Microbial communities living in microbial mats are known to constitute early indicators of ecosystem disturbance, but little is known about their response to environmental factors in the Antarctic. This paper presents the first major study on ciliates from microbial mats in streams on King George Island (Antarctica). The objective of the study is to investigate the structure and spatial distribution of ciliate communities and to identify the environmental factors determining the structure of the assemblages. Additionally, we compared ciliate communities inhabiting streams on King George Island with other isolated islands of the maritime Antarctic. Samples of microbial mats for ciliate analysis were collected from three streams fed by Ecology Glacier. Sampling was carried out three times from 17 January to 24 February 2012. The total numbers of ciliates were dominated by small taxa recognized as cosmopolitan, also recorded on other islands of the maritime Antarctic. The species richness, abundance, and biomass of ciliates differed significantly between the stations studied, with the lowest numbers in the middle course of the stream and the highest numbers in the microhabitats closest to the glacier and at the site where the stream empties into the pond. Variables that significantly explained the variance in ciliate communities in the transects investigated were total organic carbon, total nitrogen, temperature, dissolved oxygen, and conductivity. Further research is required to explain the impact of biotic factors on the presence of ciliates, including the abundance of bacteria, microalgae, and small metazoa.