It is 16.1 mi long, and the river flows northwards from a point approximately 1.8 mi south of the Durham line in Guilford, Connecticut, into Durham and then Middlefield, meeting the Mattabesset in Middletown,[1] about 0.8 miles (1.3 km) upstream[2] of the Connecticut River.

In 2006, the Coginchaug was among Connecticut's 85 waterways cited to be of "lower quality", in view of the elevated levels of bacteria, including E. coli.

Currently, efforts are being made by the Natural Resources Conservation Service of the United States Department of Agriculture to reduce the number of bacteria introduced into the river from untreated sewage, sanitary sewer overflow, agricultural runoff, leaking septic tanks, etc.

Flowing from Myer Huber Pond, it runs slowly through thick swamps which stretch over 3 miles (5 km) and are likely to be impassable except immediately after heavy rains.

There are many[vague] portages, including those at six dams and at Wadsworth Falls, the only major waterfall.