[15]: 21  However, development of what would become the city's first subway line did not start until 1894, when the New York State Legislature passed the Rapid Transit Act.

It called for a subway line from New York City Hall in Lower Manhattan to the Upper West Side, where two branches would lead north into the Bronx.

[15]: 182 The Brooklyn Bridge station was constructed as part of the IRT's original line south of Great Jones Street.

[18][19] As such, no plans had been drawn up for the eastern portion of the Brooklyn Bridge station or its approaches by early 1903, which caused delays in ordering steel.

[23][15]: 186  The station's first-ever passenger was described by Newsday as an "anonymous middle-aged Brooklyn woman who picked up her skirt and raced down the rubber-covered stairs three at a time to beat out the rest of the crowd".

The plant consisted of four pumps at the northern end of the station, which could draw up to 300 or 400 U.S. gallons per minute (19 or 25 L/s) of groundwater; the water was then chilled and sent through ducts above the platforms.

[34][35] To address overcrowding, in 1909, the New York Public Service Commission proposed lengthening the platforms at stations along the original IRT subway.

[36]: 168  As part of a modification to the IRT's construction contracts made on January 18, 1910, the company was to lengthen station platforms to accommodate ten-car express and six-car local trains.

[36]: 168 [38] By 1914, city engineers had prepared plans for the construction of five additional entrances to the Brooklyn Bridge station: three to the street and two to nearby buildings.

[47] The New York City Transit Authority (NYCTA) also announced plans in 1956 to add fluorescent lights above the edges of the station's platforms.

[48]In the late 1950s and early 1960s, the NYCTA undertook a $138 million (equivalent to $1.44 billion in 2023) modernization project for the Lexington Avenue Line.

[49] As part of the modernization program, the NYCTA announced in early 1957 that the Brooklyn Bridge station would be extended about 250 feet (76 m) to the north and that the platforms would be widened and straightened to remove the need for gap fillers.

[7][55] The overpass and the permanent passageway to the Chambers Street station opened in June 1963,[56] and the platform extension project was substantially completed by the end of 1963.

[65] In an attempt to prevent fare evasion, the MTA added low metal fins to each arm of the Brooklyn Bridge–City Hall station's turnstiles in 2025.

[74]: 372–373 [77] Uncertainty over the building's design resulted in delays in the construction of the proposed Brooklyn loop station underneath it, even as the rest of the line was nearly completed by early 1909.

[81] The New York City Board of Estimate approved $875,000 for the station's widening that July, excluding funds for land acquisition.

[90] The BRT's Chambers Street station opened on August 4, 1913,[91][92] relieving traffic on elevated lines that had used the Brooklyn Bridge.

[14]: 4–5 At the north end of the complex, two stairs extend from the IRT underpass to the northwestern corner of Reade and Centre Streets.

[75] Two stairs and an elevator rise from the western side of the IRT mezzanine to City Hall Park, just southwest of the intersection of Centre and Chambers Streets, in front of the Tweed Courthouse.

[64] A long passageway at the eastern side of the IRT mezzanine leads to a stair within a plaza just south of the Manhattan Municipal Building.

[145] The northern BMT mezzanine contained bronze doors on the east wall, now sealed, which led to the Thurgood Marshall United States Courthouse.

[14]: 9  The largest staircase under the Municipal Building's northern section was 43 feet (13 m) wide and could originally accommodate 800 passengers per minute.

The platforms contain double-height, tile-clad columns spaced every 15 feet (4.6 m), which support the jack-arched concrete station roofs.

[148] Before the extension to Broad Street opened, the two westernmost (now southbound) tracks ramped up to just before the portal from the Brooklyn Bridge, ending at a wooden gate.

The spaces above the alcoves contain black-on-green plaques with back-to-back "B"s, which alternate with white-on-green tablets with the words brooklyn bridge in Arial font.

[153]: 31 As part of the MTA Arts & Design program, Mark Gibian created a sculpture for the station, titled Cable Crossing, in 1996.

[156] The sculpture consists of numerous cables in the fare control area of the IRT mezzanine, a reference to the nearby Brooklyn Bridge.

[158] In creating the sculpture, Gibian said he wanted it to represent "the controlled power of the subway and its network of metal and concrete that undergirds the city".

[159] As a major hub for the IRT and BMT, the Brooklyn Bridge and Chambers Street complex was the subway system's busiest station when it was built.

[166] The high ridership at the complex contributed to the closure of the IRT's City Hall Loop in 1945, when the Brooklyn Bridge station still had 14 million annual passengers.