The schooner Margaret A. Muir was built by Hans M. Scove in 1872 for Captain David Muir of Chicago, who named the vessel after his oldest daughter. After a few days after its launch on November 7 the Margaret A. Muir was struck by schooner J. & A. Stronach, carrying away its bowsprit (the spar extending from a vessels bow). The Margaret A. Muir mainly shipped on the lower great lakes, moving various cargoes including coal, gypsum, lumber, foodstuffs, and crops. The vessel maintained excellent insurance ratings throughout most of its sailing work, consistently maintaining some form of an "A" rating and higher valuation. In May, 1880, Captain Muir sailed onto Lake Michigan with cargo from the Union Iron Company thinking a storm had cleared when a sudden lull in the wind caused the booms and gaffs to swing violently, snapping the foremast and mainmast. The Margaret A. Muir drifted until 3:00 a.m. when the schooner was towed by steambarge R.J. Hackett to Port Huron. The iron ore being shipped at the time was refused due to a drop in price between the time of the contract and the delivery, leading to Muir suing the Union Iron Company for losses.

Captain Muir often had conflicts with unions after the incident, leading to the Margaret A. Muir being caught between the two often. On July 12, 1883, two crewmembers filed a complaint against Muir about their pay being reduced to cover medicine costs. Further, on September 18, a group of unionized sailors stormed the ship, driving the non-union crew off of the vessel and forcing the schooner to remain at the port. This happened once more before the crew was able to finally get the vessel away, where it was subsequently damaged in a three-ship collision and thus forced to remain at port for repairs. On September 8, 1886, a back-and-forth occurred between union crew and Muir involving raising their pay by 5-cent increments (per 1,000 feet of lumber) as they unloaded lumber; Muir, being anxious to unload, conceded three times before the crew walked off after the fourth attempt. Muir hired non-union crews into 1891 when, due to being unable to find a crew, he was forced to apply at the Seamen's Union in Cleveland. That same union staged an attack on the ship in an attempt to remove non-union members in late August. Finally, unionized crews at Point Edward, Ontario, cut the Margaret A. Muir's lines on July 14, 1892.
While sailing with 650 tons of salt on Lake Michigan, the Margaret A. Muir was functioning well throughout the night of September 29, 1893. However on the morning of September 30, about three miles off Ahnapee, Wisconsin, the ship fell into a trough of the sea and a ginormous wave washed over the deck. The captain and crew were able to escape on a yawl just as the schooner keeled over and sank. The crew of seven made their way to the beach. David Clow, the then-captain of the ship, announced his retirement as the Margaret A. Muir was the third ship he had lost in the last three years. The vessel's masts were left standing and posed a hazard to navigation, leading to it eventually being dynamited on July 15, 1894.
The wreck of the Margaret A. Muir lies broken under 57 feet of water only a few miles outside the entrance to Algoma. Most of Margert A. Muir's hull components and deck machinery are present at the site. In May, 2024, the vessel was relocated by maritime historians Brendon Baillod, Bob Jaeck, and Kevin Cullen of the Wisconsin Underwater Archaeology Association (WUAA) in a deliberate search. It was subsequently investigated by the Wisconsin Historical Society (WHS) State Historic Preservation Office (SHPO) maritime archaeologists and volunteers in May and July, 2024. The ship has been broken in such a way that one can see the interior of the vessel. The Margaret A. Muir has not been visited by any divers outside of WUAA and WHS SHPO, leading to even better preservation.