In this study, the transport model for a transient contaminant(nitrate as NO3-N) is developed using groundwater flow model to calculate the time evolution of nitrate concentration and estimate how much nitrate flux discharges from the Yeosu Industrial Complex to Kwangyang bay calibrating the model using six groundwater monitoring data. The nitrate flux budget analysis through different boundaries (Kwangyang Bay) after 10 year transient model simulation is carried out. The increment concentration of nitrate at six groundwater monitoring sites in the Yeosu industrial area is increased to 1.7 mg/L. The nitrate flux budget analysis calculates that 6.1*104 g/d (22.3 tonne/year) of nitrate flux is estimated to discharge from groundwater to Kwangyang Bay through constant first-kind boundary in the next 10 year.