In the early 1940s The Air Ministry requisitioned land for the construction of Earls Colne Airfield to the north of the Estate. The old deer park at Marks Hall (now the Arboretum) was also requisitioned to serve as a base for fighter and bomber forces, hosting RAF Squadrons and US Air Force Divisions. 

Numerous military buildings and installations were constructed and Marks Hall Estate was peppered with prefabricated units providing shelter for some 3,000 personnel.  A network of concrete roads, some of which are still visible here today, connected Nissen huts, air raid shelters, a hospital, workshops and the mansion, which was adapted to serve as an Area Headquarters.

Between 0600 hours and 0750 hours on 24th March 1945, a force of 440 gliders of the Glider Pilot Regiment, towed by 440 tug aircraft of the Royal Air Force, took off from airfields across East Anglia, including those based at Marks Hall, to take part in Operation Varsity