The main focus of this study was to evaluate the copper sensitivity of Euplotes vannus, Euplotes crassus, and their naturally associated bacteria from Guanabara Bay, a Brazilian polluted bay, during 96 h of laboratory assay. In the control, both microorganisms did not appear to be negatively affected, and E. vannus and E. crassus produced the highest biomass at 48 h (6.3×102 and 1.14×103μg C cm−3). With 0.001 mg Cu L−1, E. vannus and E. crassus showed the highest biomass (1.90×10−1 μg C cm−3, 24–72 h, and 8.52×102 μg C cm−3, 24 h), while their bacteria showed highest biomass at 24 h with exposition of 0,1 mg Cu L−1 (1.32 μg C cm−3, E. vannus) and with 0.001 mg Cu L−1 (1.90×10−1 μg C cm−3, E. crassus). However, E. crassus showed more resistance and both following bacteria showed better adaptation to higher copper concentration, possibly due to previous environmental selection. The basis of the microbial loop may be active under copper stress and facilitates the biomagnification process.The Euplotes resistance was evaluated with their naturally associated bacteria to copper. The association of Euplotes and bacteria positively influenced bacterial survival during copper stress.