Abstract Adult long-tailed ducks ( Clangula hyemalis) were collected from nine locations across their breeding grounds in northern Canada and measurements of stable isotopes of carbon ( δ 13C), nitrogen ( δ 15N) and sulfur ( δ 34S) in bone collagen were used to investigate if relative use of freshwater habitats such as the Great Lakes (with expected depleted stable isotope profiles) compared with coastal marine environments (with expected enriched stable isotope foodweb profiles) could explain tissue trace element profiles. Contrary to expectation, all three stable isotopes did not covary in our sample, suggesting that mechanisms other than simple freshwater vs. marine isotopic gradients were involved among populations. All three stable isotopes varied significantly with collection location and both δ 15N and δ 13C values varied significantly between sexes suggesting that males exploit either a different food base or occur in different geographic areas than females for at least part of the year. The δ 34S data, in particular, suggested that many of the birds breeding in the western Canadian Arctic probably overwinter in the Great Lakes along with many of the birds breeding in Hudson Bay. Males at the majority of collection locations had higher concentrations of hepatic Hg (1.1–8 μg/g dw), Cu (25–40 μg/g dw), Se (7.3–27 μg/g dw) and renal Cd (33–129 μg/g dw) than females. Concentrations of Hg, Cu and Cd were well below toxicological threshold levels found in the literature. However, hepatic Se concentrations in 64% of the females exceeded 10 μg/g dw and concentrations in 8% of the birds measured exceeded 33 μg/g dw suggesting levels of potential concern.