The objective of this study is to investigate the modelling of porosity and hydraulic conductivity changes in saturated porous media induced by the biological growth in pore space. Three different relationships between porosity changes and hydraulic conductivity changes as well as microorganism transport were implemented in the three- dimensional model for multi component reactive transport with variable density groundwater flow PHWAT. The model was then validated through data from laboratory sand box experiment found in the literature. Simulations show that the model is able to represent the behaviour of clogged media; however parameter estimation is needed to improve reliability. A brief investigation on bioclogging effects on soil heterogeneities has also been performed; the growth of biomass in the pore spaces seems to reduce permeability differences within the medium and to limit the forming of preferential paths.