Compacted clay soils are widely used as a barrier to protect environment from leachate migration. The suitability of clay soil for liner material, depends on resistibility to increase in hydraulic conductivity and contaminant transport. In this article, the influence of compaction energy and permeated leachate properties on the hydraulic conductivity were investigated. Natural attenuation capacities of clays compacted both standard and modified compaction methods were also evaluated. With this purpose, a series of laboratory tests were conducted with soil and real leachate samples obtained from Sile-Komurcuoda Organized Landfill Site. DI and real leachate samples were percolated through the laboratory-scale column reactors that were filled with compacted clay samples prepared according to Standard and Modified Proctor method. During percolation, the hydraulic conductivity and natural attenuation capacity of the clay liner were determined by hydraulic conductivity calculation and chemical oxygen demand (COD), suspenden solids (SS), total Kjeldahl nitrogen (TKN), total phosphorus (TP) monitoring, respectively. According to the hydraulic conductivity measurements using leachate, it is shown that hydraulic conductivity decreased in both compacted clay prepared by Standard and Modified Proctor methods, possibly associated with biological and chemical clogging mechanisms. It is thought that clogging formed due to biofilm growth and/or suspended solids accumulation between the particles of the clay soil. When the variations of the COD, SS, TKN, and TP were examined, it was observed that the removal efficiency of the clay compacted by the modified compaction method was greater than the one compacted by the standard compaction method, especially for SS.