The islands were first settled roughly 11,000 years ago when the continental ice shelf began to recede at the end of the Last Glacial Period.

[8] Archeological evidence suggests hunting and gathering on the islands between 6,000 and 8,000 years ago, and shell middens found in both English and American Camp areas indicate there were thriving villages before the arrival of Europeans.

[7][8] An excavation by a team from the University of Washington's Burke Museum of Natural History and Culture established extensive evidence of various human uses of the area around English Camp, but was inconclusive as to whether it was a site of year round settlement.

[8] The Lummi Nation, among those Coast Salish tribes whose ancestors inhabited the islands, are engaged in efforts to re-start traditional uses of the English Camp area, including reef net fishing.

[7] The Haro and Rosario straits defined the competing territorial claims of the United States and Great Britain after the Oregon Treaty of 1846 settled most of the northwestern border.

The period of military occupation was peaceful; a road was built between the two camps, and Americans in the village of San Juan engaged in commerce with both encampments.

Today the Union Jack still flies there, being raised and lowered daily by park rangers, making it one of the very few places without diplomatic status where US government employees regularly hoist the flag of another country.

The American Camp site is on the island's southernmost peninsula, and partially overlaps the original Hudson's Bay Company farm.

The park property also includes the original site of San Juan village on the north shore of the peninsula, which was abandoned after the dispute ended and was entirely burned in 1890.