In the mid-1950s, the Port of New York Authority (PA) prepared a transportation master plan that proposed the development of six new heliports in the metropolitan area, including one at the southern tip of Manhattan near The Battery or Wall Street.

[3][4][5] The PA opened the West 30th Street Heliport in 1956 (one of the locations identified in the master plan) and New York Airways began operating helicopter shuttle service between that heliport and area airports, but passenger demand was much lower than projected and thought to be a result of competition by other forms of ground transportation.

It was believed that a helicopter landing pad in Lower Manhattan would attract more passenger demand, which led to the PA to study the feasibility of a new heliport.

[13] When the airline resumed operations in Lower Manhattan in April 1978, it did so at a temporary heliport built on landfill in Battery Park City.

[22] Although the PA's lease with the city covered an area of approximately 8 acres (3.2 ha) and allowed for significant expansion of the heliport's operational area, the replacement pier was built to the same dimensions as the old pier and a barge was added to provide parking for helicopters (considered to be an anchored floating structure), which avoided the need for the preparation of a lengthy environmental assessment.

[23] As part of the project, tests were made using a Microwave Landing System (MLS) at the Battery Park City Heliport and at a pier near Wall Street.

[24] Plans to install a permanent MLS were abandoned when the site in Red Hook, Brooklyn on which the transmitter was to be located was put up for sale by the PA.[25] A semi-automatic fire protection foam system was installed that provided full coverage of the pier and could be remotely operated from the terminal; it was the first public heliport to include such a system.

[29][31][32] After the new facility opened, the PA experienced a problem with seagulls dropping clams onto the heliport to break open the shells and feared that the birds could get caught in helicopter rotors and bring aircraft down or the contents of the clam shells on surfaces could cause helicopters' landing gear to skid or passengers to slip and fall.

The new operator was also required to implement a refueling system available for helicopters using the facility; previously the heliport did not have any fuel services.

[48] The change in the heliport's operator resulted in a five-month suspension of US Helicopter's scheduled flights from the Downtown Manhattan Heliport to EWR and JFK because FirstFlight did obtain approval from TSA for a passenger security screening plan and then demanded higher rent from US Helicopter after a security plan was approved.

[51][52] Traffic at the Downtown Manhattan Heliport increased to 58,021 total flights in 2014; the New York City Economic Development Corporation (NYCEDC) estimated that over 56,000 of these were sightseeing trips.

[52][54][55] As a result of the agreement, the Downtown Manhattan Heliport is now capped at accommodating a maximum of 29,651 tourist flights per year.

[56] To protect Lower Manhattan from future flooding associated with coastal storms and projected sea level rise, NYCEDC and the Mayor's Office of Climate Resiliency commissioned the preparation of a master plan for climate resilience in the Financial District and Seaport areas.

The plan was released in 2021 and included strategies to rebuild the East River waterfront from The Battery to the Brooklyn Bridge such as the addition of a floodwall.

[57] The master plan projected that the existing deck of the Downtown Manhattan Heliport would be flooded on a monthly basis by the 2050s and proposed for a replacement heliport to be built at a higher elevation near its existing site with access the pier for emergency and service vehicles provided via a flood gate.

In the year ending December 30, 2003, the airport had 10,002 aircraft operations, an average of 27 per day: 90% general aviation and 10% military.