Abstract A transect that extended 40 km offshore across the continental shelf off Perth, Western Australia, was sampled monthly during 1997 and 1998. Zooplankton was sampled at 5 km intervals with a 300 micron-mesh bongo net deployed vertically to within 3 m of the bottom, or to a maximum depth of 70 m. Numbers of species of chaetognaths and siphonores were quantified, as were abundances of the common species from these groups and of the hydromedusae Auglaura hemistoma. The potential influences of four environmental variables (sea-level, sea surface temperature, salinity and chlorophyll concentration) on variability in diversity and abundance were assessed using generalized additive modeling. A combination of factors were found to influence the seasonal and spatial biological variability and, of these factors, non-linear relationships always contributed to the best fitting models. In all but one case, each of the environmental variables was included in the final model. The seasonally variable Leeuwin Current, whose strength is measured as variations in local sea-level, is the dominant mesoscale oceanographic feature in the study region but was not found to have an overriding influence on the shelf zooplankton. This contrasts a previous hypothesis that subjectively attributed seasonal variability of the same taxa examined in this study to seasonal variations in the Leeuwin Current. There remains a poor understanding of shelf zooplankton off Western Australia and, in particular, of the processes that influence seasonal and spatial variability. A more complete understanding of potential causative influences of the Leeuwin Current on the shelf plankton community of south-western Australia must be cognizant of a range of biophysical factors operating at both the broader mesoscale and at smaller scales within the shelf pelagic ecosystem.