Karst aquifers are important water resources but highly vulnerable due to their heterogeneous and complex characteristics. Various hydrological aspects (recharge, flow behaviour) have to be known in detail to develop a sustainable concept for water collection, distribution and treatment. In the karst area of Gunung Sewu (Java, Indonesia) such a concept was to be implemented within a German-Indonesian joint IWRM project. The basic hydrogeological conditions and water quality aspects were characterized on a regional scale through hydrochemical monitoring of springs, wells, subsurface and surface rivers. More detailed information about the recharge, flow and storage behaviour was obtained from high resolution monitoring of T, EC and discharge in one large underground river system. The water quality is well below any guideline values with regard to inorganic pollutants during dry season. During rainy season, dissolved Al concentrations are frequently above the Indonesian guideline value. Slow matrix flow is the most important recharge component during dry season, thus assuring the year-round water availability in the subsurface karst. During rainy season, quick infiltration of the surface water is a dominant recharge component. Rapid response of discharge, T and EC to heavy rain suggests the presence of point recharge that feeds a highly karstfied conduit system with fast conduit flow and short transit time of water. The strong variations in discharge and hydrochemistry are particularly challenging for technical water usage and treatment facilities. Piston flow is indicated to be the third important flow component and is induced by heavy rainfall.