This paper presents the results of studies on the structure of the ciliate population in a freshwater lake. The classification of the ciliated communities based on the analysis of the distribution of ciliate population density in the lake along the oxygen gradients, taking into account their oxygen preferences, was proposed. It was shown that the distribution of ciliated protozoa in the space of a reservoir is determined not by such spatial units as the water column, bottom, and periphytal, but by the oxygen gradients. Four types of habitats with different oxygen regimes were distinguished: With stably high oxygen concentration, stably low oxygen concentration, stably oxygen-free conditions, and conditions with a high amplitude of diurnal oxygen variations. The location of these habitats in the space of the lake and their seasonal changes were determined. On the basis of the quantitative development of ciliate populations, zones of optima and tolerance ranges of some ciliate species in the oxygen gradient were established. The oxygen preferences were established for the species from four distinguished assemblages: Microoxyphilic, oxyphilic, euryoxyphilic, and anoxyphilic (anaerobic). The presence or the absence of a certain type of assemblage in the reservoirs depends solely on the parameters of the oxygen gradients. The diversity of the ciliated protozoa in water bodies also depends on the stability and diversity of the oxygen gradients.