The effects of two contrasting environmental conditions in nearshore waters off central Chile on the diet and morphospace of two cohorts of larval labrisomid blennyCalliclinus geniguttatuswere studied using geometric morphometrics and gut content analysis. The two environmental conditions corresponded to (a) a cold period with upwelling-favourable southwesterly winds and a mixed water column of cooler water and (b) a warm period with calm winds and stratified warmer water. During the cold period, fish larvae had a more hydrodynamic head shape, longer jaws and a higher feeding incidence, suggesting a greater food supply due to upwelling events and a possible increase in encounter rates in the turbulent environment. In contrast, the larvae from the warm period had a more robust head shape with smaller jaws and a lower feeding incidence, which was related to higher water temperatures and lower wind intensities. The present study suggests that larvae have a rapid response to environmental changes on a short time scale (i.e., from weeks to months), showing a link between environmental conditions and changes in the phenotypic traits and diet of the larval stages of this cryptobenthic species.