Earth’s diverse soil microbiomes host bacteria within dynamic and highly fragmented aqueous habitats that occupy complex pore spaces and often restrict the spatial range of ecological interactions. Notwithstanding recent advances in resolving global drivers of soil bacterial biogeography, the spatial distribution of bacterial communities within soil volumes remains largely unknown. Here, we propose a framework for representing submillimeter-scale distributions of soil bacteria based on physical constraints supported by individual-based model results and direct observations. The spatial distribution of bacterial cell clusters modulates various metabolic interactions and soil microbiome functioning. For dry soils with prohibitively long diffusion times, interactions are highly localized among sparse communities. Frequently wet soils promote long-range trophic interactions between dense cell clusters through aqueous pathways. Biomes with high carbon inputs support large and dense cell clusters where anoxic microsites form even in aerated soils. Micro-geographic considerations of yet unobservable processes can improve interpretation of data from bulk soil samples.