Waterhouse made his AFL debut in round 3, 1996 against the reigning premiers Carlton. Despite Carlton being on an 18-game winning streak, Fremantle won by 53 points. Waterhouse was quiet, with only two kicks, but did manage a goal. He vacillated between the Dockers and Swan Districts for the remainder of the year, finishing with 11 AFL games for nine goals, though he did kick nine goals against South Fremantle in the twelfth WAFL round. 1997 and 1998 were inconsistent seasons for Waterhouse, and he was dropped from the team and injured numerous times. Despite only playing 16 games in 1998, Waterhouse was Fremantle's leading goalkicker, with 30 goals. 1999 saw the recruiting of Adelaide Crows star full forward, Tony Modra to Fremantle. Modra and Waterhouse would make a dangerous pairing for the following two seasons, combining for over 100 goals each year. Waterhouse played all bar one game and finished third in the best and fairest award in those two seasons before injuries took their toll from 2001 onwards. He also represented Australia in the International rules series against Ireland in 1999. Round 21, 2000 would be Waterhouse’s greatest on-field moment. In the infamous Demolition Derby against West Coast, Waterhouse sparked a last half comeback from being 42 points behind 6 minutes into the third quarter. His career high seven goals earned him three Brownlow Medal votes and helped Fremantle to their greatest ever comeback to win by 1 point.
Injuries and career decline
A broken collarbone sustained during a pre-season game against Geelong at Fremantle Oval would delay his start to the 2001 season until round 3 and repeated hamstring strains would restrict him to only six games and ten goals for the season. 2002 was even worse, with an anterior cruciate ligament injury also occurring during a preseason game at Fremantle Oval ruling him out for the entire season. Waterhouse made his return to AFL football in round 4, 2003, but he couldn’t recapture his form from 1999 or 2000 and was dropped after kicking only seven goals from eight games. Having played 99 games to this point, and with Fremantle going on to make the finals for the first time, many thought that Clive would be marooned one game short of the century. However, Waterhouse was named to play in the first game of 2004 to reach the milestone. He played a further six games in 2004 for seven goals before being delisted at the end of the season.
Post-AFL career
Waterhouse then returned to Adelaide in 2005 where he continued to play football, rejoining in the SANFL and becoming the team's leading goalscorer for 2005 with 71 goals. In 2007 Waterhouse again injured his anterior cruciate ligament while playing in the SANFL. Wearing Guernsey number 26 from throughout his AFL career, he was the first player to score 100 goals for Fremantle. He retired with 178 goals, a then-club record.
