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 because they look almost identical from the air. It was estimated that the greater scaup made up about 11% of the continental scaup population. Since the 1980s, scaup populations have been steadily decreasing. Some of the primary factors contributing to this decline are habitat loss, contaminants, changes in breeding habitat, and a lower female survival rate. The 2010 American scaup population survey was 4.2 million scaup, however, the worldwide greater scaup population survey estimated 1,200,000 to 1,400,000 mature greater scaup. Along with the aerial population surveys, there is a banding program for the greater scaup. Metal leg bands are placed