The Silver Line runs under Atlantic Avenue on the middle level, with two side platforms serving the busway.

[5] An accessible passage also connects the mezzanine with the interior of the South Station terminal, served by Amtrak and MBTA Commuter Rail trains.

Silver Line route SL4 runs on the surface rather than the underground busway; it stops on Essex Street at Atlantic Avenue.

The tunnel was rebuilt with a flat ceiling, while the fare lobby was moved to the east closer to the South Station headhouse.

[9] A passageway between the Red Line lobby and the interior of South Station opened in June 1990.

[17] However, route SL4, operating to a surface stop on Essex Street at Atlantic Avenue, began service on October 13, 2009.

[7] In early 2005, a blue and white tile mosaic reading 'South Station Under' was discovered during renovations to the Red Line platform.

[18] Network, a 650-square-foot (60 m2) glass mosaic map by Ellen Harvey, was built on the interior walls of the northeast headhouse in 2019.