Multiple environmental mechanisms have been proposed to control bottom water hypoxia (<2 mg O2 L?1) in the northern Gulf of Mexico Louisiana shelf. Near-bottom hypoxia has been attributed to a direct consumption of oxygen through benthic microbial respiration and a secondary chemical reaction between oxygen and reduced metabolites (i.e. ferrous iron and total sulfide) from these populations. No studies to date have examined the metabolically active microbial community structure in conjunction with the geochemical profile in these sediments. Temporal and spatial differences in dissolved and solid phase geochemistry were investigated in the upper 20 cm of the sediment column. Pyrosequencing of reverse transcribed small subunit (SSU) ribosomal ribonucleic acid (rRNA) was used to determine population distribution. Results indicated that populations shallower than 10 cm below surface were temporally variable yet uniform between sites, while below this depth, populations were more site-specific. This suggests a potential interaction between the water column and the benthic microbial population limited to a shallow depth. The presence of dissolved reduced iron in the upper sediment column was indicative of low oxygen concentration, yet sulfide was at or below detection limits. Putative sulfate and iron reducing and oxidizing populations were metabolically active at similar depths suggesting potential recycling of products. Results from this study indicate low carbon concentrations in the shallow sediments limit general metabolic activity, reducing the potential for microbial respiration. Supplemental materials are available for this article. Go to the publisher’s online edition of Geomicrobiology Journal to view the supplemental file.