The Whale Museum in Friday Harbor is a small but substantive natural history museum dedicated to the orca and other cetacean populations of the Salish Sea. It was founded in 1979 — before the San Juan Islands were known as a whale-watching destination — and has been producing serious research on the region's Southern Resident killer whales ever since. The exhibits tell the story of these whales: their social structure, their vocalisation patterns, their diet of Chinook salmon, and the pressures they face from boat traffic, noise pollution, and declining prey.
The centerpiece display is a full-skeleton orca suspended from the ceiling — the bones are from a real animal, and the scale makes an immediate impression. Other exhibits cover grey whales, humpbacks, and the complex acoustic world of cetaceans. There is a research station in the building that runs a year-round hydrophone network, and on busy whale days the staff can tell you exactly where in the channels the pods have been sighted most recently.
The museum is small enough to cover in an hour or two, and the gift shop is genuinely good — proceeds go directly to research and conservation. It is worth visiting before a whale-watching tour to understand what you are looking for, and worth returning to afterward when the experience of watching the animals has given the research context.