The Plume and Atwood Dam in Thomaston, completed in 1960 following the Great Flood of 1955, creates a reservoir on the river and is the last barrier to salmon and trout migrating up from the sea.

[6] Various Algonquian bands, often included in the Wappinger tribe, originally inhabited the Naugatuck River Valley.

Given its rocky soil, which was not good for farming, and the high potential for water power, the Naugatuck Valley became an industrialized area in the 19th century.

After winding through rural forested areas, the two branches of the Naugatuck River enter downtown Torrington and join just north of East Albert Street at about 530 feet (160 m) above sea level.

However, occasional sewage spills continued to occur, and a 2017 study identified the presence of phthalates in the river.

The Connecticut Department of Environmental Protection stocks the river with broodstock Atlantic Salmon between Route 118 in Harwinton/Litchfield and the Thomaston Dam, and from southern Naugatuck to Beacon Falls.

It is considered a "trophy trout stream" the rest of its length between the confluence of the East and West Branches and the Kinneytown Dam in Seymour.