The Downtown and Waterfront Development Office is tasked with managing projects to develop the downtown and waterfront areas of the Port of Yonkers. It facilitates, designs, and builds, development projects for the Port of Yonkers's Department of Planning and Development.

Opened in the Port of Yonkers in 2007, the John F. Kennedy Marina Picnic and Launch issues permits through the Department of Parks, Recreation, and Conservation for the launch of canoes and kayaks, jet skis, and motorized boats. Both day passes and annual permits are available. Overlooking the Hudson River, the Pavillion is available for group functions. Boaters can dock at the Port of Yonkers Recreation Pier at the foot of Main Street.

The Port of Yonkers is a natural river harbor on the Hudson that can accommodate vessels up to 152.4 meters (500 feet) in length. The harbor offers excellent shelter and has anchorage depth of from 9.4 to ten meters (30.8 to 32.8 feet). The Cargo Pier in the Port of Yonkers has alongside depths from 4.9 to 6.1 meters (16 to 20 feet). The Port of Yonkers's Oil Terminal has depths from 7.1 to 9.1 meters (23.3 to 29.9 feet).

The Altman Stage Lighting Company owns, and the Hudson River Pilots Association operates the Station Dock in the Port of Yonkers to board and discharge Hudson River Pilots. At the rear of the dock is the Hudson River Pilots Association Station Office. This Port of Yonkers dock has berthing distance of 9.1 meters (30 feet) with alongside depth of 2.4 meters (eight feet). The second berth is 38.1 meters (125 feet) long with alongside depths of 2.4 and 6.1 meters (eight and 20 feet).

A Tarricone owns and operates the Port of Yonkers Terminal No. 1 Wharf to receive petroleum products by barge. The wharf has berthing distance of 91.4 meters (300 feet) with alongside depth of 4.3 meters (14 feet). Pipelines connect the wharf to 11 steel storage tanks with total capacity for 111.9 thousand barrels at the terminal.

Refined Sugars Inc. owns and operates the Port of Yonkers Wharves to receive raw sugar by vessel and to occasionally moor tugs. Storage buildings at the rear of the wharf can accommodate 20 thousand tons of raw sugar, and one surface rail track serves the plant and connects to the Consolidated Rail Corporation (CONRAIL). The wharves have berthing distance of 182.9 and 61 meters (600 and 200 feet) with alongside depths of 7.6, 8.5, and 9.1 meters (25, 28, and 30 feet).

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