The transport of microorganisms (bacteria, fungi, and viruses) in porous media governs many phenomena in bioremediation of environmental pollution problems and microbial enhanced oil recovery. The purpose of this study is to investigate the efficiency of microbes to modify reservoir heterogeneity and improve oil recovery. The transport of microorganisms in the subsurface formation is governed by many complicated physical, chemical, and biological phenomena, such as adsorption, interaction between microorganisms and substrate, and the growth and decay of cells. Little information exists concerning the transport, growth and metabolism of viable cells in subsurface environments. Some of the phenomena are still not well understood. This report will present our progress on development of a three-dimensional, three-phase, multiple-component numerical model to describe microbial transport phenomena in porous media.