The relationship between the ciliate community and the environmental variables in Ushuaia and Golondrina bays (54°79′S 68°22′W and 54°85′S 68°36′W, respectively) in the Beagle Channel, Argentina was investigated. The study was performed in three zones within the bays, previously delimited on the basis of their water quality. The most perturbed sites were located inshore. In order to analyse the contribution of each species to the similarity or dissimilarity between zones, similarity percentages analysis was undertaken using the Bray–Curtis similarity index. The variations in species composition and dominance in the selected zones were examined by the abundance–biomass comparison plot. We also studied the relationship between environmental and ciliates variability. The ciliate community comprised a total of 43 species belonging to 15 genera. Ciliate abundance and biomass varied temporally and spatially. A more diverse community dominated by small and opportunistic species tolerant to environmental changes was found in the most perturbed zone, while in the less stressed zone the community comprised bigger species, probably adapted to more stable environmental conditions. A community comprising species from both zones was found in a transitional area. We conclude that the structure of the community varied closely with environmental conditions.