Watson began his coaching career in 2004 with the Canadian national team system where he held assistant positions with the U-20 and senior squads. Watson served as assistant coach for Canada at the 2004 CONCACAF Men's Olympic Qualification Tournament and was an assistant when the team finished third in the same tournament in 2008. He also spent four seasons on the staff of his former playing club Charleston Battery as an assistant to Mike Anhaeuser from 2006 to 2009, helping lead Charleston to the final of the 2008 Lamar Hunt U.S. Open Cup.