Bioirrigation of marine sediments by benthic infauna has the potential to increase both the rate and depth of bacterial mineralization of polycyclic aromatic hydrocarbons (PAHs) by recirculating oxygenated bottom water into sediment burrows. Rates of heterotrophic bacterial production and mineralization of PAHs (naphthalene, phenanthrene, and fluoranthene) were measured in sections of sediment cores sampled from stations in San Diego Bay. Data suggest that rates of PAH biodegradation and bacterial heterotrophy were influenced by bioirrigation by benthic infauna. PAH mineralization and heterotrophic production were higher in core sections where sulfide was not detected relative to core sections containing sulfide. Depth-integrated capacity of the upper 17 cm of sediment to mineralize PAHs was 4 to 10 times higher at the station with bioirrigation coefficients that increased with depth. Remedial dredging of sediments to remove contaminant mass (and presumable lower ecological risk) will also remove benthic infauna. Removal of infauna and the subsequent lowering of bioirrigation in surface sediments would be expected to lower the capacity of intrinsic PAH bioremediation. This could cause local increases in ambient PAH concentration and consequently increase the ecological risk at the site and potentially degrade the health of the ecosystem by removing a sink for PAHs.