Deep Run is an 11.9-mile-long (19.2 km) tributary of the Patapsco River in central Maryland in the United States. The main stem arises in the vicinity of Ellicott City, starting in the Montgomery Meadows housing development, and the lower course forms part of the border between Howard and Anne Arundel Counties. It passes underneath Route 100 twice, Interstate 95 once, and Route 1 once as well.