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 of James Bay and the Great Lakes. Notable breeding concentrations, with more than half a million birds at the height of the season, can be found in Alaska, in the woodlands of the McKenzie River valley and on the Old Crow Flats. These birds migrate south (mostly via the Central and Mississippi Flyways) when the young are fledged and return in early spring, usually arriving on the breeding ground in May. Lesser scaup typically travel in flocks of 25–50 birds and winter mainly on lakes, rivers and sheltered coastal lagoons and bays between the US–Canada border and northern Colombia, including