Throughout the War of 1812 the practice of naval medicine in Kingston (the headquarters of British naval forces on the Great Lakes) was beset with adversity. Dependent for years upon the army, the Provincial Marine’s medical resources were minimal, with problems increasing exponentially after the expansion of the Royal Navy’s forces on the lakes in early 1813. Naval surgeons in Kingston faced almost constant shortages of personnel, supplies and facilities, issues which were not fully resolved until the very end of the war. Yet although the standard of care under these conditions has earned a poor reputation in the past, naval medical officers in fact strove to ensure the comfort and recovery of their patients. This article follows the development of naval medical infrastructure in Kingston during the conflict, demonstrating that despite adverse circumstances the care provided was often both sophisticated and effective.