The influence of natural populations of the sub-surface deposit-feeding amphipod Victoriopisa australiensis on sediment biogeochemistry was assessed by randomly collecting 21 sediment cores in a zone of Coombabah Lake, southern Moreton Bay, Australia, where the benthic infauna was dominated by this species. Cores were incubated sequentially to determine sediment-water column fluxes of oxygen, dissolved inorganic carbon and inorganic N species, followed by incubations to determine rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) using the isotope pairing technique. Finally, each core was sieved in order to determine the population and biomass of amphipods present. Whilst all measures of overall benthic metabolism (sediment oxygen demand, and effluxes of inorganic carbon and nitrogen) showed increased with amphipod density, with rates being stimulated 70-220% at the highest categorised density range of 2,500-3,500 ind m-2, only the correlation with dissolved inorganic carbon was statistically significant. In contrast, there were no discernable trends between amphipod densities and any of the N-cycle processes with the slopes of all correlations being very close to zero. These results highlight the differences in mesocosm simulations of fauna effects, which primarily relate to shifts in rates of organic matter turnover, compared to natural sediments where fauna effects relate more to induced changes in rates of organic matter deposition. Therefore, while mesocosms represent a powerful tool to investigate the mechanisms by which fauna influences microbial metabolism in the sediment, only studies of natural sediments can determine to what extent these mechanisms function in situ.