In the archipelago, fifteen islands are accessible by public ferry. Public ferries serve nine Gulf Islands and six San Juan Islands.
Today, the San Juan Islands are an important tourist destination, with sea kayaking and orca whale-watching by boat or air tours, two of the primary attractions. Part of the charm that attracts tourists and residents to the San Juan Islands 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 San Juan Islands make up San Juan County, Washington, though some of the furthest east of the islands are in the mainland counties of Whatcom and Skagit, including Lummi,Guemes, and Cypress Islands.
The majority of the San Juan Islands are quite hilly, the tallest mountain being Mount Constitution at almost exactly a half-mile (800 m) elevation (see Orcas Island), 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 (Arbutus) grace much of the shorelines while evergreen fir and pine forests cover large inland areas.
The San Juan Islands get less rainfall than Seattle, about 65 miles (105 km) to the south, due to the rain shadow of Olympic Mountains to the southwest. 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.
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.