Small copepods and protozoa are major contributors to heterotrophic biomass in Antarctic waters. They produce small (< 300 µm) faecal pellets, the fates of which are largely unknown. We examined the distribution and abundance of microzooplankton and small faecal pellets in Ellis Fjord, east Antarctica. We determined statistical relationships between the abundance of microzooplankton and pellets, and examined pellet morphology and ultrastructure using light and scanning electron microscopy. Our results indicate species-specific differences in the morphology and fate of pellets produced by small copepods: Oithona similis and harpacticoid pellets were retained in upper waters, while Oncaea curvata and Paralabidocera antarctica pellets sank to depth. Protozoan pellets did not sink to depth irrespective of their source or morphology and despite the fact they can be larger than those produced by small copepods. The majority of microzooplankton pellets, composed of phytoplankton that otherwise may have directly sedimented to depth, was retained in near surface waters and probably recycled and remineralised. Despite producing faecal aggregates, heterotrophic activity of most microzooplankton do not contribute to vertical flux but instead support respiration of matter in upper waters. This may reduce the vertical flux of particulate matter to depth, thereby reducing the capacity of Antarctic waters to act as a carbon sink, with implications for global climate.

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Ellis Fjord, located in the Vestfold Hills of East Antarctica (68.5°S, 78°E), exhibits a range of environments, from essentially marine at its sea‐ward end, to permanently stratified basins with hypersaline brines at its inland end. The drainage basin of the fjord contains small areas of mosses and lichens, but no higher plants, and supplies fresh water to the fjord in ephemeral summer melt streams. Direct anthropogenic inputs are negligible or non‐existent, as are those from other mammals and birds. The fjord exhibits unusual biological and chemical properties, and offers the opportunity to study oceanic processes in isolation and at small scales. It also has the logistical advantage of proximity to the facilities of Australia's year‐round Davis research station.

Knowledge of copepod abundance and distribution has been limited, particularly in the Indian Ocean sector, as the use of coarse sampling gear has meant that copepods were frequently lost from the catch. This study analyses samples obtained from Prydz Bay using a fine mesh (300 μm) Rectangular Midwater Trawl (RMT1) net during summer 1992–93. Results demonstrate that a net of mesh 4.5 mm used in previous studies underestimates total copepod abundance by a factor of 38. The abundance of the smaller species has been underestimated the most. New estimates of copepod biomass indicate that copepods represent approximately 27% of krill biomass. Copepod and krill distributions are shown to be discrete at 82.4% dissimilarity. Mean temperature accounted for 33.6% of the variation in copepod distribution while two of the species showed a slight correlation with chlorophyll a pigment data. These results highlight the numerical importance of copepods and the species' distributions in the East Antarctic marine ecosystem.