Watson was selected at pick 40 under the father–son rule in the 2002 national draft. He was initially coached as a key forward by Kevin Sheedy, who also coached his father Tim. His poor kicking by AFL standards drew criticism, and it was determined that he would be more suited to the midfield at Essendon. At the time, his weight was criticised by the media, as he was overweight for an AFL player. Over the next two seasons, he began to develop his craft in the Essendon midfield and became one of the competition's elite midfielders.