The main stem empties into Penobscot Bay near the town of Bucksport. The river's total fall from Penobscot Lake on the South Branch is 1,602 feet. The river's West Branch from Ripogenus Dam to the Pemadumcook Lakes is famous for its numerous falls and rapids which provide outstanding whitewater rafting and angling for wild landlocked Atlantic salmon. Like all of New England's major rivers, the Penobscot has been grossly polluted with untreated industrial and municipal waste for most of the 20th century. Water quality on the main-stem and lower tributaries has improved markedly since the 1970s.
Terrain ranges from steep mountains including Maine's highest, Mt.
Katahdin, rolling hills and extensive bogs, marshes and wooded swamps. Most of the watershed is forested, intensively harvested for pulp and saw logs and sparsely settled. The only major urban area in the watershed is the riverfront cities of Bangor and Brewer. Paper mills are located on West Branch at Millinocket and East Millinocket, and on the main-stem at Lincoln, Old Town, Brewer and Bucksport. The Penobscot is home to many fish, including native brook trout, landlocked salmon, smallmouth bass, white perch and chain pickerel are prevalent resident species.