The fate and distribution of six phthalate esters (PAEs) in a municipal wastewater treatment plant (WWTP) employing an anaerobic/anoxic/oxic (A2/O) process were investigated. The process achieved relatively high removal efficiencies of PAEs in the range 55–97%. It illustrated that biotransformation and sludge-adsorption were major elimination pathways by analyzing the mass balance and flux of PAEs. About 83% of ∑PAEs was entirely removed by A2/O bioreactors indicating biotransformation is the dominant removal mechanism. PAEs with shorter alkyl chain length and higher water solubility were more biodegradable. Less than 6% of ∑PAEs were removed by excess sludge adsorption. The sludge-adsorption capacity of PAE depends on its hydrophobicity. The levels and fluxes of PAEs were analyzed by monitoring different sites of the receiving river of the WWTP effluent to clarify the potential impact of discharge. Daily flux of PAEs upstream and downstream of the discharging point were 113 kg·d−1 and 205 kg·d−1, respectively, which were higher than the effluent devotion value of 6.67 kg·d−1. It suggested that the emissions from the WWTP appeared to be less than those from the other possible sources, such as potential untreated discharge and surface runoff. Improvement of wastewater collection efficiencies is necessary to eliminate the PAE load in the urban river.