The viaduct takes a curving path, passing behind the former Victorian Railways headquarters at 67 Spencer Street, taking a relatively sharp 90 degree turn east from Spencer Street, swinging southward around the back of the former Melbourne City Markets[a] (now Northbank Place), with the former Fish Market on its south side (now the west end of Batman Park), then north-east to avoid the former turning basin for ships on the Yarra River, before passing over the Banana Alley Vaults, and entering Flinders Street station.

At the same time, a number of country railway lines had been built to the north and west of Melbourne, using Spencer Street station (now Southern Cross) as their terminus.

[2] The ground-level tramway was removed, although a short section was retained as a siding to serve the new Melbourne City Markets on Flinders Street, not being lifted until 1929.

From December 1894, suburban traffic on the Williamstown and Essendon line began to use the viaduct, after the construction of additional platforms at Spencer Street station.

As part of the City Loop project, each of the existing four tracks were integrated into the four independent tunnels around the Melbourne central business district.

[4] Unlike the earlier viaduct tracks, the new ones were able to take a straighter path because the turning basin had long been disused and partly filled in.

[10] In 1997, the Northbank area was redeveloped, with the turning basin partly restored and the newer viaduct bathed in blue light by night[11] in an artwork titled 'Blue Line' by Peter McNeill-Stitt, that includes 1,400 metres (4,600 ft) of neon tubing.