The widespread contamination by polycyclic aromatic hydrocarbons (PAHs) has created a need for cost-effective bioremediation processes. This research studied a chronically PAH-contaminated estuarine sediment from the East River (ER; NY, USA) characterized by high concentrations of PAHs (approximately 4-190 ppm), sulfide, and metals and a marine sediment from New York/ New Jersey Harbor (NY/NJH; USA) with only trace quantities of PAHs (0.1-0.6 ppm). The focus was to examine the relationship between bioavailability of PAHs and their biological removal in a slurry system. Freshwater and marine sediment toxicity tests were conducted to measure baseline toxicity of both sediments to amphipods, aquatic worms, fathead and sheepshead minnow larvae, and a vascular plant; to determine the cause of toxicity; and to evaluate the effectiveness of the biotreatment strategies in reducing toxicity. Results showed the ER sediment was acutely toxic to all freshwater and marine organisms tested and that the toxicity was mainly caused by sulfide, PAHs, and metals present in the sediment. In spite of the high toxicity, most of the PAH compounds showed significant degradation in the aerobic sediment/water slurry system if the initial high oxygen demand due to the high sulfide content of the sediment was overcome. The removal of PAHs by biodegradation was closely related to their desorbed amount in 90% isopropanol solution during 24 h of contact, while the desorption of model PAH compounds from freshly spiked NY/NJH sediment did not describe the bioavailability of PAHs in the East River sediment well. The research improves our understanding of bioavailability as a controlling factor in bioremediation of PAHs and the potential of aerobic biodegradation for PAH removal and ecotoxicity reduction.