This research area is located within the most essential underground river system of Gunung Sewu Karst, Indonesia. Thewater sampling focused on Bribin Cave and Baron Resurgence, where around 300.000 of people depend on this system. Timeserieswater sampling was conducted to assess the contaminant composition within the system. In addition, another objectiveis to identify the possible contamination recharge area of this system.Several samples have been analyzed to identify the contaminations in the underground river. In addition,geomorphological approach and field survey were conducted to describe the potential recharge area of the system includingcatchments of autogenic / allogenic stream and the spatial distribution of sinkholes around the system. Afterwards, thesanitation procedure of waste disposal in the recharge area is also evaluated.The result shows that nitrate, heavy metals, and coli bacteria contaminated some samples over the whole time. Theinvestigation also confirms that there are three possible contaminations of the recharge: (1) urban activity in Wonosari Basin,(2) settlement inside the conical karst, and (3) usage of fertilizer within the karst valley farmland adjacent to the sinkholes.Next, the most intensive source of contamination is the way in which Wonosari City residents dispose their waste withouttreatment into the allogenic river.