Activated carbon filter is often used as the pretreatment process of nanofiltration or reverse osmosis membrane system, especially when the content of organics and free chlorine in influent water is high. However, a lot of microorganisms often rapidly reproduce in the activated carbon filter after continuous operation, resulting in a large number of bacteria in the effluent. So when the activated carbon filter was used as pretreatment of membrane systems, membrane fouling caused by biological contamination often occurred. The objective of this paper was to discuss how to effectively control the activated carbon biological contamination. Three different control methods—water backwashing, hot alkali treatment and ultrasound treatment were compared. Results showed that ultrasound treatment was the most effective. A relatively high removal efficiency of biomass (above 90%) was obtained when 40 kHz ultrasound was applied at 90 W for 20 min. Bacterial count in the effluent can be decreased from 3.90×104CFU•mL-1 to 8.5×103CFU•mL-1. After 3 days of continuous operation, bacteria count increased from 8.5×103CFU•mL-1 to 4.06×104CFU•mL-1. After ultrasound treatment, the removal efficiency of CODCr increased from -386.3% to 73.8%.