The geospatial distribution of benthic organisms at cold seep sites in the Gulf of Mexico provides an ideal opportunity to study the coupling of seafloor biological activity, supported by microbially-mediated alteration of seafloor-derived substrates, and the geochemical processes which govern their distribution. Chemosynthetic communities are dependant upon primary production by endosymbiotic and free-living chemoautrophic bacteria.  The activity of thiotrophic organisms supports a complex community that includes vestimentiferan tubeworms, bathymodiolid mussels, and vesicomyid clams. The ecology is intimately linked to the geology and ultimately, the geochemical component of the sedimentary sulfur cycle.  Chemosynthetic sites are often established where hydrocarbons, associated with salt diapirism, vent to the seafloor.  Benthic organisms, living on the upper slope sediments, alter the geochemical distribution of porewater constituents and determine the porewater chemistry characteristic of specific biogeochemical relationships.  The average sulfide concentration from two white sulfur oxidizing bacterial mat cores (1.2 ± 1.0 mM) is significantly different from the interstitial sulfide concentrations in three red microbial mat cores (6.3 ± 3.2 mM; p < 0.001).  Whereas mat color is related to the predominant microbial population, it is evident that porewater profiles and authigenic pyrite provide a geochemical indicator of the biological processes occurring in the sediment.  A survey of porewater compositions, including dissolved sulfide, sulfate concentrations and isotopic compositions as well as ¹³C, ¹⁵N, and ³⁴S of benthic organisms, at both seep and non-seep sites, are used to contrast geochemical constraints on the ecology across large spatial scales.  The stable isotopic compositions of bulk tissues reflect and distinguish the sources of C, N and S assimilated by an organism. The sulfur isotopic signature of gastropods (-8.2 ± 0.1‰) grazing on the white microbial mat is similar in ³⁴S to the dissolved sulfide below the mat (-6.7 ± 3.7‰), suggesting that isotopically depleted sulfides are incorporated into the snail diet and further establishes the link between the geochemical composition of the sediments and the organisms that inhabit the substrate.