On July 11, 2002, he was signed as a free agent by the Vancouver Canucks. After one season with the Canucks, he was placed on waivers and picked up by the Pittsburgh Penguins on October 3, 2003. However, after just five games with the Penguins, he was placed on waivers again and reclaimed by Vancouver on November 1. Playing with the Canucks' AHL affiliate, Baumgartner captained the Manitoba Moose in the season of 2003–04 and scored, 27 points. As the Moose began play at the newly opened MTS Center in 2004–05, Baumgartner earned the distinction of scoring the first ever professional goal at the arena, on November 17, 2004. When NHL play resumed the following season, Baumgartner cracked the Canucks regular lineup and set NHL career highs in every statistical category, as well as leading all team defencemen with 34 points.