The mechanisms linking changes in biodiversity to variation in ecosystem functioning are poorly understood because we lack empirical data to describe the functional traits of herbivorous reef fish in many coastal settings. This study used black rabbitfish (Siganus fuscescens) to test whether variation in species abundance and morphological trait diversity were linked to changes of environmental condition. Fish were surveyed at fourteen inshore coral reefs, which were distributed along gradients of water quality, reserve protection and latitude, throughout Central Queensland, Australia. Data were collected with a stereo diver-operated video and we developed an approach for measuring fish morphological traits from video footage using EventMeasure. Rabbitfish abundance was negatively correlated with coral cover and coral functional diversity and positively linked to reef area, macroalgae cover and the proximity of adjacent estuaries. Variation in morphological traits was also correlated with coral functional diversity, with the head length, mouth length, eye diameter and pre-orbital length of rabbitfish declining as coral functional diversity increased. The results demonstrate phenotypic plasticity in the head and face attributes of rabbitfish, which might be indicative of changes in feeding preferences from macroalgae to turf algae with increased coral functional diversity.