The boat basin, first proposed in 1924, was constructed in 1937, during the tenure of Robert Moses as Parks Commissioner, to offer a place for boats to dock during the summer. It was built as part of a project to cover over the tracks of the New York Central Railroad's West Side Line which also included a grand architectural multi-level entry and exit from the Henry Hudson Parkway, all under the name of the "79th Street Grade Crossing Elimination Structure". The multi-level structure was designed by Gilmore David Clarke. The Works Projects Administration provided $5.1 million for the project, which created the Freedom Tunnel, an underground parking garage, a restaurant, and the marina. By the 1960s, though the restaurant was long gone, the majority of slips were occupied by year-round boaters.
In 1979, the city sought to cancel a 1977 concession agreement with Nichols Yacht Yards to operate the marina, claiming that Nichols had underreported revenue and had acted as an "absentee slumlord". Boat owners would manage the marina until a suitable operator would be found. Though Nichols obtained an injunction blocking the dismissal in December 1979, the firm's operation of the facility ended in 1982, with Nichols having spent $250,000 in legal fees to battle the city and counter a rent strike by boat owners.
In 1992, a five-year agreement was signed with boaters and the city, tying increases of nearly 25% in docking fees to improvements in facilities at the marina, such as new docks and electrical lines. By 1996, year-round residents had complained that the 18-month-long project, implemented at a cost of $1.4 million, had been done in shoddy fashion.
The city stopped issuing new year-round permits in 1994, seeking to make space available for seasonal boaters among the basin's 116 slips. After complaints were received, the Parks Department agreed to an increase to 52 year-round spots, which start at a yearly fee of $5,000, based on the size of the boat. By May 2009, the Department was to require that all boats be seaworthy. As of February 2008, there were 19 boats that were considered unseaworthy and that would need to make operational "in case of an emergency evacuation".
Year-round residents have included Mad Magazine writer Dick DeBartolo who uses a boat as his office. Mario Puzo and Frank Sinatra have all used the basin to moor their boats. In the 1960s, Roy Cohn docked his 95-foot (29 m) yacht here, and used it to entertain the city's political leaders.
By summer 2012, several boaters noticed that the basin was in a state of disrepair and asked the city to fix it.
Rules and regulations covering the 79th Street Boat Basin also apply at the Sheepshead Bay Piers and the World's Fair Marina.
The Boat Basin is also used as a launch site for kayaks, canoes and sailboats. The Hudson River sloop Clearwater often docks here, as part of its mission of informing the public about environmental and pollution issues in the Hudson River. As of May 2012, seasonal docking fees are $120 per linear foot (or a minimum of $3,000) for the summer (May 1 to October 31) and $105 per linear foot (or a minimum of $2,625) during the winter (November 1 to April 30). Total dock fee revenue was over $240,000 in 2007, with more revenue taken in from the higher fees paid for part-time boaters. As of February 2008, there was a waiting list of 450 boaters seeking part-time docking privileges during the summer. Fees were raised again in December 2011.
The granite and fieldstone open rotunda surrounded by a vaulted Guastavino tiled arcade overlooks the marina, and is the site of the open-air O’Neals’ West 79th Street Boat Basin Café. A boat pump-out system connects directly to boats to allow for sewage disposal. Along with a fresh-water line system, the service is provided at no additional cost by the Parks Department. All other services, including electricity, telephone, television, and Internet access, must be paid for by boat owners, individually.
The 79th Street Rotunda, planned and built by former New York City Parks Department Commissioner Robert Moses during the West Side Highway's conversion into a parkway, is a traffic circle that sits next to the boat basin. between the Hudson River and the Henry Hudson Parkway at the western edge of 79th Street. There are two ways to access the site by foot: one way is to walk along Riverside Park, and the other is to walk west on 79th Street. Drivers briefly drive atop the rotunda’s traffic circle as they exit the Henry Hudson Parkway or enter the Parkway from 79th Street. The rotunda's interior, open-air courtyard is able to block noise and views of the highway, while blocking noise and views of the highway for the park and boat marina below. Moses viewed the project with grand monumentality, while believing it would add to the grandeur and allure of New York City as viewed from across the Hudson River from New Jersey’s Hudson River Palisades. The Rotunda was a core part of the project.
The Riverside Park runs through the boat basin and rotunda. The 79th Street Rotunda was built to allow easy access and exit to and from the Henry Hudson Highway. Additionally, it provided for safe transit of electrically powered trains into Manhattan by covering the electrified West Side Line railway tracks in a tunnel now called the Freedom Tunnel. It also provides an internal, sheltered parking garage for boat basin users. The internal courtyard and seasonal café were built after the initial design and conception.
The structure is constructed primarily out of concrete. Above ground, the concrete is clad in cut stone to give the structure a smoothened-out look. Below ground in the parking garage, however, the concrete is more roughened. The initial McKim, Mead and White plan had called for rough-cut, dark stone to be applied to the exterior of the building; however, Clinton Loyd, the principal architect and engineer, modified their plan and used lighter, finer cut stone. Loyd believed it would give the building a cleaner and more refined look. The structure of the Rotunda was designed to hold large loads.
The Boat Basin has been a popular filming location. The Parks Department's web page for the basin lists details for obtaining film permits among things to do at the marina. The 1986 film 9½ Weeks, starring Kim Basinger and Mickey Rourke, includes scenes shot at the marina and inside a houseboat moored there. The 1998 film You've Got Mail has Tom Hanks and his relatives living on yachts in the basin.