Biodegradation was a major mechanism for removing oil resulting from the Exxon Valdez oil spill in Prince William Sound, Alaska. For three field seasons, we examined the hexadecane, phenanthrene, and naphthalene mineralization potentials of hydrocarbon-degrading microorganisms and the accompanying hydrocarbon concentrations from intertidal and shallow subtidal sediments. We found that mineralization potentials were not directly dependent on sediment substrate concentrations, but environmental factors influenced the ability of microbial populations to mineralize polycyclic aromatic and aliphatic compounds. These factors included the intensity of physical mixing experienced, the treatments received, and the availability of alternative carbon sources. In 1989, when the Exxon Valdez oil was relatively unweathered and before shoreline treatment was begun, the mineralization potentials of aromatic hydrocarbons were high at many sites even in the presence of alkanes at higher concentrations. However, by 1990, mineralization potentials for alkanes were greater than those for aromatics at oiled sites exposed to terrestrial bio-waxes or fatty acids from the bioremediation process. Therefore, our study shows that sediment chemistry data alone cannot predict the persistence of hydrocarbons following the Exxon Valdez oil spill and demonstrates the need for systematic ecosystem-level studies of the abiotic and biotic factors influencing biodegradation.