The earliest inhabitants to the San Juan Islands were Indians, mostly of the Lummi nation. British and Spanish explorers discovered the islands in the 18th century, but settlement by whites didn't begin until the 1850s. First to settle here were a few British trappers and sheepherders, and some Americans returning, disappointed from searching for gold in Canada's Caribou country.

Conflicts between British and Americans came to a head in the so-called Pig War of 1859. An American settler on San Juan, Lyman Cutlar, shot and killed a British-owned hog that persisted in invading the American's potato patch. The language defining the boundary between Canada and the United States being unclear, and with both nations claiming jurisdiction, U.S. troops were sent to confront British authorities when they attempted to arrest Cutlar. British warships then appeared off the San Juan coast and a shooting war appeared imminent.

Fortunately the two governments agreed to a joint occupation of the San Juans until a boundary could be agreed to. Finally the question was submitted for arbitration by the Kaiser of Germany who decided in 1872 that the Americans had the stronger claim to the islands. This ended the last territorial conflict ever between the United States and Great Britain.

Waters surrounding the San Juans remain open to navigation by boaters from both countries. On the whole, the islands have historically been populated by hard-working farmers, fishermen, seafarers. Beginning in the 1970s these demographics began to change. Traditional occupations had become less profitable and the tourist business was becoming more important, even as increasing numbers of mainlanders came looking for alternatives to the problems of big-city life. Today with improved transportation and with better services and living standards, the islands are less remote and more liveable than ever before. Besides increasing numbers of retirees, many in the San Juans today are artists, writers, and others able to live where they like.