After school, he decided on a career in the British Army, enrolling at the Royal Military College, Sandhurst, and after completing his officer training was commissioned into the Duke of Cornwall's Light Infantry.
That survey made Holt's name as an ichthyologist; he published not only several papers on the eggs and the early larval stages of fish but also wrote the general report of the expedition.
As a result of Green's and Holt's work, the government instituted a formal program of fishery surveys under the auspice of the newly formed Congested Districts Board in 1892.
Holt joined the Marine Biological Association (MBA) and worked until 1894 at Grimsby, where he was in charge of a newly opened research station for the North Sea.
Nevertheless, E. W. L. Holt maintained his ties with Ireland, and in 1895 he purchased a dismasted brigantine named Saturn for the Royal Dublin Society and had it equipped as a marine biology research station.