In Korea, the aquifers at the coastal areas are mostly shallow alluvial unconfined aquifers. To simulate the flow and dispersion in unconfined aquifer, a FDM model has been developed to solve the nonlinear Boussinesq equation. Related analysis and verification have been executed. The iteration method is used to solve the nonlinearity, and the model shows 3-D shape because it is a 2-D model that consider the undulation of water table and bottom. For the verification of the model, the output of flow module is compared to the 1-D analytic solution of Lee (1989) which have the drawdown or uplift boundary condition, and the two results show almost the same value. and the mass balance of dispersion module shows about 10% error. The developed model can be used for the analysis and design of the flow and dispersion in the unconfined aquifers. The model has been applied to the estuary area of Ssangcheon watershed, and the parameters have been deduced as a result : hydraulic conductivity is 90 m/day, and longitudinal dispersivity is 15 m. And the analysis with these parameters shows that the wells are situated in the influence circle of each others except for No. 7 well. Groundwater discharge to sea is 3700 m3/day. And the chlorine ion ( concentration at the pumping wells increase at least 1000 mg/L if groundwater dam is not exist, so the groundwater dam plays an important role for the prevention of sea water intrusion.