With his colleagues he often travelled around Canada, especially to the wilderness of Ontario, which was a major source of inspiration for Thomson. His first exhibition was in 1913. One year later he acted as a firefighter and guide in Algonquin Park in Northern Ontario. His first trips to Algonquin Park inspired him to follow the lead of fellow artists in producing oil sketches of natural scenes on small, rectangular panels for easy portability while traveling. Between 1912 and 1917, Thomson produced hundreds of these small sketches, many of which are now housed in such galleries as the Art Gallery of Ontario in Toronto and the National Gallery of Canada in Ottawa.

Many of Thomson's major paintings, began as sketches before being expanded into large oil paintings at Thomson's "studio"--an old utility shack with a wood-burning stove on the grounds of an artist's enclave in the Rosedale area in Toronto. Although Thomson sold few of these paintings during his lifetime, they formed the basis of the posthumous exhibitions, including one in London, England, that eventually brought international attention to his work.

During the height of his popularity as an artist and while he was reaching a fevered pitch in creating great powerful canvases, he disappeared during a canoeing trip in Algonquin Park on July 8, 1917. His body was not discovered until July 16, the official cause of death was drowning, but there are still questions about how he actually died. It has been speculated that he was murdered by a romantic rival or due to gambling debts; however, no one was ever tried for causing his death. He was buried at Canoe Lake in Algonquin Park the next afternoon, but at the request of his family his body was exhumed and reinterred in the family plot beside the Leith Presbyterian Church on July 21.