The point was named by captain George Vancouver after visiting the site in May of 1792 and spotting the clay that can be seen in the bluffs above the point.
About October 1 1888 a lens lantern with a red light was mounted on a pole to mark the eastern entrance to Port Townsend Bay. In 1892 the Lighthouse board recommended a large fog bell be installed to warn of the sharp turn in the course when entering for leaving Puget Sound. $3,500 was allocated by Congress on March 3 1893 and a one and one half story six-room keepers house with a fog bell tower was built and put into operation on April 7, 1896. The huge 1,200 pound bell would strike twice every fifteen seconds during periods of fog or low visibility.
Seventy-year-old former sea captain Osmore H Morgan was the first keeper. He had spent the prior fourteen years as head keeper at the New Dungeness Lighthouse. His daughter, Nettie Race took over after his passing in 1907. A few months later Axel Rustad was appointed keeper and he and wife Karen took over. They stayed for ten years raising four sons in the keepers quarters. The only water for the family was rain water collected and stored in a 5,000-gallon redwood tank which was located in a shed behind the house.
In July 1903 the North Pacific, a side wheel steamer struck Craven Rock off Marrowstone Point in a dense fog. The steamer had 14 passengers aboard who were taken to shore by lifeboats and the tug boat C. B. Smith. Lighthouse keeper Morgan fed and sheltered them until they were taken aboard the steamer Mainlander which had run aground on Marrowstone Point that same morning but was afloat again at high tide. The North Pacific was a total loss as it sank in deep water.
In 1907 construction of Fort Flagler was completed. Fort Flagler joined with the guns at Fort Casey on Admiralty Head and the guns at Fort Worden near Point Wilson to form a "Triangle of Fire" to prevent enemy vessels from entering Puget Sound
Dense fog caused another mishap in August 1908. The 502-foot-long armored cruiser USS Colorado ran aground on Liplip Point the southeast tip of Marrowstone Island. This incident cast light on the need for more navigational aids in Puget Sound. On October 22, 1913 Congress appropriated $30,000 for improvements.
Marrowstone Point received a new fog signal and light in 1914. An experimental acetylene gun was installed in a wooden building thirteen yards northeast of the bell tower and took the place of the fog bell. Mariners were asked to report the efficiency of the gun to the lighthouse inspector in Portland.
A new acetylene gun was installed atop a concrete structure just two months later. At the same time, the light was changed from a fixed red to a quick two red flashes every six seconds. The acetylene fog gun was the first of its kind to be used in the United States.
Several improvements were made over the years until 1962 when it was automated. In 1972 the Coast Guard transferred the property to the Bureau of Sport Fisheries and Wildlife in the U.S. Fish and Wildlife Service to be used as a research facility. The keepers house is now used as a guest house for scientists who visit the Marrowstone Marine Field Station.
Still standing at the waters edge are the structure that held the light and fog signal and the light tower. The flashing white light is still functioning but the fog signal is no longer being used. The station is now being used as a marine ecosystem health and marine fish health research facility.
Fort Flagler is now Fort Flagler State Park . A military museum is located in the park. The Marrowstone Point Light is visible from the park's beach but it is not open to the public.