Before the Whitehall Terminal was built, ferry service in New York Harbor was provided as early as the 1700s by individuals (and later private companies) with their own boats.

[6] The B&O refused to sell their terminals to the city, prompting municipal officials to announce in 1904 that they would acquire the sites through eminent domain.

[37] In 1951, Manhattan borough president Robert F. Wagner Jr. asked the New York City Planning Commission to provide $132,000 for a footbridge between the terminal and Battery Park, crossing over West Street.

[42][44] The Department of Marine and Aviation's ferry bureau, which had been housed on Whitehall Terminal's upper stories, relocated to St. George in January 1954.

The New York Times described it as a "squat, washed-out green hulk in which function vanquished form"; the American Institute of Architects called it "the world's most banal portal of joy.

"[52][14] The Whitehall Terminal's renovation was the first part of urban planner Robert Moses's proposal to redevelop the area around South Ferry.

[53] The NYCTA decided in early 1959 to overhaul the adjacent South Ferry subway station, adding a wide stairway that connected with one of the terminal's entrance ramps.

[58] In January 1980, city officials began adding elevators and escalators to the Whitehall Terminal as part of a $5.75 million modernization program for the Staten Island Ferry.

[62] The city government announced plans in 1985 to sell the Whitehall Terminal as part of the South Ferry Plaza project.

[63][64] The Whitehall Terminal would be replaced, and the developer would restore the adjacent Battery Maritime Building, an official city landmark that could not be demolished.

[76] South Ferry Plaza was canceled in January 1991 due to a decline in the real estate market,[77] and the terminal's renovation was delayed as a result.

[85] The EDC selected six finalists that August:[84][86] Venturi Scott Brown, Rafael Vinoly, Aldo Rossi, Polshek Partnership, Hardy Holzman Pfeiffer Associates and Skidmore, Owings & Merrill.

[86][87] The next month, city officials also announced that they would permanently ban vehicles from the Staten Island Ferry to reduce vehicular congestion at the rebuilt terminal.

[92][93][94] The winning design featured a barrel-vaulted waiting room similar in size to Grand Central Terminal's Main Concourse.

[92][93] The Journal of the American Institute of Architects wrote: "The facades on the east, west, and north are almost Miesian in character, but are more utilitarian than elegant.

[95] After Rudy Giuliani won the 1993 New York City mayoral election, he reversed the decision to ban cars from the rebuilt Whitehall Terminal,[100][101] which not only raised the cost by $500,000[101] but also delayed the project by about six months.

[106] Venturi Scott Brown subsequently redesigned the terminal, removing the planned clock and adding windows facing Lower Manhattan and a large indoor LED display.

[95][107] In mid-1995, Venturi Scott Brown presented a revised proposal, which was publicly nicknamed the "zipper" because the plan included an electronic sign along New York Harbor.

[108] Venturi Scott Brown left the project in late 1996 after the city government downsized the design to a simple steel-and-glass facade, in an attempt to reduce the terminal's cost by $30 million.

[107] It includes access to the New York City Subway's South Ferry/Whitehall Street station, served by the 1​, N, ​R, and ​W trains, as well as bus services at Peter Minuit Plaza.

[150] Access to bicycle lanes and other water transport, including the Governors Island ferry at the neighboring Battery Maritime Building, is also available.

[153] Justin Davidson wrote for Newsday that the hub was "an elegant addition to [the] city's architecture" and a destination in its own right, saying: "The panorama of lower Manhattan from the top of the escalators, the vast windows framing the Statue of Liberty, the upstairs deck with views of the harbor – these are reasons to take shelter here for a little longer than the ferry schedule makes strictly necessary.

"[154] According to Contract magazine, the terminal was intended as a "destination spot where visitors can sit outside, have lunch, and take in the views of the Statue of Liberty and the Brooklyn Bridge".

[159] The terminal has a technologically advanced heating and air conditioning system, partially powered by solar panels that overhang the observation deck.

The terminal building has a glass curtain wall on three of its sides, which is supported on steel columns measuring 21 inches (530 mm) deep.

[119]As part of the Percent for Art initiative, the city's Department of Cultural Affairs[161] purchased and installed sculptured granite benches created by artist Ming Fay, entitled Whitehall Crossing, in the waiting room.

[162] The installation includes a series of twenty-eight granite benches divided into three serpentine rows, suggesting the carved seats of a "floating, organic form over a water theme terrazzo floor.

[163]In parallel with the construction of the new terminal, Peter Minuit Plaza was completely reconfigured to provide easy accommodation for pedestrians, buses, and taxis.

[137][138] The plaza includes the "New Amsterdam Plein and Pavilion" (a gift from the Kingdom of the Netherlands), an area to showcase art, design, and horticulture.

[164] This area was conceived as an "outdoor living room" where scheduled and spontaneous activities can take place alongside public markets and a state of the art food and information pavilion.