By nightfall, the animal was clearly in trouble, then quickly died, NY1 and CBS television reported.
"Myself & an ecologist were there at the moment the dolphin died. He cried out. Lifeless breached on concrete piling. Police put up tape," tweeted witness Aaron Stewart-Ahn.
The US Environmental Protection Agency calls the Gowanus Canal "one of the nation's most extensively contaminated water bodies," and cites coal tar, heavy metals and the results of "years of discharges, storm water runoff, sewer outflows and industrial pollutants."
The canal was named a Superfund site in 2010, meaning that federal funds will be available for a cleanup.
In December, a large whale was discovered washed up on a New York beach, still alive, but fatally ill.