Water quality has been found to significantly influence the flotation operations due to the alteration of surface properties of minerals. The effect of cations on the flotation of RE minerals has been studied, however, there are still very limited information regarding the effect of anions. The present study examined the impact of specific anions such as Cl−, SO42−, and HCO3− on the flotation performance of rare earth (RE) ore. This study integrates flotation experiments, rheology measurements, entrainment experiments, zeta potential measurements and settling experiments. It is observed that an increase in the concentration of these anions lead to a decrease in the recovery of RE minerals and an increase in the recovery of FeO minerals and thus negatively affecting flotation efficiency. This adverse effect is most pronounced with Cl− and least noticeable with HCO3−. An increase in the non-selective entrainment of gangue minerals is observed when the flotation pulp has higher viscosity. The reduction in the zeta potential of fine particles in the presence of these results in a higher pulp viscosity due to increased attractive forces between particles. These findings were verified by settling experiments and calculations based on the DLVO theory.