[4] Initially opened as Keilor Road, this station was renamed to Sydenham on 1 April 1887, then was given its current name of Watergardens on 26 January 2002.

Sydenham station originally opened on 1 March 1859, shortly after the railway line was extended from Sunshine to Sunbury.

[5][6] In 1926, interlocked gates were provided at the former Melton Highway level crossing, which was located at the down end of the station.

[5] In 2002, as part of the extension of the electrified network from St Albans, Sydenham was closed, and a new station was built approximately 600 m (1,969 ft) in the up direction.

[7] In 2015, the Level Crossing Removal Authority announced the grade separation of the highway and railway line.