The present study introduces a reactive transport modeling approach to determine the influence of pore-scale heterogeneities on biogeochemical processes in porous media. For this purpose, a pore network model, which simulates flow and advective–diffusive transport of chemical species in heterogeneous pore networks is developed and coupled to the Biogeochemical Reaction Network Simulator (BRNS). The resulting coupled model (PNBRNS) is able to simulate the reactive transport of solutes in heterogeneous pore assemblies. The PNBRNS model is applied for the simulation of a test case of bioavailability and effective biodegradation rate of a dissolved contaminant in different pore networks, built using a discrete set of geostatistically derived pore-size or biomass distributions. Results show that the heterogeneity of the pore-size distribution has a significant impact on bioavailability while the heterogeneity of the biomass distribution only leads to minor effects. The model also includes intra-pore bioavailability restrictions using diffusion-limited biodegradation kinetics. The results indicate that intra-pore limitations lead to extra constrains on the biodegradation of contaminants, even in the presence of larger-scale structural heterogeneities.