There are many biogeochemical factors simultaneously influencing the fate of chemical compounds in soil; abiotic factors like grain/pore size distribution, saturation state and pore connectivity and biotic factors such as the diversity of microbial community in terms of having aerobic/anaerobic as well as their activities and metabolic pathways. Primary aim of this study is to establish a novel reactive transport modelling approach covering the full range of spatio-temporal heterogeneity at pore scale to assess underlying biogeochemical phenomena in porous media.