In this study, modelled groundwater actual flow times in intermediate and deep aquifers, covered by regional scale impermeable aquitards, were compared with 4He and 81Kr age dating results. To improve the reliability of the steady state 3D groundwater flow model, the isotopic ages of deep groundwater were compared to the MODPATH modelled travel times. The highest helium values in groundwater reservoirs coincide with fault zones in the crystalline basement and sedimentary cover near Rapakivi granite massifs. Insights into isotope-geochemical anomalies of the Baltic Artesian Basin intermediate and deep groundwater support their main distribution peculiarities in the flow path towards the Baltic Sea coast lowland and seabed depression as the regional groundwater discharge area.