Individual variation in behaviour within populations may be explained in part by demographics and long-term, stable individual psychological differences. We examined the relation between boldness (taken as the time to emerge from a shelter and explore a novel environment) and body size in eight populations of the poeciliid Brachyraphis episcopi originating from sites upstream and downstream of waterfalls in four rivers that run into the Panama Canal. The relation between body size and time to emerge from a shelter was positive, with larger fish taking longer to emerge. This relation differed between downstream and upstream sites, being significant in the upstream populations only. These results are best explained by a metabolic hypothesis whereby juvenile fish are compelled to emerge earlier in order to resume feeding. In the downstream sites this effect was slightly offset by the relatively greater predation threat for smaller fish, such that they delayed their emergence from cover. We discuss the underlying importance of variation in boldness and its effects on other behavioural and life history traits.