The combined lesser scaup (Aythya affinis) and greater scaup (A. marila) population in North America has steadily declined from an average of 7.5 million breeding birds in the 1970s to an all-time low of 3.39 million in 2005. Bioaccumulation is widely known as the means of elevated levels of toxins in vertebrates. Our goal was to determine whether chromium and selenium were factors contributing to the continental scaup population decline by identifying wetlands used by scaup that potentially contain dangerous concentrations of chromium and selenium. We hypothesized that zebra mussels (Dreissena polymorpha) would contain the highest concentrations of selenium and chromium because they are filter feeders, whereas amphipods would contain the lowest concentrations because of their short life span. We collected zebra mussels, fingernail clams (Sphaerium transversum), chironomid larvae, snails (Gastropoda), and amphipods on randomly selected traditional lesser scaup staging and breeding wetlands. We found higher chromium concentrations in zebra mussels from Iowa, USA, than in those from Wisconsin, USA (P = 0.0074). In addition, selenium concentrations in zebra mussels from Wisconsin were higher than in those from Iowa (P < 0.0001). Higher selenium concentrations in amphipods were associated with sampled wetlands surrounded by developed land. Invertebrates with >5 μg/g selenium and >1 μg/g chromium are potentially hazardous for scaup. Chromium concentrations in Iowa were the highest for most species examined, whereas they were the lowest in Minnesota, USA. Based on our results, lesser scaup probably accumulate the highest concentrations of selenium on Lake Onalaska, Wisconsin, whereas they probably accumulate the lowest concentrations in Iowa. Waterfowl biologists are searching for explanations to the scaup decline; we propose chromium and selenium concentrations in amphipods and fingernail clams may be a factor.