Waterhouse made his representative debut in the 2004 State of Origin series, playing in games I and II off the bench for the New South Wales Blues. Selected again in 2009, Waterhouse was sent off after coming into a fight between Steve Price and Brett White during game III of the State of Origin series. He became the first Blues player to be dismissed from an Origin game, however was not suspended due to the nature of the incident. He was the first player since Gorden Tallis to be sent off in an Origin match. His dismissal capped off a horror year for NSW as they lost their fourth (of an ongoing eight) straight Origin series.
On 29 June 2011 it was announced Waterhouse had signed to join English Super League club Warrington from 2012 on a three-year deal. Waterhouse played in the 2012 Challenge Cup final win over Leeds Rhinos, scoring a try in the first half, and the 2012 Super League Grand Final loss to the Leeds Rhinos.