Knowledge about the coastal zooplankton of the south-eastern Indian Ocean is limited, with few studies having compared assemblages across the latitudinal range of the western seaboard of Australia. The dominant oceanographic feature in this region is the Leeuwin Current, which transports warm, lower-salinity, tropical waters southward along the shelf-edge. This study examined data collected by Australia’s Integrated Marine Observing System at three coastal National Reference Stations located at 22°S 114°E, 32°S 115°E and 34°S 122°E. Spatial and temporal patterns in zooplankton abundance, composition and diversity were investigated, and differences in assemblage structure, particularly with respect to copepods, were related to oceanographic conditions. Clear dissimilarities among copepod assemblages were observed, becoming weaker in winter owing to enhanced connectivity of species driven by alongshore and cross-shelf transport in the Leeuwin Current. Both physical and biogeochemical factors were significant in structuring copepod assemblages, with seawater density, incorporating temperature and salinity, exerting the greatest influence. The results suggest that both broad-scale latitudinal gradients and mesoscale events contribute to variation in zooplankton assemblages in these waters. This study provides the first detailed comparison of zooplankton assemblages among the north-west, south-west and southern coastal waters of Western Australia, and enhances understanding of the processes influencing zooplankton distribution and structure.