day for COD, 300 kg/day for DIN and 18.0 kg/day for DIP, respectively.