[2] The river rises in Reading, flows roughly south through Woburn and Winchester, and empties into the Mystic Lakes.

The river's 25 square mile watershed covers most of Woburn and about half of Winchester, as well as portions of the surrounding communities of Lexington, Burlington, Wilmington, Reading, Wakefield, and Stoneham.

The Aberjona River was first identified by Europeans shortly after 1631, when Captain Edward Johnson explored the area.

A 1995 study by Spliethoff and Hemond analyzed sediments of the Upper Mystic Lake with industrial records, and determined that high concentrations of arsenic, cadmium, chromium, copper, lead, and zinc were deposited by chemical and leather industries dating from the early 1900s.

In the 1995 bestseller A Civil Action (and 1998 film starring John Travolta), a 15 acres (6.1 ha) parcel of forest, field, and marshland on the banks of the Aberjona River is recalled by witnesses as the place where workers from abutting industrial plants (owned by W.R. Grace & Co. and Beatrice Foods) dumped trichloroethylene (TCE) and other toxic chemicals into trenches, or "swimming pools", "within a few inches of the water."