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.
In the infamous Demolition Derby against the West Coast Eagles, Waterhouse sparked a last-half comeback from being 42 points behind, six 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.
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.