In this book a conceptual model of solute transport with bioremediation processes using sawdust as a matrix to improve the efficiency of bioremediation in the porous media was developed. The transport part of the model solves the advection-dispersion partial differential equations and the reaction part describes the heterotrophic metabolisms of several groups of bacteria. The model considers biological clogging effects, by calculating changes in porosity through converting biomass into volume, which directly reduces porosity of porous media. Unwanted substances rich in wastewater are usually deficient in electron donor and require external addition of electron donors in order to achieve complete reduction. In this study possible source of carbon is the solid carbon supplied to system in the form of sawdust. The results of this study indicate that sawdust could be employed as low cost material to enhance the bioremediation processes and increase the permeability of porous media. Feasibility and applicability of model was assessed by conducting laboratory soil-sawdust columns experiments and comparing the simulated results with experimental data.