In this study, pumping capacity in the area of natural river estuary is estimated by the quantitative analysis using finite element method. The study area is Iga-ri pumping station in the estuary of Seojung-chun which runs to the East coast. First of aH, hydraulic properties and effects of different seawater levels are analyzed in this area. Variations of groundwater level caused by pumping and properties of seawater intrusion are analyzed, then compared the case of reinforcing the existing intake weir with the case of setting up an weir at the upper stream. The observed data of groundwater drawdown caused by pumping during drought period and seawater intrusion are compared with results of the analysis done by groundwater model using finite element method, and it is found that both are similar. Accordingly, groundwater model used in this study reflects well the variation of groundwater level caused by pumping.