The train connects Long Island City in Queens with the Greenpoint section of Brooklyn.
It was flooded with three million gallons of salt water during the storm.
It was one of nine tunnels flooded during the storm.
Repairs will cause G train subway service to be disrupted for the next 12 weekends.
For riders, that means finding alternative routes.
Greenpoint Avenue, 21st Street and Court Square stations will be closed, beginning this weekend. Shuttle bus service will be provided.
The weekend closures will be in effect from 12:01 a.m. Saturday through 5 a.m. Monday.
Trains will run between Nassau Avenue and Church Avenue only.