McGowan occupied one of the most responsible positions on the USS Varuna during the attacks on Forts Jackson and St. Philip and in action against the rebel ship Morgan on 24 April 1862. Although guns were raking the decks from behind him, McGowan remained steadfast at the wheel throughout the thickest of the fight, continuing at his station and rendering service with the greatest courage and skill until his ship, repeatedly holed and twice rammed by the enemy, was beached and sunk.