The ferry will stop next to the Brooklyn Army Terminal at 58th Street in Sunset Park.
The temporary ferry, which runs weekdays from Rockaway, Queens, was started in the wake of Superstorm Sandy.
The Brooklyn stop will begin Aug. 5 as the MTA begins a projected 14-month closure of the Sandy-damaged Montague tube. The closure will disrupt R train service between the two boroughs for 65,000 riders.
Ferries that leave from Beach 108th Street and Beach Channel Drive in the Rockaways will make the Brooklyn stop before continuing to Pier 11, near the South Street Seaport, and East 34th Street in Manhattan.
A one-way trip is $2.