Colchester police said they received a call around 3:25 p.m. reporting that human remains were seen off the shore of Colchester Point Road.
Responding officers found the skeletal remains approximately six feet from shore, police said, and the department's marine unit was called to the scene to recover them.
The body was taken to the chief medical examiner's office for identification and autopsy.
Crews from across New England have been assisting Vermont following severe flooding this week.
Police said foul play is not indicated at this time, though noted it is early in their investigation. No other information was immediately available.
Recovery efforts have remained underway in Vermont following the intense storms that brought torrential rain to the area last week, and there was more precipitation Sunday, with additional flash flood warnings in the state.