In many instances, dynamic, potential status and geochemical characteristics of groundwater discharging through natural springs are not well known. Present study has assessed the deep groundwater in the form of thermal and non-thermal spring in artesian condition in the selected zones in Sri Lanka, using isotope and geochemical characteristics. The results revealed that evaporation-fractional crystallization and cation-exchange in the sedimentary aquifers while rock-water interaction in crystalline deep aquifers, are the significant mechanism that control the groundwater chemistry. All the deep groundwater recharged from meteoric water at different elevations and further influenced by either evaporation or rock-water interaction during the subsurface flow. Artesian aquifers in the sedimentary terrain in the north-western coastal zones showed the recharging elevation as from 100 to 200 m amsl. They are not mixed with sea water and slightly impacted by the locally evaporated surface waters. Almost all these waters are comparatively old; indicating slow movement along the regional flow paths. Considering the recharge and discharge conditions of artesian non-thermal waters in the Southern lowlands of crystalline terrain can be classified as non-mixed, non-evaporated and young groundwater with higher elevation recharge. The artesian non-thermal waters in the East North Central lowlands, have shown the same characteristics but with evaporated conditions. All artesian thermal waters are tritium free, hence they are older and deep percolated. Intensive rock-water interaction and higher altitude origin were observed in some thermal springs. Some spring clusters in the weathered overburden have shown significant mixing with recent local rains. Non-mixed, non-evaporated and less rock-water interacted nature is a significant in two thermal springs that emerges through (chemically inert) quartzite bed rock. Both thermal and non-thermal water with artesian condition have clearly indicated that they are originated from a common recharge source but with different flow paths in different penetration depths and travel distances, resulting different chemical characteristics. Fresh water springs are mostly young and recharged from local rains followed with shallow percolation.