It is predicted that global warming and climate change will affect both of global and regional water environment in future. Local downpours or serious drought may be brought in an unexpected region. It is suspected that these impacts finally affect on the groundwater flow and water quality. Therefore, investigation and analysis of the water budget and the material balance in basin-wide are important for conservation and utilization of the water resources. In this study, two-dimensional model of groundwater flow and quality was prepared for evaluation of groundwater environment in Kyoto basin. This model has good performance for simulation of groundwater level and it has acceptable performance for simulation of T-N concentration observed in Kyoto basin. So, this model was used for the impact assessment on the groundwater system in Kyoto basin by global climate change in future using of MRI-AGCM20 outputs.