A microscale model for the transport and coupled reaction of microbes and chemicals in an idealized two-dimensional porous media will be presented. The model includes the flow, transport and bioreaction of nutrients, oxygen, and microbial cells within a saturated granular porous media. Bacterial cells are predominately attached to the solid matrix but may also be found within the bulk fluid. Attachment of bacterial cells to the solid matrix and growth of bacteria can change the local permeability and thus alter the microenvironment. The coupling of mass transport and bioreaction can produce spatial gradients of nutrient and oxygen concentrations. A numerical methods associated with the model will be described along with results of several example simulations.