In the Falklands War in 1982, 10 Harrier GR.3s of No. 1 Squadron operated from the aircraft carrier HMS Hermes. As the RAF Harrier GR.3 had not been designed for naval service, the 10 aircraft had to be rapidly modified prior to the departure of the task force. Special sealants against corrosion were applied and a new deck-based inertial guidance aid was devised to allow the RAF Harrier to land on a carrier as easily as the Sea Harrier. Transponders to guide aircraft back to the carriers during night-time operations were also installed, along with flares and chaff dispensers.

As there was little space on the carriers, two requisitioned merchant container ships, the Atlantic Conveyor and Atlantic Causeway, were modified with temporary flight decks and used to carry Harriers and helicopters to the South Atlantic. The Harrier GR.3s focused on providing close air support to the ground forces on the Falklands and attacking Argentine positions; suppressing enemy artillery was often a high priority. Sea Harriers were also used in the war, primarily conducting fleet air defence and combat air patrols against the threat of attacking Argentine fighters. However, both Sea Harriers and Harrier GR.3s were used in ground-attack missions against the main airfield and runway at Stanley.

If most of the Sea Harriers had been lost, the GR.3s would have replaced them in air patrol duties, even though the Harrier GR.3 was not designed for air defence operations; as such the GR.3s quickly had their outboard weapons pylons modified to take air-to-air Sidewinder missiles.[88] From 10 to 24 May 1982, prior to British forces landing in the Falklands, a detachment of three GR.3s provided air defence for Ascension Island until three F-4 Phantom IIs arrived to take on this responsibility. During the Falklands War, the greatest threats to the Harriers were deemed to be surface-to-air missiles (SAMs) and small arms fire from the ground. In total, four Harrier GR.3s and six Sea Harriers were lost to ground fire, accidents, or mechanical failure.[96] More than 2,000 Harrier sorties were conducted during the conflict—equivalent to six sorties per day per aircraft.

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