Greater scaup faces numerous threats, the most significant challenge to their survival is habitat degradation caused by a mix of human development and runoff. Greater scaup, when moulting and during the winter, are threatened by escalated levels of organochloride contaminants. Oil and sewage pollution also threaten this duck. Since 80% of the greater scaup population winters in the urbanized part of the Atlantic Flyway, these ducks are subject to high levels of organic contaminates, along with increased levels of heavy metals in foods and habitat. A joint group of American and Canadian scientists researching scaup migration across the Great Lakes found that
Lesser scaup well as seeds and other parts of aquatic plants like sedges and bulrushes (Cyperaceae), "pondweeds", widgeon-grass ("Ruppia cirrhosa"), wild celery ("Vallisneria americana") or wild rice ("Zizania"). In winter, but less so in summer, other aquatic animals—crustacean, insect and their larvae and small fishes—form an important part of their diet. It has been reported that both the lesser and the greater scaup have shifted their traditional migration routes to take advantage of the presence of the zebra mussel ("Dreissena polymorpha") in Lake Erie, which was accidentally introduced in the 1980s and has multiplied enormously. This may pose a risk to these