The hydraulic conductivity defines the displacement of liquids inside porous media and affects the fate and transport of contaminants in the environment. In this research the influence of microbial growth and decay inside soil pores on hydraulic conductivity is analysed. Long-term tests performed in silt–bentonite mixtures permeated with distilled water and a nutrients solution demonstrated that hydraulic conductivity of compacted silt–bentonite samples decreases with time of permeation as a bioclogging mechanism develops. The injection of antibiotics and antifungals in the specimens produces a rebound in the hydraulic conductivity associated with the decay of microbial activity. These results show that biomediated reactions can be used to control the flow rate through compacted soil liners.