He spent much of his spare time sketching the architecture and scenery of the area, until he was recalled to England in 1835 by his father, to assist on the Start Point lighthouse project in Devon.

[2] Aberdeen had a tidal harbour at the time Abernethy arrived, and he spent a year dredging and building embankments to improve the access channel.

[2] The Preliminary Enquiries Act was passed to ensure that major new schemes were competently assessed before being implemented, and Abernethy worked as one of its Surveying Officers for eight years until 1852.

He acted as a consultant to the Swansea Harbour Trustees from 1847, and became their Engineer-in-chief in 1849, but continued to live in Aberdeen until 1851, when he moved to Birkenhead, where he held the same post as well.

He produced plans for improvements to the Irish Bann Navigation in 1851, and for the Dean Forest, Monmouth, Usk and Pontypool Railway in the following two years.

[3] He set up an office in London in 1853, and acted as consulting engineer for a large number of schemes, while still maintaining his regular oversight of the docks at Cardiff, Fraserburgh, Newport and Swansea.

He expanded his work to include overseas projects in 1862, although a number of his recommendations were not implemented, and the scheme that was eventually built at Alexandria harbour was rather less satisfactory than his own design.

[3] Major harbour schemes included those at Silloth, Portpatrick, Falmouth, Port Natal in South Africa, Watchet, Boston and the Alexandra Dock at Kingston upon Hull.

In 1883, he reported on the three rival schemes for the Manchester Ship Canal, finding in favour of the one by Sir Edward Leader Williams.

[6] Although he only presented a single paper to it, he contributed to the discussions on a wide range of subjects, He was also made a fellow of the Royal Society of Edinburgh.