Several experiments were performed in the laboratory condition using an SBR bioreactor modelling the expected conditions, created by malfunction of certain bioreactor elements, thus the different oxygen condition. In the course of the experiments, the concentrations of ammonia nitrogen, nitrates(III), nitrates(V), TOC, and TC were systematically measured. Besides physico-chemical parameters, the structure of activated sludge community was analyzed. In the samples, the number and species composition of protozoa (ciliates) were determined. Each of the three measuring series conducted for various types of process conditions was repeated three times. The activated sludge used for inoculation of the bioreactor was sampled at Hajdow WWTP in Lublin. The results obtained are the average of three repetitions of every experimental series. On this ground, we may conclude that the number of ciliates shows a high correlation with the O2 concentration, pH and TOC.