Mytilus edulis were collected intertidally from three locations in Halifax Harbor, Nova Scotia, on five occasions during spring and summer 2000. Bioindicators of health (lipid content), condition and gonad indices (CI and GI), and sex ratio, as well as vitellins, were compared with the bioaccumulation of polycyclic aromatic compounds (PACs) including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), coprostanol, and metals. Twice as many male as female mussels were collected from a downtown site (M8) close to numerous raw sewage effluents and a naval dockyard. Males from M8 had a high lipid content, and females had a delayed production of vitellins. These mussels also displayed the highest levels of PACs, coprostanol, Ag, and Sn. Coprostanol and silver are sewage markers in sediments, and their presence in mussels confirms exposure to sewage effluents. Female mussels were more abundant in an area outside the industrialized part of the harbor that had higher marine traffic (M14); displayed higher levels of vitellins in gonads; had similar time trends for CI and GI; and had some similar metals compared with mussels from M8. The lowest variability in biomarkers was observed at a site in a mostly residential arm of the harbor (M12), which was expected to be more pristine based on an earlier investigation. Compared to mussels in M14, the mussels of M12 had the lowest condition indices and PCB concentrations and low but similar levels of lipids, PACs, and coprostanol. They also displayed the highest concentrations of Cd, Cu, Pb, and Hg, and females had the highest gonad indices early in the season.