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 100% of female greater scaup, and 77% of female lesser scaup, had escalated levels of selenium in their bodies. Selenium is an occurring semimetallic trace element that occurs naturally in some soils and minute amounts are necessary for animal life. However excessive selenium can cause reproductive harm and is highly toxic. On their migration across the Great Lakes, greater scaups are at risk of ingesting selenium by eating the invasive zebra mussels, which can render a hen infertile. This sterilization of hens is causing the population to decrease. In a study of 107 scaup, they all had traces of iron,