That line then amalgamated with the Swindon, Marlborough and Andover Railway to form the M&SWJR.

Cirencester became a through-station in 1891, with the opening of the northern extension of the line between Cirencester and the junction at Andoversford with the Great Western Railway (GWR)'s Cheltenham Lansdown to Banbury line, which had opened in 1881.

Cirencester was the biggest station on this section of the line; it was home to the M&SWJR's locomotive and wagon workshops, and a large goods yard.

There was also a huge water tank, atop a stone building on the up platform, which supplied water that was loaded into rail-mounted tankers and taken to the stone-crushing plant at Foss Cross, the next station to the north.

Despite the size of the station, Cirencester Watermoor never achieved the passenger or goods traffic that was attracted by the Great Western station in the town, Cirencester Town, and its status was further diminished when, following the Grouping of 1923, the M&SWJR line was allocated to the GWR, which promptly closed the workshops.