The station was opened on the 4th. January 1939 under the command of Group Captain F.J. Vincent as a station of 2 Group, Bomber Command. It was built as part of the R.A.F. expansion programme of 1935 / 1936 on farmland that was well known locally as good mushroom land and under the right conditions mushrooms are still to be seen in quantity in the area.
The first two Squadrons to be based here were Nos. 21 and 34 flying mainly training flights until in August of 1939 No. 34 Squadron was posted to Egypt and replaced by No. 82 Squadron, who with 21 Squadron formed No. 79 Wing. These two Squadrons remained until mid 1942. 79 Wing operated from both Watton and Bodney flying from grass flying fields.
The role of the Wing changed from Photo-Reconnaissance to Maritime-Reconnaissance during the “Cold War” but with the German invasion of Norway the missions became more aggressive and the Wing concentrated on targets in France and Belgium in support of the B.E.F. until Dunkirk and then focused their attention on the invasion ports and targets in Germany.
Twice during the summer of 1940 No.82 Squadron lost eleven out of twelve Blenheims dispatched on raids in daylight and it was not until the middle of 1941 that the fighter escorts were available for operations.
In 1942 No.21 Squadron exchanged their Blenheims for Mitchels although they did not fly any operations with these aircraft and in October of that year the Squadron moved to Methwold. At the same time No.82 Squadron transferred to the Middle East and Watton was occupied by No.17 Advanced Flying Unit. They were equipped with Miles Masters and performed advanced flying training. In July 1943 No.17 A.F.U. left and the Americans moved in.
Soon after their arrival the Americans expanded the airfield and built the single runway at Watton and in July 1944 the 25th B.G. commenced operations these were mainly to do with weather and photo recon., but also some O.S.S. (secret service) missions supporting the resistance organisations in Europe. Sharing the runway were also the 3rd Strategic Air Depot, operating on the South side of the Airfield at a site they called Neaton, their purpose was to provide engineering support for the 8th Air Force and many crippled aircraft landed at Watton to be repaired by them. The Americans remained until August 1945 when the camp was returned to the Royal Air Force.