​At the outbreak of the Second World War, Waddington was fully operational. No. 44 and No. 50 Squadrons were based here with their Hampdens and immediately went into action on the day Britain declared war, attacking German naval targets at Kiel. 

​On 9 May 1940, war came to the village and its residents with a German air raid on the village and airfield. This resulted in the church and nineteen houses being destroyed by two parachute mines. The airfield was also hit, resulting in the death of four personnel in an air raid shelter and eight women who were in the NAAFI (Navy, Army and Air Force Institutes), the organisation that ran the canteen. The manageress was one of the casualties, and the rebuilt mess was named in honour and memory of her. 

​On 17 April 1942, six Lancasters of No. 44 (Rhodesia) Squadron from Waddington, along with six Lancasters from No. 97 Squadron from Woodhall Spa, took part in a raid. The target was the MAN diesel engine factory at Augsburg, Germany, and the attack would be conducted in broad daylight and at low level. The raid proved very costly, with the plant being hit but production continuing. Only two Lancasters of No. 44 Squadron and three of No. 97 Squadron returned. Of the 85 aircrew who undertook the operation, 49 were reported missing. Squadron Leader John Nettleton, who led the raid and returned to Waddington, was awarded a Victoria Cross for his actions. 

​Today the airfield is still in operational use by the RAF and is currently home to the RAF Aerobatic Team, the Red Arrows. Memorials and a heritage centre can be found around the main base and are open to the public, but booking by prior appointment is required.