A model simulating reactive transport in natural filter using sawdust as materials to improve the efficiency of filter is developed. The transport part of the model computes the changed in concentration over time caused by the processes of advection and dispersion. The kinetic sub model describes the heterotrophic metabolisms of several groups of bacteria. To model a complete redox sequence (aerobic oxidation, denitrification, Mn (IV) -reduction, Fe (III) -reduction and sulfate reduction) four functional bacterial groups (X1, X2, X3 and X4) are defined. The growth and metabolisms are formulated using the Double Monod kinetic equation. The model takes into account the exchange between the different phases (mobile phase, bio phase and matrix phase). The results from a laboratory soil-sawdust columns experiments are used to verify the simulation results of the model. While the availability of organic carbon is one of the most important factors that affects bacterial activity in natural filter. This study demonstrates that using sawdust as a carbon source can improve the biologically mediated redox processes.