Since mid-November 2008, it has been owned by the Port Authority of New York and New Jersey, which acquired it for about $16 million as a step in a process that might see a Cross-Harbor Rail Tunnel completed.

Since freight trains are not allowed in Amtrak's North River Tunnels, and the Poughkeepsie Bridge was closed in 1974, the ferry is the only freight crossing of the Hudson River south of the Alfred H. Smith Memorial Bridge, 140 miles (230 km) to the north of New York City, in a process known as the Selkirk hurdle.

On the Bay Ridge, Brooklyn end, the 6-acre (2.4 ha) 65th Street Yard connect to the Long Island Rail Road's freight-only Bay Ridge Branch, which is operated by the New York and Atlantic Railway, and the New York City Transit Authority's South Brooklyn Railway.

The Port Authority began working with government agencies in New York and New Jersey to bring NYNJ to a state of good repair.

[11] In May 2010 the Port Authority announced that it would purchase Greenville Yard and build a new barge-to-rail facility there, as well as improving the existing rail car float system.

[16] The railroad north along First Avenue was refurbished and new tracks laid to support operations at the South Brooklyn Marine Terminal, including an automobile import pier and a new municipal recycling plant.

[17] On October 29, 2012 Hurricane Sandy caused major damage to the Greenville facility, undermining the transfer bridge gantries and sinking one of the car floats.

Built by Metal Trades, Inc., the four-track barge can carry up to 18 rail cars of 60-foot (18 m) length, with up to 2,298 long tons (2,335 tonne) of cargo.

[24] In July 2017, the Port Authority announced a $35 million study to build a Cross-Harbor Rail Tunnel, suitable for freight.