Hydraulic conductivity (HC) is perhaps the most important unique parameter determined in the laboratory for predicting mobility of leachates through clay liners. Typically, HC must be < or = 1 x 10(-9) m/s for soil liners and covers used to contain hazardous waste, industrial waste, and municipal solid waste (MSW). Soil samples used in this study were obtained from the Kemerburgaz landfill in Istanbul. The study presents change in clay HC brought about by the chemical reactions between clay and a permeant. Any change induced by such a reaction in the microstructure (microfabric) of the clay was studied by scanning electron microscope. In order to determine the removal capability of the natural clay, COD, SS, VSS, Total P, TKN, Cu, Mn, Fe are also measured in the influent and effluent of the lab-scale reactor.