A tornado watch is in effect until 9 p.m. Friday for coastal waters from Montauk to Martha's Vineyard, the weather service says.
A flash-flood warning for Suffolk County also has expired, according to the National Weather Service. About 2:45 p.m., doppler radar had shown rainfall of 1 to 2 inches an hour, which the service said could lead to flash flooding on roads.
As storms hit the Island, numerous calls came in, mostly related to flooded conditions at numerous intersections, said Nassau County police, who also got a report of a tree falling into a house at Luddington Road and Preston Road in East Meadow.
A flood advisory, since canceled, had been issued earlier for Suffolk and Nassau counties.
And two earlier tornado warnings, also no longer in effect, had been issued for Suffolk County.
Thunderstorms and isolated showers began early Friday that were forecast to bring severe thunderstorms with damaging winds, the National Weather Service said.
The Upton-based service had predicted rain for most of Nassau and Suffolk counties beginning noon Friday through early Saturday morning. New rainfall amounts could range between one-quarter inch to one-half inch, the service said.
As of early Friday afternoon, storms were affecting airport traffic with arrivals at LaGuardia delayed an average of 2 hours, 49 minutes, with departures held up about 1 hour, 45 minutes to 2 hours, according to the Federal Aviation Administration.
Arrivals at JFK were delayed an average 2 hours, 25 minutes, the FAA said, with departures held up an average 2 hours to 2 hours, 15 minutes.
Long Island MacArthur Airport reported delays of about 1 hour and a half to close to four hours on departures to nearby airports, the FAA said.
Strong to severe thunderstorms are possible Friday night, the service said in a hazardous weather outlook for the first part of the weekend. Among the main threats is damaging winds, said David Stark, a meteorologist with the service.
Stark said if storms are severe, wind gusts could range from 35 mph to 58 mph. He said the chance of such winds are small, and most forecasts for the weekend call for winds between 10 mph and 15 mph.
"If we do get a severe storm, winds could be a lot higher than that," Stark said. "Right now, we're calling for the rain, realizing there is a possibility of severe storms."
The wet weather is the result of a low pressure system from the Great Lakes moving east and a cold front across eastern Pennsylvania and upstate New York, Stark said. Those two systems are luring moisture from the South.
The worst of the storms should end early Friday night, with some isolated showers falling overnight into Saturday, Stark said.
On Saturday, showers are likely, with chance of precipitation at 60 percent to 70 percent in the morning to 40 percent at night.
Temperatures call for highs in the low 80s, nighttime lows in the 70s with high humidity, Stark said.
By Sunday morning, most of the stormy weather will be pushed northward and out to sea, Stark said.
Also moving out with the storms will be the humidity. Sunday's high temperature is expected to be in the mid to high 80s, with low humidity and sunny skies, Stark said.