Groundwater is an important resource for water use in the alluvial coastal lowland plain. In the Shiroishi lowland plain, southwestern Kyushu Island of Japan, land subsidence and salinity intrusion due to intense withdrawals of groundwater have become the main environmental issues for public concern. In this study, an integrated surface and groundwater model was established and applied to the Shiroishi site to simulate groundwater flow hydraulics, aquifer compaction and solute transport in the alluvial lowland plain. Moreover, a groundwater optimization model was also formulated to search for an optimal safe yield of groundwater extraction without violating salinity intrusion and other constraints. The simulated results show that groundwater levels in the aquifer greatly vary in response to varying climatic and pumping conditions. Consequently, land subsidence has rapidly occurred throughout the area with the central prone in Shiroishi basin. As a result of pumping and land subsidence, seawater has been intruded along the coast. In case of relative sea level rise, seawater intrusion appears to extend much farther in land from the coast. From the viewpoint of agricultural water management, pumping for irrigationwith an optimal pumping amount that is a new finding from the optimization model will sustain groundwater quality in the study area.