The 12-inch main broke around 3:30 p.m. at 156 Montague Street in Brooklyn Heights.
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The water flowed into the Court Street subway station, causing R trains to skip Court Street in both directions.
Q trains are also delayed.
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Commuters can use the B26, B38 or B52 bus service as an alternative.
Once the water is drained, MTA officials said they will inspect the infrastructure.
A DEP crew shut off the main and stopped the leak just after 4:30 p.m., and repair work is ongoing.
About 100 customers and 25 businesses are without water service until repairs are completed. Water is expected to be restored by Friday.
Several businesses in the area had flooding in basement.