Originally the land was occupied by the Algonquians, and was eventually settled by European farmers and saw mill owners. The lake was known at that time as Lower Trout Lake, but was eventually named Canonto Lake after North and South Canonto townships were formed.

Historically, the lake had a smaller shoreline than it did today. Like many lakes in Frontenac, Canonto was tamed by damming. When the Canonto townships were mapped out, the lake’s shoreline was smaller; rock shoals were rocky islets and the lake’s largest island, Arcol Island, was a peninsula.

As farms became unsustainable and the best logging was gone, the original farming families subdivided their lots and new people have come to Canonto Lake as cottagers and residents. The Cartwrights, a farming family who had been allowing the public access to the lake via their property, sold their property to the Mississippi Valley Conservation Authority so that the tradition could continue. A system of trails was developed, and is now leased to the township of North Frontenac.