Seamounts are recognised as hotspots of biodiversity, attracting large numbers of top predators, but the underlying mechanisms are still unclear. We studied mesozooplankton abundance and size distribution at three shallow seamounts (60m, 240m and 18m deep) in the South West Indian Ocean, along a latitudinal gradient (19°S, 27°S and 33°S). Samples were analysed using a ZooScan, allowing the use of a size-based approach. Differences were observed between seamount areas, but overall zooplankton communities did not seem to be affected by the changes in topography. Only in the lee of La Pérouse seamount was the zooplankton community slightly more concentrated than upstream, suggesting that zooplankton were flushed downstream of the seamount. The southernmost and shallowest seamount, Walters Shoal, had low abundance and its size spectrum differed greatly from the two other seamounts further north. These differences were attributed to seasonality and mesozooplankton population dynamics, whereas the other two seamounts exhibited a more “typical” oligotrophic pelagic ecosystem, at equilibrium and dominated by small organisms. At the time of sampling, the unnamed seamount south of Madagascar was influenced by a mesoscale dipole that impacted the zooplankton distribution, potentially masking any seamount effect. The normalised biomass spectrum approach contributed to a better understanding of the ecosystem dynamics (i.e. equilibrium vs. non-steady state) but revealed little variability within a stable oligotrophic environment.