As Euroamericans conquered the North American continent, their most effective weapons were not guns or steel, but microbes. Smallpox in particular had devastating effects on Natives, who had no natural immunity to the disease.
According to historian Edmund S. Meany, Smallpox Bay got its name when “many Indians Infected with the disease at Victoria died there. Their bodies were burned with kerosene by American Officers there in 1860." There is little other evidence of the event, but that is hardly unusual. Reports can be found when white individuals and communities had an outbreak of smallpox on the Islands, but little was recorded when native communities experienced an outbreak. This makes it harder to determine smallpox casualties in native communities.
What we do know is that smallpox radically reduced the American Indian population by upwards of 90 percent across North America. In the Pacific Northwest, the earliest record of a smallpox outbreak was in the late 1770s. It is believed to have been the deadliest smallpox epidemic in the relatively isolated northwest. Anthropologists tracking the cultural changes of Natives in Washington State discovered that two or three Lummi villages in the San Juan Islands were almost completely obliterated in the late 18th century because of smallpox. Survivors of that outbreak returned to their mainland territory, leaving behind remnants of their seasonal hunting and gathering lands. Stories of relocation due to disease are common amongst Coast Salish and Northern Straits Indians. Unfortunately, this adds another layer of complexity when trying to figure out how many people were affected by smallpox in the Pacific Northwest.
At least four other smallpox epidemics occurred in the Pacific Northwest following the initial outbreak in the late 1770s; 1801-02, 1836-38, 1853, and 1862-63. While not all of these epidemics reached the San Juan Islands, the latter does align with the rumors of bodies being burned at Smallpox Bay. The mystery around the name may never be solved, though, the bay stands as a reminder of the devastating effects that smallpox had on Native American and First Nation peoples.