Bands of rain -- some of them heavy -- will be affecting the area overnight Monday and later Tuesday, according to the National Weather Service.
"We can expect this to continue for the next several hours," said David Stark, a meteorologist with the National Weather Service in Upton said at about 9:30 p.m. Monday.
"Rain is moving to the east and it looks like portions of eastern Suffolk will see some of this activity. There will be moderate to heavy rain at least until midnight," he said.
He said the rain will taper off and then pick up again Tuesday afternoon or early evening.
An incoming cold front coupled with a lingering surface trough is the culprit, said Tim Morrin, a meteorologist for the weather service.
"The atmosphere is so moist and humid these showers could pop up randomly and dump lots of rain in one area in a short period of time," Morrin said.
That scenario is why the service also issued a flash flood watch through 6 a.m. Wednesday for Nassau and Suffolk counties.
The chance of rain is 60 percent to 70 percent in most areas through Tuesday night, dropping to between 30 percent and 60 percent through Wednesday morning.
Conditions could produce " total rainfall between 2 to 3 inches," the weather service said in a statement. "Locally higher amounts can be expected. This will increase the flash flood potential."
Clearing is likely to begin Wednesday in the afternoon, as high pressure builds and produces a stretch of cooler, drier conditions, the service said.
Daily highs in the mid-70s and lows in the high 60s are likely from Wednesday and continuing into the weekend, the service said.