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Although the overall form of the estuary remains unchanged from the time of Giovanni da Verrazzano's visit in 1524, no part of it remains unaffected by human activity, and some parts, such as Hell Gate and Ellis Island, have been almost completely altered. In the greatest hidden change, the navigational channels have been deepened from the natural 17 feet (5.2 m) depth to 45 feet (14 m), in some places requiring blasting of bedrock.
There is an extremely complex system of tides and currents. Both the Bight and the Sound are essentially marine bodies with both tides and saltwater, but the Sound compared to the Atlantic is about 20-30% less saline (as an estuary), and the tide is about 3 hours later with as much as 70% more variation. Rivers add a fresher, non-tidal inflow although the tide and brackishness extend well up rivers  throughout the extended hydrologic system from Albany to Montauk Point to the Hudson Canyon region of the New York Bight. The New York Harbor Observing and Prediction System (NYHOPS) utilizes information from sensors, weather forecasts, and environment models to provide real-time forecasts of meteorological and oceanographic conditions in the area.
The lists below includes features of the Port of New York and New Jersey with a waterborne emphasis, starting with natural features. Where possible the list proceeds from the Lower Bay entrance approximately clockwise around the Harbor. The alternative sorting is by jurisdiction.
Ellis Island--All of the landfill portion of Ellis Island beyond its 1834 waterfront is in Jersey City, New Jersey, as is all water surrounding Liberty and Ellis Islands. The original island is an exclave in New York State.
^NOAA Tides and Current web site FAQ page. See discussion of hydraulic currents 
^Muka, Samantha (August 11, 2015). "Building Beaches: Beach Nourishment in the United States". Retrieved 2017. New York State has the longest history of nourishment in the country. The first beach nourishment project was the construction and expansion of the shoreline off of Coney Island and Brighton Beach.
^Reports of Channel ConditionsArchived 2008-10-29 at the Wayback Machine., USACE, Nov. 2004: "Partial Anchorage Channel: Starts approximately 3,990 Ft. seaward of Red Gas #2; Ends approximately 1,660 Ft. landward of Red Light & Bell #21. Authorized project: Width: 2000 ft, Length: 2.34 nmiles, Depth 45 ft.... Shoaling exists and begins approximately 2,230 Ft. seaward of Red Gas #2 and proceeds landward with a length of approximately 600 Ft. and a width of approximately 60 Ft."
^Boundaries extend to mid-Hudson on the west, into the Upper Harbor south of Governors Island, to the far pierhead line of the East River, Harlem River and Spuyten Duyvil. The exceptions are the additional areas of Marble Hill section included north of the Harlem River (bounded approximately by Johnson Avenue, West 230 Street) and Liberty and Ellis Islands to their original 1834 waterfront. River