Waters was recruited as the Eagles' first-round draft pick in the 2003 National Draft with pick 11. Eagles recruiting manager Trevor Woodhouse described him as ready to immediately step into the Eagles' team: "Beau Waters, we rate him pretty high, he's a skilled left-footer. We're looking for him to step into the fore reasonably quickly, but there's no pressure on him to play next year." He made his debut for the Eagles against at the Telstra Dome in Round 3 of the 2004 AFL season, gathering ten possessions and four marks in a game the Eagles lost by six points. He played nine more games in his debut season, gathering 25 possessions and eight marks as the youngest player in an Eagles win against the in Round 18. Waters did not play a game in the 2005 season after being ruled out with osteitis pubis. A week after he had recovered from the injury, he was hit by a taxi he was trying to flag down after a night out in Subiaco. Rushed to Sir Charles Gairdner Hospital, it was initially thought no damage had been done, but it was later revealed he had injured his lateral ligament, ruling him out for six weeks during the pre-season. Waters returned to the side in 2006 as a key part of the squad, playing 23 matches throughout the season. He scored his first AFL goal in Round 3 against Richmond. He gained his first Brownlow votes in Round 18 against St Kilda for a 34-possession game. Waters played in every one of the Eagles' finals matches. He gathered 26 possessions and took ten marks as the youngest member of the Eagles' premiership side in the Grand Final win over, in the process gaining a vote in the 2006 Norm Smith Medal. Waters played 20 games in 2007 and eight games in 2008 before suffering a season-ending elbow injury. He resumed full-training in May of 2009 but then re-injured the same elbow, ruling him out for the remainder of the 2009 season. Waters was awarded the Chris Mainwaring Award for Best Clubman in 2009 for his work for the club while off injured. Waters made a long-awaited return in the 2010 season, after one-and-a-half years out due to injury. He was one of the Eagles best players in a year where the club finished last, averaging 21 possessions and seven marks in a 20-game season. Waters also captained the club for a number of games after regular captain Darren Glass was ruled out for the season with a knee injury. Waters gathered two Brownlow votes for a 33-possession game in a loss against in Round 11, and finished third overall in the West Coast Eagles Best & Fairest. Waters was named the Eagles sole vice-captain for the 2011 AFL season. He retired in February 2015 due to ongoing injury.
