One of the most consistent motifs of Canyons is that of running. The act of running takes on multiple symbolic and literal meanings throughout the text. On the literal level, Brennan is obsessed with running, as for him it is a way to escape the surroundings he perceives to be dreary and depressing. However, running also has a metaphorical meaning to Brennan, as through obsessing over the skull and trying to find its origins, he begins to spend less time at home with his mother and Bill; Brennan literally runs away from his issues, but he also metaphorically runs away by distracting himself.

Coyote Runs also has a relationship to running. On the raid, the Apache people never meant to harm anybody but rather to steal horses. To that end, when they’re caught, their only recourse is to flee, which leads to Coyote Runs’s demise. Through the motif of running, Canyons demonstrates how people flee from their problems and flee from danger, but it also shows how that fleeing can lead to greater problems—avoiding one’s issues does not address them, and Brennan is only able to achieve a measure of peace once he ceases compulsively running. In Canyons, running can be shown to be a method of fleeing literal danger—capture by soldiers or by park rangers—but also a method of fleeing internal danger.