ABSTRACT: In the work the hydrogeological structure of thermal waters in Sklené Teplice Spa is evaluated on the basis of new knowledge from deep geological and hydrogeological wells. The genesis of waters chemistry is evaluated according to hydrogeochemical indices, geochemical factors and isotopes of 18O, 34S, 14C. The regime of thermal waters is evaluated in relation to precipitation and springs of cold waters in the assumed catchment area. In the protection zone of 1st degree the outflow area is protected and in the protection zone of 2nd degree the accumulation zone of thermal waters.