It is essential for a full-scale treatment plant processing saline wastewater to understand the effects of salt on an activated sludge system and the performance of pollutant removal. For this purpose, a bench-scale modified university of cape town (MUCT) process was tested to treat real saline sewage with salt concentrations of 5, 8, 10 and 15 g/L. The experimental results indicated that salt in sewage significantly affected nutrient removal compared with organic removal. Total phosphorous removal efficiency in MUCT deceased from 92% when treating freshwater to 72% when treating 8 g/L saline wastewater, while total nitrogen removal efficiency decreased from 75% to 62%. Vital number of aerobic heterotrophic bacteria shrunk when salt concentration in wastewater was over 15 g/L, resulting in decreased organic removal efficiency. Obvious nitrite accumulation in the aerobic tank and denitrifying nitrite by polyphosphate accumulating organisms (PAOs) in the anoxic tank occurred in the MUCT treating saline sewage containing over 8 g/L NaCl. Elevated salt level enhanced the carbon requirement for phosphorus release. Population shift in biological community (aerobic-heterotrophic, nitrifying, and denitrifying organisms) in treatment system was observed in response to salinity inhibition, which contributed to an insight into the nature and the magnitude of the salt effects.