Hydro-chemical and isotopic data from different aquifers in the Great Hungarian Plain (the central part of the Pannonian Basin) were evaluated down to a depth of 2,740 m. The chemical and isotopic composition of water is influenced by its origin and by chemical and mixing processes. The analytical data and chemical considerations, together with geology, pressure conditions and evolution history of the area, explain the evolution of the subsurface water. Most of the samples are of meteoric origin, but there were some samples with a non-meteoric contribution, as indicated by the water stable isotopes, and these were identified as seawater trapped during the sedimentation in Lake Pannon. The sea contribution is traceable by the shifts in δ18O and δ2H and the chemical composition of the water, and is explained with an upward-driving force. Chemical considerations and spatial variability of the dissolved components suggest that distinct water bodies, each with a specific origin and chemical evolution, can be separately identified. Although in the Quaternary layers there are water bodies that can be considered to display complete flow systems (from recharge to discharge), in most water bodies present infiltration was not identified. The lack of recent recharge to several water bodies in various places and depths suggests a separation of the recharge and the discharge that occurred not in space, but in time. A possible explanation of the cessation of recharge is a significant change in the hydraulic circumstances, probably the surface elevation.