Riley, 26, only played in one game for the Wolves this season, before being sent out on loan to Wakefield, while Waterhouse has spent the last three seasons at the Halliwell Jones Stadium.
Also leaving are first team coaches Willie Poching, who is joining Hull KR, and Richard Marshall, strength and conditioner Chris Baron, sports scientist Andy Holleyhead, soft tissue therapist Amanda Turner and joint U19s community coach Danny Fullerton.
Head of coaching and rugby Tony Smith added: “All of these players and coaches have been a pleasure to work with over their time at the club and have contributed to our continuing success. We’ve all built up a great relationship and anybody who has been part of the Warrington family will always be welcomed back. We wish them all well for the future and look forward to our paths crossing in the future.”
Warrington-born Riley has scored 120 tries in 180 appearances since his debut in 2005 and has been part of the three Challenge Cup winning teams in recent years.
Waterhouse, who joined at the start of 2012 from Penrith, has scored 19 tries in 78 appearances for the Wolves.