He was appointed Commander-in-Chief, Pacific Station in on 8 July 1857, with his flag aboard . Baynes arrived as the gold rush in the British Pacific Northwest was happening and the Royal Navy was expected to enforce the laws enacted by the Governor of the Colony of Vancouver Island, James Douglas. While Baynes was away at Callao, Peru, the San Juan border dispute erupted. On 27 July 1859, United States troops under the command of Brigadier-General William Selby Harney landed on San Juan Island off the Colony of Vancouver Island at the behest of 22 American settlers who claimed to be threatened. The settlers had killed a pig that belonged to the Hudson's Bay Company, and feared British punishment. San Juan Island was British territory, and though the British Ambassador to the United States Lord Lyons initially sought to conquer an American-held island that the British also laid claim to, he ordered Baynes to assist but not to escalate the issue. Douglas also sought military intervention, who demanded the landing of Royal Marines on the island. Baynes refused and his patient handling of the situation led to joint-occupation of the island until a formal decision could be made. In 1872, the British recognized American sovereignty over the island.