Daytime service operates between 71st Avenue in Forest Hills, Queens, and 95th Street in Bay Ridge, Brooklyn, making all stops along the full route; one northbound a.m. rush hour trip terminates at 96th Street on the Upper East Side of Manhattan instead of 71st Avenue in Queens.

Overnight service short turns at Whitehall Street–South Ferry in Lower Manhattan from Brooklyn and does not operate to and from 71st Avenue.

[10] At that time, the 2 service was rerouted from the Manhattan Bridge to the Montague Street Tunnel, running local from Queensboro Plaza in Queens to 86th Street–Fourth Avenue in Brooklyn.

[12] During this time, rush-hour specials to Chambers Street were sporadically added and removed, eventually becoming an addition to the line.

[11] At one time, including during 1931, additional midday service operated local between 57th Street and Whitehall Street–South Ferry.

[13][17] On November 27, 1967, the day after the Chrystie Street Connection opened, the RR was moved back to Astoria–Ditmars Boulevard on the BMT Astoria Line.

[16][17] The RJ designation was only used from November 1967 until July 1, 1968, when it was cut back to Chambers Street and renamed as additional RR rush-hour peak-direction service.

[18] On January 24, 1977, as part of a series of NYCTA service cuts to save $13 million, many subway lines began running shorter trains during middays.

[23] Starting on April 28, 1986, R service on the Nassau Street Line was extended to Metropolitan Avenue for layups and put-ins from Fresh Pond Yard.

[37]: 9–10 [38] A modified version of the second plan was decided upon: some E trains would run from 179th Street instead of Archer Avenue during morning rush hours, though all E trains would run to Archer Avenue during the afternoon rush hour to reduce confusion for Queens-bound riders.

[24] On September 11, 2001, after the attack on the World Trade Center, the BMT Broadway Line was damaged, and the R service was cut back to run only south of Court Street.

[48] Late night service was cut back to 36th Street when the north side of the Manhattan Bridge reopened on February 22, 2004.

On December 21, full service was restored between Manhattan and Brooklyn after the Montague Street Tubes were drained.

[50][51] However, from August 2, 2013, to fall 2014, the tunnel was closed again so that extra repairs could be completed, bringing back similar storm changes to the R train.

On weekends, the R train ran its full route via the Manhattan Bridge, skipping all stations between Canal Street and DeKalb Avenue.

Originally slated to open by October 2014, the tunnel reopened a few weeks early, on September 15, 2014, and several million dollars under budget.

[55][56][57][58] Beginning on November 5, 2016, late-night R service was extended north to Whitehall Street-South Ferry in order to provide a one-seat ride into Manhattan.

[60][61][62][63] During late weekend evenings, every other R train short turned at Whitehall Street, resulting in waiting time doubling along the entire Brooklyn portion of the route.

[3] Starting November 6, 2017, one northbound R trip was diverted to serve the then-new Second Avenue Subway in order to increase service on that line during the morning rush hour.

[68] On March 17, 2023, New York City Transit made adjustments to evening and late night E, F and R service to accommodate long-term CBTC installation on the Queens Boulevard Line between Union Turnpike and 179th Street.

[69] In August 2023, it was announced that midday headways on the R would be reduced to eight minutes[70][71] although the MTA delayed the service increase until early 2024.