Laboratory-scale sequencing batch reactors (SBR) with activated sludge were used for co-treatment of municipal wastewater and two drilling fluids the polymer-potassium (DF1) and polymer (DF2) types. The influence of two doses of each types of drilling fluids, 1% and 3% of total added wastewater volume, on the wastewater treatment processes and community of eukaryotes in activated sludge was examined. During 6 cycles, the response of ciliate (distinguishing bacterivorous and predatory ciliated protozoa), naked amoeba and total eukaryote was observed. At 1% concentration, DF2 negatively affects the eukaryotic community, however DF 1 does not reliably affect the structure of the activated sludge eukaryotic population. At parallel, the increase in DF1 concentration in the sixth cycle induces significant structural changes in the eukaryotic population, similar to the effects of DF2.