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 more often than those of the greater scaup—particularly during flight—but their call is weaker, a guttural "brrtt, brrtt". Lesser scaup are often hard to distinguish from the greater scaup when direct comparison is not possible, but in North America a large scaup flock will often have both species present. Females, juveniles and drakes in eclipse plumage are hard to identify; there is considerable overlap in length between the two species, but greater scaup are usually noticeably more bulky. Lesser scaup females and immatures tend to have less white around the bill, but this too varies considerably between individual birds. The