Aberdeen Waterloo station is/was built on the site of the Aberdeenshire Canal basin at Waterloo Quay (Aberdeen Harbour). Initial plans for the Great North of Scotland Railway were for the Aberdeen terminus to be at Guild Street (joined with the existing Aberdeen Railway, but the high construction costs of this route prevented this and after a short period the railway was extended down the narrow canal bed to Waterloo Quay, where a passenger station was opened in 1856 (Goods traffic first ran to Waterloo on 24 September 1855, the delay in passenger services was due to the need to construct suitable buildings). Upon completion of the new station at Waterloo the GNSR moved their company offices to the site from Union Street.

The only connection between the Great North of Scotland Railway at Waterloo and the Aberdeen Railway at Guild Street was through the harbour tramway lines, which were only suitable for the conveyance of goods traffic. This inevitably led to difficulty for passengers making connections between the two stations - indeed it is said that the GNSR frequently locked the gates of Waterloo Station to ensure punctual departures! Eventually the arrangements proved so inadequate that a new line was constructed from Kittybrewster (the original terminus of the GNSR) to Guild Street, and a new joint station was provided for the services of both railway companies. Aberdeen Waterloo ceased to be a passenger station in 1867 when the new railway was opened, and the GNSR company offices soon transferred to new buildings opposite the new station.

Aberdeen Waterloo continued to handle goods traffic until the 1960s, today the site finds use as a pipe yard. Interestingly at least two of the sidings from the former goods station at Waterloo are still "in situ", covered over with sand(?). This is rumoured to have come about as the land was initially sold to the GNSR with the express instruction that it must be used for railway purposes, and hence the fact that the sidings are still in situ (although completely out of use) means that, technically, the site is still being used in line with the Harbour Board's wishes. The redevelopment of the goods yard at Guild Street was also delayed for some time due to the fact that the land was initially sold for railway purposes only.

The Kittybrewster-Waterloo branch suvives, mostly out of use though retained for occassional calcium carbonate traffic which is sometimes taken to a private siding at Waterloo. Railtours have on occassion travelled down the Waterloo branch as well.