Using remote underwater stereo-video systems we examined fish behaviour towards a stationary SCUBA diver at temperate (Rottnest Island) and sub-tropical (Houtman Abrolhos Islands) reefs in Western Australia. Changes in species richness, relative abundance, fish length, and the mean distance of individual fish from stereo-video cameras, in the presence and absence of a SCUBA diver, were assessed to infer changes in behaviour. Results show that a stationary SCUBA diver may obtain accurate measures of species richness and of the composition of fish assemblages in an area. However, the usefulness of these measures to reflect changes in fish behaviour appears limited as responses of fish towards the stationary SCUBA diver were highly species specific. Several species differed in their mean relative abundance (Heterodontus portusjacksoni, Coris auricularis, Thalassoma lunare), length (Ophthalmolepsis lineolatus, C. auricularis), and the distance to which they would approach the stereo-video systems (Kyphosus sydneyanus, Scarus schlegeli) when a SCUBA diver was present. Here, species-specific changes in the behaviour of several common and abundant fish species towards a stationary SCUBA diver advises caution to avoid biases when interpreting results obtained by SCUBA divers.