In order to control of water quality in Jeju harbor, variation of physical oceanographic environments was estimated using material cycle model. It is composed of the three-dimensional hydrodynamic model for the simulation at water flow and material cycle model for the simulation of water quality. The three dimensional hydrodynamic model simulation of the circulation and mixing in Jeju Harbor has been conducted forced by Sanzi River Discharge, Tidal elevation, wind and Solar heat in case of August and November, 2000 and February and May, 2001, respectively. The results of numerical model and observation show that the model can produce realistic results of current in the harbor. The monthly variation of velocity pattern are not so much changed are found In Jeju Harbor. The residual current was forced by temperature, salinity, density, wind and tidal current. The residual current of August, 2000 are the strongest among four month. It can be explained that the density effect can be important role in residual current at Jeju Harbor. As the results of salinity distribution simulation, very low concentration of all levels were simulated in August, 2000. The flowrate of Sanzi river was investigated 77,760 ㎥ /d in August, 2000. Therefore, pollutant loadings from Sanzi river should be considered for water quality management in Jeiu harbor.