In its natural state, it also drained Allagash, Chamberlain, and Telos lakes, but in the 1840s dams were built which diverted their drainage into the East Branch of the Penobscot River, to facilitate the shipping of logs south to coastal Maine.

In 1857 Henry David Thoreau, along with his Concord friend Edward S. Hoar and Penobscot guide Joseph Polis, made a canoe journey which led him to the source of the river, i.e. Heron Lake.

His account of the excursion called "The Allegash and East Branch" was published posthumously as the third chapter of The Maine Woods (1864).

In 1970 the waterway became part of the National Wild and Scenic River program of the U.S. federal government.

The expansion of recreational access to the river through new roads and docks has remained a controversial topic in recent years.