The Black River originates at North Lake in the foothills of the Adirondacks, in Herkimer County, about east of Boonville. The river flows west into Oneida County then north, past Forestport and Boonville into Lewis County. At Lyons Falls, it is joined by the Moose River from the east just above the eponymous waterfall, where the river drops over a gneiss cliff. Near Glenfield the Black River receives the smaller tributaries of Otter Creek and the Independence River, also from the east. Further north, it passes Lowville, then receives the Beaver River from the east, then the Deer River, its only major western tributary. Starting above Carthage the river briefly divides Lewis and Jefferson Counties before crossing entirely into Jefferson County, where it turns sharply west toward Lake Ontario, flowing past Great Bend, Black River and Watertown. Below Watertown it enters a canyon, well known for its challenging rapids.
The river ends at Lake Ontario in the village of Dexter, about west of Watertown, where it empties into the Black River Bay and Marsh, which are parts of the Golden Crescent. For the last few miles it forms the boundary between the Towns of Brownville and Hounsfield.
Dams
There are at least 17 dams on the Black River, with eight in the upper part above Lyons Falls, and nine below Watertown. The upper and lower reaches of the river have a steep gradient and were originally developed to provide mechanical power for mills, such as the old Georgia-Pacific paper mill in Lyons Falls, and later hydroelectricity. In contrast the middle of the river have practically no gradient and are not suitable to the development of head for industrial or hydropower projects. The three uppermost dams, forming North Lake, Kayuta Lake and the smaller Forestport Reservoir are the only structures forming significant impoundments. The other dams are run-of-the-river, with no appreciable storage capacity, so power generation is entirely dependent on the natural flow of the river combined with releases from upstream reservoirs, which is relatively consistent except for drought years.
Sporting activities
The river is an excellent location for fishing. Abundant trout, salmon, bass, and pike are present in the stream, and salmon is the most favored. Whitewater rafting and kayaking are popular on some stretches of the river, notably the Black River Canyon, which begins in Watertown and ends in Brownville. The Black River Canyon is one of few whitewater streams which have reliable flows throughout the summer. The "Canyon" itself is not actually present until you reach Brownville and ends in the Dexter Reservoir.
Environmental issues
A number of streams and lakes in the watershed have been impaired as a result of acid rain. Elevated levels of mercury have led to restrictions on the consumption of fish in some areas. In August 2005, the Black River was contaminated by a spill from a manure lagoon on Marks Dairy Farm when a retaining wall gave way, allowing the contents of a waste holding pond to spill. About of pollution flowed into the river. An estimated 280,000 to 375,000 fish were killed. As of August 3, 2006 a settlement has been reached and Marks Dairy Farm, originator of the spill, was ordered to pay $2.2 million.
