In the current study, sequential nitrification and anoxic experiments in synthetic municipal wastewater were exposed to 0.5 to 100 mg/L of chlortetracycline for 24 h to evaluate acute impact on the nitrification, and denitrification processes of biological treatment. Both processes were significantly (p < 0.05) inhibited at >50 mg/L of chlortetracycline, and the results revealed that nitrification was adversely affected by chlortetracycline compared with the anoxic process. In nitrification, chemical oxygen removal (COD) and ammonia oxidation kinetics were 50% inhibited at 10 mg chlortetracycline/L, and nitrite oxidation kinetics at 0.5 mg chlortetracycline/L. Likewise, in the anoxic process, 14 and 10 mg/L of chlortetracycline inhibited 50% of COD removal and nitrate reduction kinetics, respectively. In nitrification and denitrification, 90% of chlortetracycline was removed by adsorbing onto sludge suspended solids. In addition, a higher chlortetracycline concentration in anoxic effluent, compared with aerobic effluents, indicated a dissimilarity in the composition of sludge solids, pH, and biomass production for both processes.