Cold seeps are seafloor environments where hydrocarbon-rich fluids, including methane and hydrogen sulfide, migrate through deep-seated faults and fractures to the seabed, supporting chemosynthetic communities. Although the biological activity within and immediately around these sites can be highly elevated compared to the surrounding deep-ocean ambient sediments, little is known about whether subtle changes extend to the larger periphery, where no visible signs of seepage exist. Here we examine how geological structures, such as subsurface faults, regulate seep formation and fluid migration, and assess the influence this has on microbial distributions by combining a 2.5×2.5×1 km three-dimensional seismic survey with a 1.6 km transect study that overlies a deeply buried salt diapir. The crest of the diapir rests ~1 km below the seafloor, where it has heavily disturbed the overlying bedrock with radial and crustal faults, half-graben block displacements, and salt-tectonic-influenced anticlinal mini-basins. Rocks draping the diapir also host a subsurface methanogenic deep biosphere that produces sufficient methane to sustain a biodiverse ocean floor cold seep. A portion of the produced hydrocarbons has become trapped within ~300 mbsf block-faulted strata where they are recognizable in seismic data as a direct hydrocarbon indicator (DHI). We analyzed 52 sediment samples extending 5–575 cm below seafloor (cmbsf) from five gravity cores and one push core collected at an active cold seep. Spatial heterogeneity in cored sediments along the transect was revealed by porewater geochemistry, stable isotopes, and lipidomics. Collectively, these data resolve distinct chemosynthetic zones that form tightly coupled functional networks mediated by interlinked redox-dependent cycling of nitrogen, carbon, iron, and manganese that are comprised of ammonia-oxidizing archaea (AOA), anaerobic methanotrophs (ANMEs), and sulfate-reducing bacteria (SRB). Evidence is provided that microbial assemblages and their metabolic interactions are shaped and sustained by diffuse and largely non-detectable microseepage ascending along more deeply buried fault systems associated with the salt diapir. The results, therefore, establish a spatially resolved model for offshore geochemical surveys that link subsurface fluid flow to redox gradients and microbial activity.