He is noted for having served as sailing master of the armed tender HMS Chatham and later acting lieutenant during George Vancouver's 1791–1795 expedition to the Pacific Northwest.
[1] In October 1786 Johnstone left Britain as mate of Prince of Wales under James Colnett on a voyage to the Northwest coast of North America in search of sea otter.
In January 1789 in Macau, when Colnett decided to take another ship, Argonaut, back to the Northwest coast, Johnstone assumed command of Prince of Wales.
During the first summer, besides helping to chart Hood Canal and exploring up Bute and Loughborough Inlets, as well as Fitz Hugh Sound and Burke Channel.
[2] During the following surveying season, 1793, with first lieutenant Peter Puget having been promoted commander of Chatham in William Robert Broughton's absence, Johnstone led more of the boat surveys—often splitting them with Discovery's sailing master, Joseph Whidbey.
That spring and summer, Johnstone was sent out on at least six major boat surveys, lasting from only a few days to nearly two weeks in one case.
In January 1806 he was promoted to captain, being appointed to HMS Leopard in 1808—on which he was part of a convoy to the Cape of Good Hope, from where he continued on to the East Indies.