In June 1938, the airfield's's first military resident's were RAF Bomber Command's 5 Group who set up an Royal Air Force Volunteer Reserve training outfit. The Civil Air Guard also operated from the aerodrome. The airfield was requisitioned by the Air Ministry in May 1940. The aerodrome was then prepared through the summer of 1940 with concrete runways to accommodate bombers of No. 1 Group RAF. The aerodrome became operational in the summer of 1941 and was initially a satellite airfield for the nearby RAF Binbrook. The Wellington squadrons based at Binbrook would use Waltham as their own airfield did not have concrete runways. Throughout the war the station was under 1 Group Bomber Command. Three squadrons served at RAF Grimsby during its operation: 142 Squadron moved to the airfield in November 1941; 100 Squadron arrived in December 1942; and 550 Squadron. The first operational sortie from Waltham for 100 Squadron was on the 4/5 March 1943. The squadron's Avro Lancaster bombers were sent on mine-laying sorties along the coasts of occupied Europe. Two Lancasters were lost. The station was closed some weeks prior to the surrender of Germany and the hangars were used by No. 35 Maintenance Unit RAF for storage and the flying field reverted to back to agricultural use.
Post-Second World War
Years later the A16 was being improved and a bypass for the village of Holton-le-Clay cut into a large proportion of the station.
Memorials
Currently a memorial to 100 Squadron stands near the B1 hangar, next to the northern entrance to Holton-le-Clay. There is a memorial for 550 Squadron at the now disused station RAF North Killingholme and 142 Squadron is said to have a memorial in North Africa.
Buildings
Many of the airfield buildings still survive and are currently in use by a haulage firm and mechanics. Much of the original runway arrangement remains and is tarmaced. They have been painted with road markings in areas, for use with learner drivers, and provide a circuit regularly frequented by dog walkers. Out of the thirty plus dispersals built only one remains to this day. It is still possible to see the outlines of some from the air. Notable surviving buildings include the control tower, crew locker and dryer rooms, the pre-war B1 and T2 hangars; however much of the station is in a state of disrepair and is also victim to fly-tipping. Old unused farm equipment also litters the station, it is overgrown with weeds and strewn with rubble. A golf course, golf driving range and a go-karting track have been built on the station and a coal merchants stands on what was once the fuel dump. The bomb dump has totally disappeared and various buildings in the village of Waltham, Lincolnshire such as accommodation huts no longer exist. The only remaining building in the village is the Women's Auxiliary Air Force canteen and kitchen which currently house the Museum of Rural Life and RAF Grimsby Exhibition at the Waltham Windmill. This building has been extended.
