The sophisticated research and management problems of the Estonian water environment are considered by means of holistic modelling. The model elaborated is based on the computer code Visual MODFLOW Classic. The model encompasses the entire Estonian Artesian Basin (EAB) and the border districts of Russia and Latvia. It involves all main aquifers and aquitards on an area of 88,000 km2. The main hydrogeological and hydrological characteristics of the study area, including the time-dependent three-dimensional distribution of groundwater heads, the direction, velocity and rate of subsurface fluxes, itemised water budgets, volumes of hydrogeological units, and durations of groundwater exchange have been determined by modelling. The palaeohydrological situation during the last continental glaciation of the EAB was reconstructed and the principal problems of the sustainable management of water environment were elucidated. The model has been used to simulate the local and cumulative rates of the base flow.