In 1924, the Boston Transit Department implemented a long-planned project to convert the tunnel from streetcars to high-floor metro trains, with high platforms added at the station.

On January 28, 1949, a welder ignited a grease fire that exploded down an elevator shaft, killing three people and burning numerous others.

The platforms were lengthened for six-car trains, new entrances were added west of Atlantic Avenue, and the station was made fully accessible.

Since the renovation, the station has had water leakage issues; it also occasionally floods during high tides and storm surges.

Aquarium station is located under State Street at its intersection with Atlantic Avenue, near the edge of Boston Harbor.

[4][5] The older eastern part of the platform level has an arched ceiling, which widens to a triple vault in the newer western section.

[9] Not until July 25, 1901 did the Commission determine that the Tunnel would run under State Street, with a station at Atlantic Avenue next to busy Long Wharf.

[11] At the east end of each platform was a 18 by 32 feet (5.5 m × 9.8 m) space for elevators and stairs; these two rooms and the trackway between them occupied the lowest chamber.

[12]: 35  The rough work of the station vault was completed on August 28, 1903, with the tilework finished on January 19, 1904, and the granolithic platforms on February 10.

[13]: 55  The Paris Métro train fire in August 1903 led the BTC and BERy to desire emergency exits from stations with only a single headhouse.

Because the elevators needed to serve the separated platforms and the narrower headhouse, they were built with an angled section with approximately 6.5 feet (2.0 m) of vertical travel.

)[18] The BTC awarded the contract for the headhouse on August 15, 1904, with completion scheduled for December 15; however, manufacture of the steel components was severely delayed.

[7]: 16 [16]: 7  The Atlantic Avenue and State Street stations had separate fare gates; a paper transfer was required to change lines.

[19] The East Boston Tunnel was originally planned to be operated with high-floor metro rolling stock and connected to the then-planned Cambridge Elevated line.

[20]: 19  Large bi-loading streetcars (with high floors but capable of loading from low platforms), which incorporated many attributes from metro cars used on the Main Line El, began use in 1905.

[22] The next year, the BTD board approved the construction of high-level platforms at Atlantic Avenue, Devonshire, Scollay Under, and Bowdoin.

[28] In 1948, the Boston Transit Department awarded a $350,000 contract to add the new escalators, remove the elevators, and construct a new headhouse on the north side of State Street.

[32] Three people died in the headhouse: two passengers who missed the ground-level exit in the smoke while climbing the stairs and became trapped on the second floor, and one construction worker.

[34][35] The new headhouse was a rectangular structure made of limestone and granite in the Stripped Classical style, with four escalators replacing the old elevators.

[41][42] In the 1970s, part of Atlantic Avenue was relocated a block to the west under the Central Artery for redevelopment, which left Aquarium station on the east side of the realigned street.

[44] In 1988, the MBTA began a major renovation project to lengthen Blue Line station platforms for use of six-car trains.

[45] On February 14, 1990, the MBTA board voted to move the renovation of Aquarium station—including a new entrance on State Street—into final design.

The revised design called for a reinforced box structure, in which the new Central Artery tunnel would sit, on top of the station arch.

[47] The work took place during the Big Dig, which moved the Central Artery to the new tunnel and built the Rose Fitzgerald Kennedy Greenway on the surface.

[4] The fare mezzanines on each end of the station have red slate floors, and aluminum panels cover the walls and ceilings.

[53][54] Since the 1996–2003 reconstruction, Aquarium station has been plagued by water leaks, which may have been caused either by the renovation or by adjacent Big Dig construction.

)[15]: 18  The location of the east headhouse near Boston Harbor has resulted in additional flooding during king tides and storm surges.

[58] A $1.7 million project, which took place from August 2020 to March 2021, added supports for aluminum planks that can be temporarily installed during high water events.

It was originally proposed to run deep beneath the Central Artery, passing under Aquarium station at a depth of 130 feet (40 m).

[61] In 2003, the MBTA released the Major Investment Study/Draft Environmental Impact Report, which considered two-track and four-track NSRL designs with or without an intermediate Central Station.