ABSTRACT: The paper gives results from regional hydrogeological investigation of the Žilina Basin carried out in the frame of the regional programmes of the Ministry of Environment of the Slovak Republic. Paleogene flysch sediments fill in the major part of the Inner-Carpathian basin forming an aquiclude to underlaying basal layers of the carbonate Paleogene conglomerates and breccias or Triassic limestones and dolomites. These form important confined aquifers of high quality groundwater. Groundwater flow conditions, chemistry and possible impact of recent climate changes upon the water balance as well as groundwater protection measures are discussed.