The water in the Hudson River Park Estuarine Sanctuary currently supports a wide range of in-water activities including the operation of large commercial and military vessels, ferries, historic ships, recreational motorized boating, non-motorized boating, fishing, habitat pile fields (Piers 32, 34, 42, 46, 49, and 72), and natural habitats. The Estuarine Sanctuary Management Plan clustered similar water uses for appropriate locations, management efficiency, and resource protection. The four water use categories are shown on the Water Use Restriction Map as water play (31%), motorized boats (45%), reserve (15%), and economic development (9%).

The water play category allows non-motorized interaction with the Hudson River in areas of expansive Park waterfront. Most motorized areas serve small to medium recreational powerboats while some delineate passenger ship terminals and wharves. Marine Reserves include significant areas of marine and benthic habitat. Non-motorized boating is currently permitted in most of the reserves. Economic Development areas often surround privately owned piers or piers managed by other public agencies (Piers 78, 79, 88, 90, 92 and 94). HRPT may restrict access to portions of the Sanctuary for emergencies, dangerous conditions, events, or degradation of resources.