Planktonic ciliates are important microzooplankton in pelagic ecosystems. Previous studies in Antarctic waters have only investigated ciliate assemblages in different habitats without considering water masses. In this article, we report the characteristics of ciliate assemblages in different water masses in open waters near Prydz Bay (East Antarctica) during austral summer. Three water masses were identified according to temperature and salinity: Summer Surface Water (SSW), Winter Water (WW), and Circumpolar Deep Water (CDW). SSW was further divided into SSW Chl a < 3 (in vivo Chlorophyll a > 3 mg m −3) and SSW Chl a < 3 (in vivo Chlorophyll a < 3 mg m −3). Ciliate abundance and biomass in water masses decreased in the order: SSW > WW > CDW. SSW Chl a > 3 had a higher proportion (38.2%) of tintinnids to the total ciliate abundance and larger aloricate ciliates (ciliates in the 10-20 µm size class were < 15% of the total aloricate ciliate abundance) than in other water masses. WW had a higher proportion (> 30%) of Southern Ocean endemic tintinnid species in total tintinnid abundance than in other water masses. Each water mass had the following indigenous tintinnid species: SSW, Salpingella sp., Codonellopsis gaussi; WW, Salpingella costata, S. faurei, Cymatocylis affinis/convallaria forma drygalskii, and C. vanhoeffeni. Laackman-niella naviculaefera and C. affinis/convallaria forma cristallina were present at high abundance in both WW and SSW Chl a > 3. Upwelling caused discontinuity of the ciliate distribution. Our results will help predict the spatial and temporal variations of ciliate assemblages and other plankton according to the dynamics of water masses in Antarctic waters.