During the next decade changes are expected in the western area of the active part of the Estonia oil shale deposit since Ojamaa mine started to dewater the oil shale layer and environmental impact assessment is in the process of estimating the influence of dewatering on the site of Uus-Kivioli mine. Aidu open cast is planned to close down in 2013 as the resources of oil shale indicated in the mine permission are ending. Closing of Viru mine in 2015 has been discussed. As the oil shale resources at Aidu and Viru area end, the mine sites will be closed and flooded. Therefore the groundwater table will increase in closed sites and will decrease in prospective areas. To estimate and visualise the situation, computational modeling of groundwater flow has been applied in most cases to estimate the future situation. The current analysis describes the process of groundwater modelling as well as offers possibilities of estimating the accuracy of the model and of the model calibration process. Water inflow rate into Estonia mine has been analysed.