The Komesu underground dam is the first fullscale underground dam constructed to prevent saltwater intrusion in Japan. Although the cutoff wall of the dam effectively reduces the movement of saltwater into the reservoir area, saltwater masses remained behind the dam at the time of its completion, and saltwater can intrude beneath and diffuse through the wall, particularly when the reservoir level is below the sea level because of high pumping levels during the drought years. Therefore, it is necessary to estimate in advance whether the saltwater concentration in the pumped water is likely to exceed or not the permissible salinity level because of an increase in the residual saltwater mass as a result of saltwater intrusion and to take necessary measures to suitably manage the saltwater level behind the dam. To analyze saltwater intrusion, we first selected the optimal program suitable for the analysis of saltwater intrusion. Second, we examined the longitudinal dispersivity and the effect of the cone of depression around the pumping wells. Then we analyzed saltwater intrusion into the reservoir area in detail by using a two-dimensional convective-dispersive analysis. The results of the analysis make it possible to improve management of saltwater in the reservoir area behind the underground dam.