Zooplankton plays an essential role in marine ecosystems as the link between primary producers (phytoplankton) and higher trophic levels in food webs, and as a dynamic pool of recruits for invertebrates and fish. Zooplankton communities are diverse with a patchy distribution at different spatial scales, influenced by oceanographic processes. The continental shelf of eastern South Africa is narrow and exposed to the western-boundary Agulhas Current, with some shelter against strong directional flow provided by the broader KwaZulu-Natal (KZN) Bight, a coastal offset adjacent to an estuary. We compared zooplankton species richness, diversity and relative abundance of key taxa among sheltered and exposed shelf areas using metabarcoding and community analysis, to explore the ecological role of the bight in a highly dynamic ocean region. Metabarcoding recovered higher richness and diversity at a finer resolution than could previously be achieved with traditional microscopy. Of 271 operational taxonomic units (OTUs) recovered through metabarcoding, 63% could be matched with >95% sequence similarity to reference barcodes. OTUs were dominated by malacostracan crustaceans (161 spp.), ray-finned fishes (45 spp.) and copepods (28 spp.). Species richness, diversity and the relative abundance of key taxa differed between sheltered and exposed shelf areas. Lower species richness in the bight was partly attributed to structurally homogenous benthic habitats, and an associated reduction of meroplanktonic species originating from local benthic-pelagic exchange. High relative abundance of a ray-finned fish in the bight, as observed fish eggs and read counts, confirmed that the bight is an important fish spawning area. Overall, zooplankton metabarcoding outputs were congruent with findings of earlier ecological research using more traditional methods of observation.