After nine years building his confidence at sea, Mouat joined the HBC on 31 August 1844. He was soon transferred to the Cadboro but, after two years, was removed by the captain when a mutiny occurred. The problem started when Mouat hit steward William Maydle as he had refused him water to wash himself with. When he arrived in San Francisco on 31 January 1847, he apologised and was reinstated to the post he had been deprived of. However, tensions were still high and when the ship landed in Fort Victoria in February, five crew members mutinied because of Mouat’s presence. He was then sent to Fort Vancouver, and later to Fort Rupert on the Mary Dare but, during the summer of 1849, his soured reputation among the lesser shipmen got the better of him and he spent that time under his captain’s (William Henry McNeill) protection.
On 16 October 1849, he set out for California. He made his way back by 1851, and within three years he had purchased a lot in Victoria, shortly returning to England soon after as master of the Mary Dare. On that trip, he beat another mate which proved unsavoury. However, his quick temper was no match for his usual kindness and generosity, and so he won himself a bride: Mary Ann Ainsley (born 1826). They returned to Victoria in 1854. He was given the position of master of the Otter, a position which employed him until 1862 when he transferred to the Enterprise and made her first trip to the Fraser River. Four years later, he purchased 200 acres and, by 1860, was living at Clifton Cottage. Unfortunately, the vessel he was captaining in 1866, the mail carrier Labouchere, struck a reef on its way to San Francisco and sank. Later, after successfully investigating possible routes for transporting gold a year earlier, he captained the steamer Marten on Kamloops Lake. However, the intended source of gold failed, and so he was promoted to take charge of the HBC post at Fort Rupert. He died making his way from Knight’s Inlet to there, and was buried at the Quadra Street Cemetery (Pioneer Square), leaving several landmarks with his name (including the Mouat Islets near Gillies Bay, Texada Island). Mary Ann carried on as a widow until 1896.
Mouat and his wife produced seven children together. The couple were socialites, especially Mary Ann, who accompanied other notable Victorians, like Mr. Cridge, on the piano.