 In November 2006 he was appointed the league coach, after Peter German accepted an assistant coaching position with the Fremantle Football Club.In late 2009, Watters signed with the Collingwood Football Club as an assistant coach for seasons 2010 and 2011.At the conclusion of the 2011 season, he was appointed the senior coach of the St Kilda Football Club following the resignation of Ross Lyon but was sacked from that position on 1 November 2013.