A new model is developed to study the effect of aqueous phase configuration on microbial growth on rough surfaces under different hydration conditions. Surface roughness is idealized using a network of conical pits (sites) on a regular lattice connected by v-shaped channels (bonds) with prescribed geometry that vary spatially. Aqueous phase distribution and connectivity within the surface network are calculated as functions of water potential or relative humidity. Microbial growth on the rough surface network is simulated using a hybrid method coupling the reaction-diffusion method for the nutrient field with the individual-based model for microbial activity. The modeling platform links variations in hydration conditions within simple heterogeneous porous media (rough surfaces) with microbial growth rates and expansion patterns. The results demonstrate effects of geometry and spatial distribution of roughness elements on aqueous phase connectivity and on effective diffusion and, consequently, control of microbial growth under different water potentials. The key parameter affecting microbial growth is the effective aqueous diffusion coefficient, which, in turn, is controlled by mean water content of the bonds in the network.