On the 6th April 1939 Wing Commander O R Gayford DFC AFC took command of the station, and on the 11th May 1939 Bristol Blenheim Mk.I bombers of 107 and 110 Squadrons arrived under No. 2 Group Bomber Command. Within a few months both squadrons had replaced their Blenheim Mk.Is for Mk.IVs. On the 3rd September 1939 war was declared and on the next day the first bombing raid of the war took place, from Wattisham.
The mission was to attack German Battleships near Wilhelmshaven. 5 aircraft from each squadron left Wattisham, 4 aircraft from 107 Squadron and 1 from 110 Squadron were lost. Flt Lt Doran from 110 Squadron was awarded the DFC for his part in the attack. Shortly after the first mission, Wing Commander Basil Embry arrived at Wattisham to take command of 107 Squadron and on 25th September flew his first sortie in a Blenheim.
All through the later part of 1939 and the whole of 1940 ground and sea targets were attacked from Wattisham with the loss of many aircraft and crews. During this period the airfield was constantly attacked by the Luftwaffe resulting in No.2 and No.3 hangars being gutted. In an attempt to stop these attacks, Hurricanes from 504 Squadron were detached from Debden for a short while. On October 30th 1940 the first “Butterfly” bombs were dropped on the airfield, killing 2 SNCOs. The most severe raid occurred on 1st November 1940 resulting in the deaths of 11 personnel.
In May 1941, 107 Squadron moved out and 226 Squadron moved in, which in turn was later replaced by 18 Squadron in December still flying Blenheim Mk.IVs. In March 1942, 236 Squadron replaced 110 Squadron which moved out to the Far East. 236 Squadron flew Beaufighters, a robust night-fighter which was armed with 6 machine guns and 4 cannons. When fitted with torpedoes, rockets or bombs it was a very effective anti-shipping strike aircraft. On 12th June 1942 a piece of World War Two folklore was written.
The French Tri-colour was thrown out over the Arc de Triomphe from a 236 Squadron Beaufighter flown by Flt Lt Gatwood, and the Gestapo HQ in Paris was strafed before running for home. On the 17th/18th August 1942, 18 Squadron sent 8 Blenheims up to attack airfields at Rheine, Trente and Vechta and all returned safely. This was the last operational flight by Blenheims in Bomber Command. Wattisham had staged the first and last Blenheim operations of the war.
In September 1942 the RAF left Wattisham airfield.