We studied the vertical distribution of microbes and meiofauna in natural hydrocarbon seep sediments to determine if there was a relationship between profiles of benthic trophic structure and the unique biogeochemical conditions present at the seep. Three stations in the Santa Barbara Channel represented a gradient of natural petroleum seepage, from very active, to moderate, to none. Seasonal differences were examined by sampling in the three major oceanographic seasons, upwelling (April), mixed (July), and Davidson (December). Densities of microbes and meiofauna were highest in July, and decreased in winter. All population sizes decreased with increasing depth in the sediment. Harpacticoids and Chl a were practically restricted to the surface sediments. Harpacticoids and Chl a were more dense (number per unit volume or strata of sediment) and abundant (number per unit area of sediment or sum of the strata) at the comparison site than at the seep sites. Density and abundance of nematodes, bacteria cell counts, and bacterial biomass were greater at the station with the most active seepage rates. Bacterial biovolumes appeared constant among sediment depths and stations, but cell biovolumes were larger in July. The data are consistent with the hypothesis that organic enrichment via petroleum utilization is responsible for increased abundances of bacteria and nematodes at the seep. There were strong correlations between densities of harpacticoids and microalgae, and densities of nematodes and bacteria. These links indicate that seeping petroleum might have an enhanced effect on the detrital (bacterial based) food web, but a toxic effect on the grazing (microalgal based) food web.