The Inupiat village of Kauwerak was located about 25 km (15 mi) downriver from Mary's Igloo. By 1900, Kauwerak was abandoned and most of its residents moved to Teller or Nome because of schools and employment opportunities. A few settled at the site of Mary's Igloo, which they called Aukvaunlook, meaning "black whale."
During the gold prospecting period of the early 1900s, non-Natives named the village "Mary's Igloo," after an Inupiat woman named Mary, who welcomed miners, trappers and others into her home for coffee. During that period, Mary's Igloo was a transfer point for supplies for the gold fields upriver on the Kuzitrin and Kougarok rivers. The supplies were offloaded from ocean boats onto barges, which were towed to their destinations. A post office and store were opened at Mary's Igloo in 1901. By 1910, Mary's Igloo was a large community of Inupiat and Anglo-Americans, who were miners, innkeepers, missionaries and support crews for the barges. It had schools, a post office and other services.
The flu epidemic of 1918 and 1919 and a tuberculosis epidemic, two years later, decimated the community's population. Catholic and Lutheran orphanages opened in the area to care for children left without parents.
The schools closed in 1948 and 1950 for lack of students and the post office and store also closed in 1952. Most of the residents moved to Nome or Teller.
The site of Mary's Igloo presently has no permanent population. It is used as a seasonal fish camp by some residents of Teller.