The microbial mineralization of six polycyclic aromatic hydrocarbons (PAHs), containing two to five fused benzene rings, and hexadecane were investigated in sediment: water microcosms which modeled degradation in two freshwater and one estuarine ecosystem. A ranking of the PAHs by order of mineralization rates along with calculated half‐lives (range in weeks) are as follows: naphthalene (2.4‐4.4) ≥ hexadecane (2.2‐4.2) > phenanthrene (4‐18) > 2‐methylnaphthalene (14‐20) > pyrene (34‐>90) ≥ 3‐methylcholanthrene (87‐>200) ≥ benzo[a]pyrene (200‐>300). PAH residues persisted from two to over four times longer in a pristine ecosystem than in an ecosystem chronically exposed to low levels of petroleum hydrocarbons. The mineralization of higher‐molecular‐weight PAHs (> four rings) totaled 0.2 to 6.5% after 8 wk. Relative differences in PAH mineralization among the ecosystems were related to hexadecane mineralization rates, the occurrence and concentration of aromatic hydrocarbon residues in sediments, and elevated populations of hydrocarbon‐degrading microorganisms. Total heterotrophic microbial populations were not good indicators of PAH mineralization rates. Chemical analyses of residues in the microcosms detected the presence of extractable polar metabolites in water and sediments which accounted for 0.1 to 6% of the original PAHs.