The San Juan Islands are a part of the San Juan Archipelago in the northwest corner of the continental United States. The archipelago is split into two groups of islands based on national sovereignty: the San Juans are part of the U.S. state of Washington, while the Gulf Islands are part of the Canadian province of British Columbia. There are over 450 islands in the entire archipelago at high tide, but fewer than one-sixth are inhabited, and only six are accessible by public ferry.

Prior to European settlement, the islands were part of the traditional area of the Central Coast Salish. Linguistically, the Central Coast Salish consisted of five groups: Squamish, Halkomelem, Nooksack, Northern Straits (which includes the Lummi dialect), and Klallam. Exploration and settlement by Europeans brought smallpox to the area by the 1770s. In 1843, the Hudson's Bay Company established Fort Camosun at nearby Vancouver Island.

The 1846 Oregon Treaty forced by President Polk established the 49th parallel as the boundary between Canada and the U.S., except in the San Juan archipelago. While both sides agreed that all of Vancouver Island would remain British, the treaty wording was left vague enough as to put the boundary between modern-day Gulf Islands and San Juan Islands in dispute. Conflicts over this border led to the Pig War in 1859. Skimishes continued until the boundary issue was eventually placed in the hands of Kaiser Wilhelm I of Germany for arbitration. The border was finally established in 1872.

Today, the San Juan Islands are an important tourist destination, with sea kayaking and orca-watching two of the primary attractions. Part of the charm that attracts tourists and residents to the San Juans is that each island seems to have a character of its own, both in terms of geography and of the lifestyle of the people who live there.

Politically, the bulk of the islands make up San Juan County, Washington, though some of the furthest east of the islands are in the mainland Whatcom County, Washington, most notably Lummi Island .

The San Juans are actually the remaining mountain-tops of a receding continent much older than the American mainland. The islands are generally quite hilly, the tallest mountain being Mount Constitution at almost exactly a half-mile elevation (see "Orcas Island" below), with some flat areas and valleys, often quite fertile, in between. The coastlines are a mixed bag of sandy and rocky beaches, shallow and deep harbors, placid and reef-studded bays. Gnarled, ochre-colored madrona trees grace much of the shorelines while evergreen fir and pine forests cover large inland areas.

The islands get less rainfall than Seattle, about 65 miles (100 km) to the south, due to the rain shadow of U.S. and Canadian mountain ranges to the west. Summertime high temperatures are around 70° F (21° C) while average wintertime lows are in the high thirties and low forties. Snow is infrequent in winter except for the higher elevations, but the islands are subject to high winds at times—those from the northeast sometimes bring brief periods of freezing and arctic-like windchills.

Three ferry systems serve some of the San Juans.

• The Washington State Ferries system serves Lopez Island, Shaw Island, Orcas Island, and San Juan Island (typically in that order), from a dock in Anacortes.
• Skagit County serves Guemes Island, also from a dock in Anacortes
• Whatcom County serves Lummi Island , from a dock near Bellingham

Beginning in about 1900 the San Juan Islands became infested with European rabbits, an exotic invasive species, as the result of the release of domestic rabbits on Smith Island . Rabbits from the San Juan Islands were used later for several introductions of European rabbits into other, usually midwestern, states.

The San Juans include:

• Barnes Island
• Blind Island
• Brown Island
• Center Island
• Clark Island
• Crane Island
• Cypress Island
• Decatur Island
• Eliza Island
• Flattop Island
• Goose Island
• Guemes Island
• Henry Island
• Johns Island
• Lopez Island
• Lummi Island
• Matia Island
• Obstruction Island
• Orcas Island
• Patos Island
• Pearl Island
• San Juan Island
• Shaw Island
• Smith Island
• Spieden Island
• Stuart Island
• Sucia Island
• Waldron Island