The aim of this study is to develop the water quality simulation model (BAYQUAL) that deal with the physical, chemical and biological aspects of fate/behavior of pollutants in the bay. BAYQUAL is a two dimensional, time-variable finite element water quality model based on the flow simulation model in bay(BAYFLOW). The algorithm is composed of a hydrodynamic module which solves the equations of motion and continuity, a pollutant dispersion module which solves the dispersion-advection equation. The applicability and feasibility of the model are discussed by applications of the model to the Kwangyang bay of south coastal waters of Korea. Based on the field data, the BAYQUAL model was calibrated and verified. The results were in good agreement with measured value within relative error of 14% for COD, T-N, T-P. Numerical simulations of velocity components and tide amplitude(M2) were agreed closely with the actual data.