Atlantic Basin is Port Authority property. It is leased to the New York City Economic Development Corporation (NYCEDC). Two of the piers are operated under and NYCEDC program called DockNYC. DockNYC is operated by BillyBey, part of the NY Waterway ferry company.  The City announced plans to completely take over Atlantic Basin from the Port Authority as part of a land swap in May 14, 2024.

DockNYC controls wharfage on Pier 11 (the east face), the inshore side of Pier 12 (the cruise terminal) and Clinton Wharf (the southern face).

Multiple marine businesses have vessels docked on Pier 11. in addition to PortSide NewYork, aboard the MARY A. WHALEN, at the south end of Pier 11.  In September 2016, there were 6 commercial vessels homeported on Pier 11 representing 3 companies.  In 2024 most of those businesses and vessels are no longer there.  Plans for a second NYC Ferry homeport displaced many along the pier.   

The asphalt and sheds around Atlantic Basin are leased to multiple tenants and some subtenants.

The NYC EDC began ferry service from Atlantic Basin's Clinton Wharf in 2017 

The north face and inshore side of Pier 10 are part of the container port.