In June 1686 Graydon was appointed lieutenant of ; in May 1688 first lieutenant of , and in October was advanced to the command of the sixth-rate 16 gun HMS Soldado previously HMY Suadadoes. In her he took part in the battle of Bantry Bay on 1 May 1689, and was shortly afterwards promoted to , which he commanded in the battle of Beachy Head, 30 June 1690. In 1692 he commanded in the action at Barfleur. From 1694 to 1695 he was appointed Commander-in-Chief, Portsmouth and with the grand fleet through 1695.