The National Weather Service has placed Rockland, Putnam and northern Westchester towns under a flood watch until noon Wednesday.
It says flooding along major parkways and low-lying areas would affect the morning commute.
According to the Journal News, Westchester police reported numerous closures along the Bronx River, Hutchinson River, Saw Mill River and Cross County parkways early Wednesday morning.
In Rockland County, Route 303 was closed between Bradley Hill Road in Orangetown and West Nyack.
While no flood advisory was issued for southern Westchester, the weather service said low-lying and poor drainage areas could experience flooding due to the heavy rain.
Rain was to continue on and off on Wednesday.