Cross-shelf differences in coral reef benthic and fish assemblages are common, yet it is unknown whether these assemblages respond uniformly to environmental disturbances or whether local conditions result in differential responses of assemblages at different shelf positions. Here, we compare changes in the taxonomic and functional composition, and associated traits, of herbivorous reef fish assemblages across a continental shelf, five years before and six months after two severe cyclones and a thermal bleaching event that resulted in substantial and widespread loss of live hard coral cover. Each shelf position maintained a distinct taxonomic assemblage of fishes after disturbances, but the assemblages shared fewer species among shelf positions. There was a substantial loss of species richness following disturbances within each shelf position. Total biomass of the herbivorous fish assemblage increased after disturbances on mid- and outer-shelf reefs, but not on inner-shelf reefs. Using trait-based analyses, we found there was a loss of trait richness at each shelf position, but trait specialisation and originality increased on inner-shelf reefs. This study highlights the pervasiveness of extreme environmental disturbances on ecological assemblages. Whilst distinct cross-shelf assemblages can remain following environmental disturbances, assemblages have reduced richness and are potentially more vulnerable to chronic localised stresses