Lithuania possesses rich resources of groundwater. However, not everywhere groundwater quality meets standards for drinking water due to its natural and anthropological contamination. To fulfil the water directives of European Commission (98/83EC, 2000/60EC), Lithuania has prepared the programm (2007-2025) focused on improving management of groundwater resources and on supplying the country population with drinking water of high quality. The program includes the task to evaluate groundwater resources by processing accumulated hydrogeological data by modern methods of mathematical modelling. For the first time, the regional hydrogeological model (HM) has been developed for the Quarternary groundwater system located in the South-East of Lithuania. This groundwater body covers one third (20880km2) of the country. The rectangular HM area has the size 290km210km= 60900km2. Local river basins comprise the active HM area of highly irregular shape. The model area 40020km2 , exterior to the active one, does not take part in simulation.