This study investigated the removal of phthalic acid esters (PAEs) from aqueous solution by the biological activated carbon (BAC) process. PAEs, such as dimethyl phthalate, diethyl phthalate, dibutyl phthalate, and di(2-ethylhexyl) phthalate, were effectively removed at a 40 mg/L activated carbon dosage by emergency activated carbon treatment for excessive amounts of PAEs. The optimal BAC process parameters were an initial PAE concentration of 10 μg/L and an empty bed contact time of 10 min. Results further showed that with higher summer temperatures, mature biofilms were formed, and CODMn, NH3-N and PAE removal efficiency tended to stabilize for approximately 1 month. During stable BAC operation, biodegradation was the primary mechanism.