This paper studies the effects of bio-clogging on hydraulic conductivity of compacted soils used as landfill liners. Landfill leachate contains a large amount of microorganism and bacterial biomass, which was likely to cause bio-clogging in landfill liners. To interpret the effect of bio-clogging on hydraulic property of compacted clays, in this study, a series of laboratory-scale hydraulic conductivity tests were conducted. The long term hydraulic conductivity of compacted clays was measured with distilled water, landfill leachate and one type of nutrient solution. The laboratory test results show that the hydraulic conductivity of compacted clays permeated with distilled water stabilized at approximately 3.77 × 10-8 cm/s, and the hydraulic conductivity of compacted clays permeated with landfill leachate or nutrient solution ranged between 1.1 × 10-8 cm/s and 5.22 × 10-9 cm/s. Such a significant difference was attributed to the effect of bio-clogging. The microorganism and bacterial biomass reduced the hydraulic conductivity up to one order of magnitude. This study indicated that the bio-clogging is approximately a feasible method to create low-cost and low-hydraulic conductivity barriers by using locally available clayed soils.