As the number of marine protected areas grows worldwide, it is important to understand how existing protected areas have functioned. Baited remote underwater video stations (BRUVS) are becoming a widely used technique for monitoring reef fish, but with few studies having so far used BRUVS in seagrass meadows, it remains unclear how they perform within these habitats. The aims of this study were to trial the use of BRUVS in shallow seagrass habitats and to compare animals observed at Pelican Lagoon Aquatic Reserve to 2 broadly similar locations on Kangaroo Island that have had no protection. BRUVS identified 47 distinguishable taxa from 5 phyla, with the majority (79%) of those being fishes. Assemblages taking into account relative abundances were not significantly different between protected and unprotected areas; however, species compositions alone varied significantly across all 3 locations. Only 2 out of 18 commercially and/or recreationally targeted species had a higher abundance within the reserve. Overall, BRUVS were found to be suitable for use in seagrass habitats; however, some limitations (particularly the potential for obstruction of the camera by seagrass blades) may exist.