The marine mammal had become wedged between a rock and a pillar below the Union Street Bridge and stopped moving shortly after 5:30 p.m., CBS-TV, New York, reported.
The animal hit its head on the pillar, then stopped moving and began floating, witnesses in Brooklyn said.
"The fact that it's here by itself in this polluted water tells me it was in trouble a long time ago. It's probably sick. It's definitely disoriented," David Kirby, who studies whales and dolphins, told CBS earlier.
NYPD Deputy Commissioner Paul Browne said the Riverhead Foundation was hoping the dolphin would free itself at the evening high tide.
The Environmental Protection Agency in 2011 called the Gowanus Canal "one of the most contaminated water bodies in the nation," the TV station noted.