Nitrate pollution in groundwater is a serious environmental problem in the Shimabara Peninsula, Nagasaki Prefecture, Japan. For efficient countermeasures and remediation of the groundwater, numerical simulation may constitute a powerful tool. Along this line, we developed a numerical model to improve the understanding of transport processes in the nitrate pollution and we evaluated the effects of remediation countermeasures by using the FREEWAT software including MODFLOW as numerical engine. The entire area of the Peninsula was represented by a 200 x 200 m grid. Based on the relationship between elevation and observed hydraulic head in steady-state conditions, boundary conditions were set for hydraulic head along seaside and mountainside boundaries. We estimated spatial variation of evapotranspiration based on spatial varying mean precipitation and temperature. Then, groundwater recharge was calculated using the UFZ package. The steady state results of groundwater flow simulations reproduced observed hydraulic head data. We then calculated distributed potential nitrate load for the solute transport simulations using statistical data from agriculture and forestry for the Shimabara City. The distribution of high nitrate loads well fit the agricultural land-use. Monitoring data confirmed that polluted groundwater is typically located downstream of high potential nitrate load areas. According to the numerical transport simulation results (performed using MT3DMS), the general trend of concentration change well agreed with observation during the past 44 years. Remediation simulations indicate that it will take about 18 years for groundwater concentrations to fall below Japanese drinking water standards. The pre-requisite is a 40% reduction in nitrate load of the source zone. In case of a 50% reduction, the nitrate concentration could be below the standard within 12 years.