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Spent drilling muds are the liquid residues of rock drilling operations. Due to a high concentration of suspended solids and potentially detrimental chemical properties, they can negatively affect microorganisms participating in wastewater treatment processes. We evaluated the addition of a potassium-polymer drilling fluid (DF) to activated sludge in laboratory sequencing batch reactors (SBRs) for municipal wastewater treatment. Ciliate assemblage, the most dynamic component of eukaryotes in activated sludge, and which is highly sensitive to changes in the system, was evaluated. The average ciliate abundance dropped by about 51% (SBR 2; 1% DF added) and 33% (SBR 3; 3% DF added) in comparison to the control (SBR 1; wastewater only). A decrease in the total number of ciliate species during the experiment was observed, from 25 to 24 in SBR 2 and from 17 to 13 in SBR 3. Moreover, a drop in the number of dominant (>100 individuals mL−1) ciliate species was observed during the experiment—from eight in the control to five in SBR 2 and four in SBR 3—signaling noticeable changes in the quantitative structure of ciliate species. The species analyzed showed different responses to DF addition. The most sensitive was Aspidisca cicada, which is bacteriovorus. In contrast, two predators, Acineria uncinata and Holophrya discolor, showed no reaction to DF addition. Our results indicate that addition of potassium-polymer DF, in doses of 1 to 3% of the treated wastewater volume, had no toxic effects on ciliates, but qualitative and quantitative changes in their community were observed.