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 zinc, manganese, copper, lead, cadmium, cobalt and nickel in their tissue samples with varying concentrations of metals in different types of tissues. Further analysis revealed that the kidneys had the highest levels of cadmium, the liver had the highest levels of copper and manganese, the liver and the stomach had the highest levels of zinc, and the lungs and liver had the highest levels of iron. There was no difference in concentration when comparing genders. Greater scaup are rated as a species of least concern by the IUCN Redlist. During aerial population surveys greater and lesser scaup are counted together,