Like the three other shared Muni/BART stations in the Market Street Subway, Civic Center has three underground levels.
The first level is a fare mezzanine, with two Muni paid areas and two BART paid areas.
The second level has a single island platform for Muni Metro, and the third level has an island platform for BART.
The station has six street entrances along its length.

A passageway formerly led to two additional entrances west of 8th Street and Hyde Street.
One - on the north side of Market Street at Grove Street - was temporarily closed in December 2016 after a sewer pipe collapsed under the escalators.
The entrance remained closed until it was permanently removed in October 2017.
The remaining entrance west of 8th Street was permanently closed on November 1, 2018, as the passageway space was needed for a new electrical substation to add redundancy and capacity to support increased Transbay Tube train frequency.
The six original entrances (all of which are significantly closer to the faregates) remained open.

Following the 2015 addition of a canopy over an escalator at 19th Street Oakland station, which reduced escalator downtime by one-third, BART decided to add canopies to all downtown Oakland and San Francisco entrances.
The canopies will protect the escalator from weather damage, improve lighting, allow the escalator to be fully closed off when the station is not open, and provide a location for real-time train arrival information displays.
The Civic Center station entrance at Market and 7th was chosen for early implementation; it was closed on December 11, 2017, with the new canopy opened on October 9, 2018.
Construction of the remaining Market Street entrances will begin in 2020, with completion in 2027.

In May 2018, BART proposed to close off a corridor that connects the 7th Street and 8th Street sides of the station because it was frequently used for drug use.
In February 2020, BART began a 12-month project to add two additional staircases to the BART platform.
Like the three other shared Muni/BART stations in the Market Street Subway, Civic Center has three underground levels. The first level is a fare mezzanine, with two Muni paid areas and two BART paid areas. The second level has a single island platform for Muni Metro, and the third level has an island platform for BART. The station has six street entrances along its length. 
A passageway formerly led to two additional entrances west of 8th Street and Hyde Street. One - on the north side of Market Street at Grove Street - was temporarily closed in December 2016 after a sewer pipe collapsed under the escalators. The entrance remained closed until it was permanently removed in October 2017. The remaining entrance west of 8th Street was permanently closed on November 1, 2018, as the passageway space was needed for a new electrical substation to add redundancy and capacity to support increased Transbay Tube train frequency. The six original entrances (all of which are significantly closer to the faregates) remained open.
Following the 2015 addition of a canopy over an escalator at 19th Street Oakland station, which reduced escalator downtime by one-third, BART decided to add canopies to all downtown Oakland and San Francisco entrances. The canopies will protect the escalator from weather damage, improve lighting, allow the escalator to be fully closed off when the station is not open, and provide a location for real-time train arrival information displays. The Civic Center station entrance at Market and 7th was chosen for early implementation; it was closed on December 11, 2017, with the new canopy opened on October 9, 2018. Construction of the remaining Market Street entrances will begin in 2020, with completion in 2027.
In May 2018, BART proposed to close off a corridor that connects the 7th Street and 8th Street sides of the station because it was frequently used for drug use. In February 2020, BART began a 12-month project to add two additional staircases to the BART platform.
Civic Center/UN Plaza station