National Disaster Management Authority (NDMA) also issued a flash flood warning in the hilly areas.
Periods of heavy rain will be possible tonight into early Thursday.
According to the Associated Press, heavy thunderstorms are flooding roads in southern Wisconsin have caused Amtrak to suspend service between Milwaukee and Chicago. Buffalo received 2.29 inches, enough to break the July 13 record of 1.86 inches, set in 1956.
Today's sunrise is at 6:09 a.m., and today's sunset is at 9:09 p.m.
The Kane County Sheriff's office said it was responding to numerous reports of abandoned vehicles in the north Starks area.
Areas expected to experience flooding include Batavia, along with the Thruway between exits 53 and 46, and Route 390 between exits 8 and 12. Do not attempt to travel across flooded roads.
By 4 a.m., rainfall estimates totaled anywhere from three to 5 inches across the area.
Flash flooding of urban areas, particularly viaducts and underpasses, will be possible.
A flash flood watch continues for much of western and central NY into this afternoon.
There's a chance of showers, and possibly an afternoon thunderstorm, again on Friday, although the temperature will cooler, dropping into the low 70s, the weather service said.
A flash food watch means that conditions may develop that lead to flash flooding.