During the reign of William and Mary, he served as Lord High Admiral (1689) and then First Lord of the Admiralty (1689–1690). Torrington played an important role in the War of the Grand Alliance, commanding the English and Dutch fleets at the Battle of Beachy Head (30 June 1690 O.S), a serious defeat for the allied fleet. He was imprisoned in the Tower of London and court-martialled for failing to support the Dutch van squadron against the French, but was acquitted. Nevertheless he lost his position as First Lord of the Admiralty. Torrington was not a popular commander, because of his reputation of being a drunk and his habit of taking several prostitutes with him to sea.
In connection with his 1690 operations against the French, the Earl is credited with being the first to use the expression, 'fleet in being'. Torrington proposed avoiding a set battle, except under very favourable conditions, until the arrival of reinforcements. By maintaining his fleet in being, he would force the French to remain in the area and prevent them from undertaking other operations.