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
Greater scaup molluscs, aquatic plants, and aquatic insects. During the summer months, the greater scaup will eat small aquatic crustaceans. There is a report of four greater scaups in April near Chicago swallowing hibernating leopard frogs (with body length about ), which they dredged out of a roadside freshwater pond. In freshwater ecosystems, the greater scaup will eat seeds, leaves, stems and roots, along with sedges, pondweeds, muskgrass, and wild celery. Owing to the greater scaup's webbed feet and weight, it can dive up to and stay submerged for up to a minute, allowing it to reach food sources that are unobtainable