Rain has already begun falling in Queens and strong winds and quarter-sized hail may follow.
The National Weather Service issued a severe thunderstorm warning for the borough warning of heavy rain, hail, lightning strikes and gusts of winds up to 60 mph.
Up to two inches of rain per hour is expected.
The NWS issued a flash flood warning lasting until 3:15 p.m. Highways, underpasses, streets and low-lying areas are at risk of flooding.