Watson was drafted 67th overall in the third round by the Denver Broncos of the 1999 NFL Draft, then the highest an Eastern Illinois player had ever been drafted. Head coach and fellow alumnus Mike Shanahan was so impressed by Watson's performance in the pre-season, he released both veteran return specialists and made Watson the starter. In his rookie season, Watson returned 48 kickoffs, and 44 punts including an 81-yard touchdown against Seattle in Week 15 (then the 5th longest in franchise history), but also fumbled 5 times and was traded to Buffalo. He was the Bills' primary return specialist in 2000, but almost exclusively as cornerback in 2001 and 2002. He was traded to the Lions before the 2003 season, but never appeared in a game.
As of 2017[update]'s NFL off-season, Watson shared the Broncos franchise record for kick returns in a season (48) with Chris Cole.