The neural basis of time perception remains unknown. A prominent account is the pacemaker-accumulator model, wherein regular ticks of some physiological or neural pacemaker are read out as time. Putative candidates for the pacemaker have been suggested in physiological processes (heartbeat), or dopaminergic mid-brain neurons, whose activity has been associated with spontaneous blinking. However, such proposals have difficulty accounting for observations that time perception varies systematically with perceptual content. We examined physiological influences on human duration estimates for naturalistic videos between 1–64 seconds using cardiac and eye recordings. Duration estimates were biased by the amount of change in scene content. Contrary to previous claims, heart rate, and blinking were not related to duration estimates. Our results support a recent proposal that tracking change in perceptual classification networks provides a basis for human time perception, and suggest that previous assertions of the importance of physiological factors should be tempered.