Wheler spent the early part of his career in the Mediterranean, eventually being promoted to command his own ships, and being particularly active against the Algerine and Salé pirates that infested the region. He went on to serve in British waters, and was knighted by King James II. Wheler remained in the navy after the Glorious Revolution and his continued good service led to the command of a squadron. He fought at Beachy Head and Barfleur, and in 1692 was promoted to flag rank. He took a fleet out to attack French possessions in the Caribbean and North America, but his attack on Martinique ended in failure when large numbers of the troops involved became sick. He floated the idea of an attack on Quebec, but insufficient troops could be found, and an assault on Newfoundland was similarly considered but rejected after the defences were found to be too great to overcome. Wheler nevertheless received another promotion, and went out to the Mediterranean in command of a large convoy. He made little attempt to engage the French warships he encountered on the voyage, but concentrated on reaching Cadiz safely. After successfully escorting the convoy Wheler attempted to navigate the strait of Gibraltar, but encountered fierce winds. His fleet was scattered and a number of ships were wrecked, while his flagship, , foundered with heavy loss of life early in the morning of 19 February 1694. Wheler was among the dead, his body being washed up two days later.