As the settlement of the west coast of North America increased during the 19th century, the San Juan Islands became a highly contested territory. Following the Oregon Treaty of 1846, which established the 49th parallel as the boundary between the United States and Canada, the San Juan Islands were jointly occupied by Great Britain and the United States pending an official water boundary. Due to escalating land and settler disputes, the San Juan Islands accumulated a strong military presence. Beginning in 1859, each nation established a military camp on opposite ends of San Juan Island. The border dispute was eventually settled in 1872 under the arbitration of Kaiser Wilhelm I of Germany, which established the border line through Haro Strait.

The first American sources to set up camp on San Juan Island were under the command of Captain George E. Pickett. After two relocations, the American Camp was eventually based north of the Hudson’s Bay Company Farm in the southern region of San Juan Island. Under the command of Lt. Colonel Silas Casey, the American Camp was effectively fortified due to the efforts of the U.S Army Corps of Engineers commanded by the 2nd Lt. Henry Martyn Robert. Lt. Col. Casey ordered Robert to create a position that could house heavy weaponry. Robert constructed the Redoubt on the open prairie of the southern peninsula of San Juan Island. While the Redoubt never saw conflict, it was an ideal defensive location in that it had a commanding view of Griffin Bay and the Strait of Juan de Fuca. Over the course of its existence, the American Camp was the post of eight companies from four regiments, and was never utilized for military action. The soldiers often went to San Juan Town (later Friday Harbor) for entertainment. The American Camp was disassembled in 1874. A memorial was erected on the Redoubt in 1904 as a testament to the American forces that had been stationed there.

In 1860, the British Royal Marines founded their camp on Garrison Bay about 15 miles northwest of the American Camp. Captain George Bazalgette was the first commander of the camp and oversaw its major construction. Bazalgette was later replaced by William Delacombe, who made further improvements to the camp and created a formal garden, which was later replanted in 1972 to commemorate the anniversary of the peaceful resolution to the border dispute. After the Royal Marines left in 1872, the British Camp was bought by Jim Crook and was owned by the Crook family for about 30 years. A memorial to the British Camp was placed in 1904, the same year as the American Camp memorial.

In addition to the Camps on San Juan Island, the town Friday Harbor, named for Hawaiian sheepherder Joe Friday, was founded by Edward Warbass in the 1870s. Warbass later became a territorial legislator and made the town an official county seat. Between the 1890s-1910s, it was a prominent location for fishing, lime quarrying, farming, shipbuilding, and agriculture. Friday Harbor became the base of notable institutions such as Jensen Brothers Sawmill, a University of Washington marine biology field station, and the Pacific American Fisheries.

The nearby Orcas Island also had a tumultuous history. It was originally inhabited by the Lummi tribe and other Salish Strait peoples. American and European settlers began arriving in the 1850s. By the beginning of the 20th century, the island had several small settlements such as East Sound, West Sound, and Deer Harbor. Between 1906 and 1909 former Seattle Mayor Robert Moran moved to Orcas Island and purchased over 5000 acres of land which encompassed a large old-growth forest and Mt. Constitution. He donated over 2700 acres of the land to the state in 1921 for the creation of Moran State Park and continued to purchase additional land in the following years. The seven mile hike to the summit of Mt. Constitution on Orcas Island is a popular tourist attraction. The Civilian Conservation Corps built several miles of hiking trails and an observation tower at the summit in 1936 to grant visitors a spectacular view of the surrounding islands.