MTA operates the following subway trains across the Manhattan Bridge:
- B Sixth Avenue Express on weekdays only, at all times except late nights.
- D Sixth Avenue Express at all times.
- N Broadway Express at all times except late nights.
- Q Second Avenue/Broadway Express/Brighton Local at all times.
For B and D trains, the stops on either side of the Manhattan Bridge are Grand Street in Manhattan, and DeKalb Avenue on the Brooklyn side.
For N and Q trains crossing the bridge, the first Manhattan stop is Canal Street. On the Brooklyn side, Q trains stop at DeKalb Avenue, while most N trains bypass DeKalb Avenue and stop at Atlantic Avenue-Barclays Center.