For the first time in the region by the example of the five streams to study the composition of the simplest ecosystems in the rivers of southern Sakhalin were conducted. Mass for the region types such as Ciliata (Ciliophora), which confirms its cosmopolitan character have been determined. Comparative analysis of representatives of Ciliophora in waterways, which showed a high degree of faunal similarities studied rivers was carried out. Impact on the distribution and abundance of ciliates environmental factors, primarily the flow rate and temperature of the water was observed.