Brooklyn Bridge-City Hall Station is now the southern terminus of the East Side Interborough Rapid Transit local service, assuming this role from City Hall station in 1945. It is a typical four track, two island platform configuration. South of the station, the downtown local track splits into three tracks. One is the loop track that returns to the uptown side, passing through the City Hall station noted above. The other two are layup tracks parallel to the downtown express track. Until the 1960's, they merged into the downtown express track north of Fulton Street station, but since then they are spurs ending a little ways north of Fulton Street. Trains are occasionally stored there. Plans are on the books to rejoin the layup tracks to the express track. The station has been recently renovated, with new tile and ADA-compliant elevator access.

This station provides transfer to the BMT Nassau Street station. This station is the zero point for the IRT East Side Chain; mile 0 is at the south end of the station.

The Brooklyn Bridge station has a number of abandoned areas as construction and service patterns have required changes to be made to the station. In addition to the two existing island platforms, there are two short local platforms on the outer edges of the station. Like those at 14th Street-Union Square and 96th Street, these local platforms were built to accommodate extra passenger volume and were built to the 5-car length of the original IRT local trains. These side platforms did not see much use as they were located at express stations that required transfer via the island platforms, and, as the trains were lengthened to their current 10 car length it was impractical to lenghten both these small side platforms and the island platforms. They were closed in 1910 after only six years in operation and walled off along the platform edges.

The side platform on the southbound side is now home to some electrical equipment and a backup control tower for the Brooklyn Bridge interlocking. The tower is functional but not normally used, because the Grand Central Station tower is the primary control point for the whole line. The interlocking board can be seen through a window along the wall along the southbound local trackway. The south end of the downtown side platform is still visible near the dispatcher's booth on the downtown island platform.

There are also some closed portions at the south ends of the existing express platforms. During the station lengthening projects it was easier to lenghten the express platform to the north. The curves at the south end proved impossible to rework so the station was lengthened northward (allowing Worth Street to be abandoned), and the curved southern ends of the express platform closed. Gap fillers and original mosaic tiles remain in the closed ends.