ABSTRACT: The caves represent specific immensely vulnerable natural geosystems. The karst waters occur in many caves and cave systems. The Slovak Caves Administration as a part of the Ministry of the Environment of the Slovak Republic carries out research of karst waters connected with caves. Waters of the vadose zone - seepage water and water of underground hydrological systems (underground rivers) are in the centre of attention. Hydrogeochemical, hydroindicative and hydrometric methods are used in the research. All results are used subsequently for protection of caves (expert statements, practical care, projects of cave protection zones).