Previous studies have revealed that chlorinated and non-chlorinated organophosphorous flame retardants and plasticisers are important contaminants in German surface waters and it has been demonstrated that wastewater treatment plants contribute to the emission of these substances. In this study temporal development as well as elimination efficiency were determined in two wastewater treatment plants (STP) in the Ruhr/Rhine area at different stages of the wastewater treatment process. The samples were analysed for the non-chlorinated organophosphate esters tri-n-butylphosphate (TnBP), tri-iso-butylphosphate (TiBP), tris-(butoxyethyl)-phosphate (TBEP) and triphenylphosphate (TPP) and the chlorinated organophosphate esters tris-(2-chloro, 1-methylethyl)-phosphate (TCPP), tris-(2-chloro-, 1-chloromethylethyl)-phosphate (TDCP) and tris-(2-chloroethyl)-phosphate (TCEP). The study showed that there were significant differences in the elimination of chlorinated and non-chlorinated organophosphorous flame retardants. The elimination rates ranged from 57–86% for TiBP, TnBP and TBEP at both STP’s. No elimination of the chlorinated flame retardants TCPP, TDCP and TCEP was observed in any of the sampled STPs. At both STPs the first treatment steps and the final filtration did not contribute to the elimination of the non-chlorinated organophosphorous flame retardants while the aeration step did. At both STPs the efficiency of the cleaning process concerning the flame retardants was comparable. Thus the type of construction of the STP was not relevant for the elimination of these substances. Additionally a strong day-to-day variation was observed, while in one STP a temporal trend for TCPP during the week was found.