In 2005, Meer was nominated for an Elizabeth Sterling Haynes Award for co-writing the surreal Sketch comedy show, Lobster Telephone (in which he also played Salvador Dalí), with the ladies of Panties Productions. In 2006, he was honored with the Sterling Award for Outstanding Performance By An Actor In A Supporting Role for playing multiple roles in Helen's Necklace, produced by Shadow Theatre. In 2011, he was nominated for five Canadian Comedy Awards, including Best Male Improvisor, for which he was also nominated in 2012, 2013, 2014, and 2015. In December 2012, Mark Meer was voted Edmontonian of the Year in an online poll held by Gig City, an Edmonton arts and entertainment website. Tiny Plastic Men, which Meer co-created and writes for Canada's Super Channel, has been nominated at the Canadian Screen Awards for Best Comedy Series in 2014, 2015, and 2016, and Meer himself was nominated for the CSA for Best Performance by an Actor in a Continuing Leading Comedic Role in 2015 for his work on the show. In 2016, Meer won the AMPIA Award for Best Performance by an Actor for the Tiny Plastic Men episode "Crisis on Infinite Octobers".

Meer appeared at Dragon*Con 2012 cosplaying as Commander Shepard, his most famous character. Though his attendance was not publicly advertised, some fans immediately recognized him.