Fish often evade predators with a fast-start escape response. Studies typically examine this behaviour in still water despite water motion being an inherent feature of aquatic ecosystems. In shallow habitats, waves create complex flows that likely influence escape performance, particularly in small fishes with low absolute swimming speeds relative to environmental flows. I examined how wave-driven water flow affects the behaviour and kinematics of escape responses in juveniles of three coral reef damselfishes (Pomacentridae) with different body morphologies. Tropical damselfishes have similar fin and body shapes during early development, with the exception of body depth, a trait deemed important for postural control and stability. Wave-driven flow increased response latency in two of the three species tested: fish with a fusiform body responded 2.9 times slower in wave-driven flow than in still water, whereas this difference was less pronounced in fish with an intermediate body depth (1.9 times slower response) and absent in fish with a laterally compressed body. The effect of wave-driven flow on swimming performance (cumulative escape distance and turning rate) was variable and depended on the timing and trajectory of escape responses in relation to the wave phase. Given intense predation pressure on juvenile coral reef fishes during settlement, interspecific differences in how wave-driven flow affects their ability to escape predators could influence the distribution and abundance of species across spatial and temporal scales.