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Laboratory-scale sequencing batch reactors (SBR) with activated sludge were used for co-treatment of drilling mud and municipal wastewater. The influence of two doses of drilling mud, 1% (SBR2) and 3% (SBR3) of total added wastewater volume, on wastewater treatment efficiency and community of eukaryotes in activated sludge was examined. Addition of drilling mud significantly decreased the efficiency of TSS removal in SBR2 and SBR3 (from 97% in control bioreactor SBR1 to 75% and 49%, respectively), COD removal (from 93% to 57% and 48%, respectively) and removal (from 93% to 56% and 48%, respectively). Values of TSS concentration in outflow from SBR2 and SBR3 greatly exceeded the limit value appointed for the wastewater discharged into the environment. Drilling mud addition led to decrease in population and diversity of eukaryotes’ groups in activated sludge, which was reflected by changes in sludge biotic index (SBI). It amounted to 10 in all the SBRs at the beginning of the experiment, and in SBR1, it remained at this same high level throughout. After 1% addition of drilling mud, a slight decrease in SBI (to 8) was observed, but 3% addition lowered the SBI to 4, reflecting serious deterioration of activated sludge quality.