Most of the architectural work at Dark Island is attributed to the prominent American architect Ernest Flagg. His client was Frederick Gilbert Bourne, president of the Singer Manufacturing Company (now the Singer Corporation), producer of the Singer Sewing Machine. His daughter, Marjorie Bourne Thayer, made additions in 1928. Flagg also designed the skyscraper headquarters for the company in New York City, the tallest building in the world at the time. Flagg is known for many major American projects, such as the United States Naval Academy at Annapolis, Maryland.
The island's castle was the last of several "castles" built at the Thousand Islands during a brief interval (1888–1905). Bourne undertook the project while the larger Boldt Castle was nearing completion nearby. The architect modeled the stone structure, planned in 1903, on Scottish models described in novels of Sir Walter Scott.
Following the 1919 death of Frederick Bourne, his daughter Marjorie (Mrs. Alexander D. Thayer) took title to the property. Her ownership was contested by a brother, but she retained title.
Upon her death, the Roman Catholic order Brothers of the Christian Schools (the Christian Brothers) acquired Dark Island along with the large Bourne country house, Indian Neck Hall at Oakdale on Long Island, which thereafter became La Salle Military Academy. Having little use for the remote island in the St. Lawrence River, the Christian Brothers sold Dark Island in 1965 for approximately US$30,000, to be used thereafter by a charitable organization of religious character, the Harold Martin Evangelistic Association.