Constructed wetlands (CWs) are regarded as a risk mitigation strategy for alleviating the risks associated with agricultural runoff that contains pesticides. We investigated the partitioning pattern of wastewater-borne chlorpyrifos, a widely used organophosphorus pesticide, in non-vegetated and vegetated CWs. Removal rates of chlorpyrifos calculated from inflow and outflow concentrations ranged from 87.65% to 96.57%. The average removal rate was significantly higher and more stable in vegetated CWs than in non-vegetated CWs. As determined using a mass-balance method, outflows, macrophytes, substrate micro-degradation, and ”other” accounted for 5.23%, 22.7%, 15.96%, and 56.11%, respectively, of the chlorpyrifos in the vegetated system. Of all Iris pseudoacorus organs examined, the rhizome was dominant in biomass and gathered the largest amount of chlorpyrifos. Except for the uptake of chlorpyrifos by plants, the primary difference between vegetated and non-vegetated CWs was that there was a relatively low potential for chlorpyrifos micro-degradation and volatilization and photolysis in vegetated CWs than in non-vegetated CWs. Identification of this partitioning pattern elucidates the mechanisms underlying chlorpyrifos removal from wastewater in CWs.