An earlier water main break snarled service along the line while crews worked to repair it.
Department of Environmental Protection crews responded to the area of 159th Avenue and Coleman Square to find the water main break just before 7 a.m.
The MTA suspended Far Rockaway-bound A train service at the station.
Shuttle buses were made available between the station and Aqueduct North Conduit Avenue.
Customers also had the option to Broad Channel and switch to the other side to take a northbound train, which was still making stops at Howard Beach.
The Port Authority says Kennedy Airport's Airtrain was not been interrupted.
Meanwhile, crews continue to pump water and remove debris from the site in order to access the water main break.
Water on-the-go drinking fountains are being set up in the area so impacted residents and businesses have access to drinking water as repair work continues
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