Watson was born and raised in Bagdad, Florida, near Pensacola. He played on the golf team at Milton High School, which had featured future PGA Tour members Heath Slocum and Boo Weekley just before he attended. Watson played golf for Faulkner State Community College in nearby Baldwin County, Alabama, where he was a junior college All-American. He transferred to the University of Georgia, the defending NCAA champions, and played for the Bulldogs in 2000 and 2001. As a junior, Watson helped lead the Bulldogs to the SEC title in 2000.