Abstract: The complex current systems of the Southern Ocean play a critical role in shaping the heterogeneity and distinctiveness of Antarctic habitats. Nonetheless, how Antarctic water masses influence ciliates, one of the most common groups of protozoa in polar regions, remains largely unknown. The present study investigated how the ciliate communities are affected by complex Southern Ocean currents by analyzing the diversity distributions, community assembly mechanisms, and co-occurrence networks of ciliates across three distinct water masses in the Scotia Sea. The findings reveal that the hydrography of the Scotia Sea significantly affects the spatial patterns of planktonic ciliates, primarily through the combination of temperature, salinity, and depth. In contract to surface waters (Antarctic Surface Water and Antarctic Circumpolar Current), ciliates inhabiting deep waters (Circumpolar Deep Water) exhibit stronger and more direct correlations with the environment parameters, alongside greater network stability. Community assembly in surface and deep-water masses is governed by stochastic and deterministic processes, respectively. Compared to other Antarctic regions documented in previous studies, the Scotia Sea demonstrated the lowest alpha diversity indices for ciliates while harboring the highest number of endemic species. A detailed re-evaluation of Antarctic ciliate community structure in the Antarctic from prior research offers valuable insights into how dynamic ocean currents shape the ecological dynamics of ciliate communities, thus providing a broader understanding of the environmental changes impacting polar marine ecosystems.