A flood watch is in effect through this evening for Putnam and Rockland counties.
In Westchester, a flood warning is in effect until 10 p.m. due to flooding of roadways and rivers reaching flood levels.
The New York Thruway authority says Exit 8 on the Cross Westchester Expressway is temporarily closed because of flooding.
The National Weather Service has also issued a high surf advisory until 9 p.m. Thursday. That means that dangerous rip currents are possible at ocean beaches.
The weather service says two to three inches of rain fell on New York City and its suburbs overnight, continuing throughout the morning. The rain is expected to taper off by the afternoon., but more rain moves in again Friday night.
The rain is threatening new flooding in neighborhoods that were underwater after Tropical Storm Irene, that have had only a few days to dry out.