Flash flood warnings were in effect in parts of New York City as well as nearby Nassau County in New York State, the local NBC station reported.
Social media posts showed cars sitting in flood waters that came to the tops of the tire wheels and people attempting to walk in knee-deep water.
In upper Manhattan, eyewitness Stephen Smith was on his way home when he shot video of the flooding at an intersection next to a subway entrance. He told Reuters the flooding came suddenly and that vehicles continued to go through the intersection even though "the water was up to their headlights".
Tropical Storm Elsa weakened as it passed over northern Florida on Wednesday afternoon but it was still strong enough to warrant a tropical storm warning from the National Weather Service on Thursday for parts of the New York tri-state area for the next day or two when it could pack winds of up to 60 miles an hour (over 96 kilometers), NBC said.