NJ Transit's option to obtain the route was acquired during the planning agreement that set the route for the Hudson-Bergen light rail line. Conrail is now moving to formally abandon the River Line south of the Weehawken Tunnel so that the next phase of the light rail can proceed.  Under the planning agreement, this abandonment triggers NJTransit's option to purchase the Bergen Arches right-of-way.

With the Hudson-Bergen line now operating through Bayonne and Jersey City on other routes, it is unclear what NJ Transit might do with the Bergen Arches right-of-way.

A troubling scenario would be a transfer of the corridor from Transit to its parent agency, NJDOT, for highway development. Jersey City mayor and gubernatorial candidate Brett Schundler wants a highway connection through the Arches to provide additional car access from the Turnpike to Jersey City's waterfront and the Holland Tunnel. An NJDOT study is looking at this and other scenarios, including passenger and freight rail use of the corridor.

CSX and Norfolk Southern railroads have said that the potential for a freight traffic boom in the NY/NJ port area, including development of the Bayonne military ocean terminal into a deep water container port, could lead to conditions where the Bergen Arches could provide needed rail freight capacity.