While the dolphin was churning up sediment and mud, it's unclear whether that contributed to its death, DiGiovanni said.
The dolphin, which appeared to be about 7 feet long, likely entered the canal from the Atlantic Ocean through the Lower and Upper New York Bays and then the Gowanus Bay, which leads to the canal. It's about 20 miles from the canal to open ocean.
Experts don't know why the dolphin wandered into the canal, but in general that can happen when one gets sick or disoriented, DiGiovanni said.
It's not uncommon for sea creatures to stray into city waters, though they don't often swim away alive.
A dolphin was found dead last August near Long Island, south of the canal. Another washed up in June in the Hudson River near Manhattan's Chelsea Piers sports complex.
In 2007, a baby minke whale that briefly captivated the city wandered into the Gowanus Bay and swam aimlessly before dying. Two years later, a 20-foot-long humpback whale took a tour of the city's waters before leaving New York Harbor safely.
AP Radio reporter Jackie Quinn in Washington contributed to this report.