One of the officers under Eliza's command, Gonzalo López de Haro, was the first European to discover San Juan Island.

The Hudson's Bay Company (HBC) established the first permanent, non-native settlement on the island on December 13, 1853, in order to create a sheep farm.

By November 1859, an agreement was reached for a joint British–American control of the island until the matter was resolved by negotiation.

In 1862, Chief Trader Charles John Griffin left the island and leased the Belle Vue Sheep Farm to Robert Firth, a shepherd, from 1864 to 1873.

[5] The 1862 Pacific Northwest smallpox epidemic swept through the region, killing large numbers of indigenous people.

Smallpox Bay, on the west side of San Juan Island, was named for victims of this epidemic.

San Juan Island is considered a "small town" community, in that it is relatively quiet rural living with few distractions or incidents aside from tourism.

One notable resident would be Lisa "Ivory" Moretti, a retired female professional wrestler of World Wrestling Entertainment fame.

In addition, many Hollywood stars and celebrities spend time on the island to avoid publicity and to seek some peace and quiet.

The waters surrounding San Juan Island are home to a variety of species including red sea urchins[12] and pinto abalone.