Although the victory at the Battle of Mobile Bay on 5 August 1864 had closed the port of Mobile to blockade runners, the city itself had not been taken. The Confederates fortified the approaches to the city and heavily mined the shallow waters surrounding it. On 27 March 1865, Milwaukee, together with several other Union ships, sortied upriver in an attempt to cut communications between Spanish Fort and Mobile. The following day she and her sister ship steamed up the Blakely River to attack a Confederate transport and forced it to retreat. While returning downriver Milwaukee struck a mine in an area previously swept. She remained afloat forward, which permitted her crew to escape without loss. Another of her sisters, , rescued the survivors.ORN, Vol. 22, p. 71
