Recent reports on the presence of persistent organic chemicals in wild and farmed salmon have left consumers and health professionals confused regarding the safety of regular fish consumption. The objectives of this study were (1) to compare concentrations of key contaminants and the essential nutrients omega-3 fatty acids between farmed and wild salmon and trout, and (2) to balance risks and benefits from regularly consuming these species. Concentrations of mercury, polychlorinated biphenyls, dioxins and furans as well as omega-3 fatty acids were determined in fillets from farmed salmon and trout bought in various markets located in Quebec, Canada, as well as in fillets from wild salmonids obtained from fishermen and various Canadian agencies. While differences were observed between market (farmed) and wild fish with regard to the concentrations of mercury and polychlorinated biphenyls, overall the concentrations of contaminants were low, such that the regular consumption of these fish would not cause tolerable daily intakes to be exceeded. Our results indicate that salmon and trout sold in Quebec markets, which as in markets located elsewhere in North America originate for the most part from Chilean farms, can be consumed regularly to achieve optimal nutritional benefits from omega-3 fatty acids, without incurring significant contaminant related health risks.