The carbonate sediments of the Western Australian shelf in the Indian Ocean host diverse assemblages of benthic foraminifera. Environments of the shelf are dominated by the southward-flowing Leeuwin Current, which impacts near-surface circulation and influences biogeographic ranges of Indo-Pacific warm-water foraminifera. Analyses of outer ramp to upper slope sediments (127–264 m water depth) at four different sites (some with replicates) revealed 185 benthic species. A shift from benthic to planktonic foraminifera was accompanied by the decrease of “larger” benthic foraminifera below the lowermost euphotic zone. Fisher α and proportions of buliminid and textularid taxa increased with water depth, as miliolids and rotalids decreased in proportion. Cluster analyses on the 125–250 μm and 250–850 μm size fractions revealed distinct assemblages, with the former distinguishing between deeper and shallower sites, and the latter distinguishing between the Carnarvon Ramp-site in the south and the three sites on the Northwestern Shelf (NWS). The assemblage shift with depth was likely caused by rapidly changing physical conditions in the upper thermocline. The assemblage differences between the NWS and the Carnarvon Ramp indicate limited horizontal transport and migration rates on the outer shelf below the influence of the Leeuwin Current. Similarity in bottom-water temperature at the studied sites indicates that water mass characteristics, biogeographic history or possibly diversity in benthic shelf habitats rather than temperature and depth are responsible for differences between the two regions.