Amtrak announced Saturday afternoon that service was restored between New York and Albany following an earlier suspension.
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Metro-North train traffic is stopped between Croton-Harmon and Poughkeepsie station due to the weather conditions.
The flooding also impacted Metro-North travelers, as Hudson Line trains are not running between Garrison and Beacon.
This disruption comes as a result of severe weather conditions after Friday night's round of rain.
The low-pressure system drenched the Tri-State region with heavy rainfall and gusty winds well into early Saturday morning, leaving some areas impacted by high tides.
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Over in Queens, streets turned into rivers in areas like Old Howard Beach, where overflowing water filled out neighborhoods Saturday morning.
Drone footage released by NYPD showed flooding had also reached parts of Far Rockaway.
Flood watches and warnings were issued for parts of New York and New Jersey ahead of the rainfall just days after a winter storm spawned the same issues on Tuesday causing downed trees and powerlines in some parts of the Tri-State area.