Evidence suggests that the diversity of microbial life in the vadose zone exceeds diversity found in all other compartments of the biosphere. Such rich diversity is believed to be promoted by complexity of resource and microenvironments and by fragmentation of aquatic habitats in unsaturated soils that limit diffusion pathways and form physically isolated niches capable of supporting diverse species within small soil volumes. We investigated the role of heterogeneity of substrate diffusion through loosely connected water films in promoting coexistence of species that otherwise would not coexist under homogeneous conditions. The mesoscale modeling approach employed in this study tracks nutrient diffusion and consumption within a domain inhabited by microbial communities that expand and move about in response to spatial and temporal variations in nutrients and hydration conditions (termed active walkers). Numerical results on hypothetical rough surfaces support the hypotheses concerning the role of diffusion limitations in sustaining nutrient gradients and sheltering less competitive species, thereby promoting coexistence in heterogeneous domains.