A brackish-water cold seep on the North Anatolian Fault (NAF) in the Marmara Sea was investigated with the Nautile submersible during the MarNaut cruise in 2007. This active zone has already been surveyed and revealed evidence of active seeping on the seafloor, such as bubble emissions, patches of reduced sediments, microbial mats and authigenic carbonate crusts. MarNaut was the first opportunity to sample benthic communities in the three most common microhabitats (bioturbated and reduced sediments, carbonate crust) and to examine their relationships with environmental conditions. To do so, faunal communities were sampled and chemical measurements were taken close to the organisms. According to diversity indices, the bioturbated microhabitat exhibited the highest taxonomic diversity and evenness despite a lower number of samples. Conversely, the reduced sediment microhabitat exhibited the lowest taxonomic diversity and evenness. The carbonate crust microhabitat was intermediate although it had the highest biomass. Multivariate analyses showed that (1) fauna were relatively similar within a single microhabitat; (2) faunal community structure varied greatly between the different microhabitats; (3) there was a link between faunal distribution and the type of substratum; and (4) chemical gradients (i.e. methane, oxygen and probably sulphides) may influence faunal distribution. The estimated fluid flow velocity (0.4-0.8 m/yr) confirmed the presence of fluid emission and provided evidence of seawater convection in the two soft-sediment microhabitats. Our results suggest that the reduced sediments may represent a harsher environment with high upward fluid flow, which restrains seawater from penetrating the sediments and inhibits sulphide production, whereas bioturbated sediments can be viewed as a bio-irrigated system with sulphide production occurring at greater depths. Therefore, the environmental conditions in reduced sediments appear to prevent the colonization of symbiont-bearing fauna, such as vesicomyid bivalves, which are more often found in bioturbated sediments. Fluid flow appears to control sulphide availability, which in turn influences the horizontal and vertical distribution patterns of fauna at small spatial scales as observed at other seep sites.