Ten times at intervals of 1–2 months, individual treatment stages of two wastewater treatment plants (WWTPs) were analyzed for the five quantitatively most widely used phosphonates. The total dissolved concentration of the investigated phosphonates in the influents was between 131 µg/L and 384 µg/L. The nitrogen-free phosphonates 2-phosphonobutane-1,2,4-tricarboxylic acid (PBTC) and 1-hydroxyethylidene(1,1-diphosphonic acid) (HEDP) accounted for an average proportion of 83–85%. Diethylenetriaminepenta(methylene phosphonic acid) (DTPMP) contributed with 13–14%, whereas aminotris(methylphosphonic acid) (ATMP) (≤15 µg/L) and ethylenediaminetetra(methylene phosphonic acid) (EDTMP) (≤11 µg/L) contents detected in the WWTP influents were comparatively low. The application of new analytical methods allowed the quantification of phosphonates in the solid fraction of the WWTP influents for the first time. High loads of phosphonates were determined (223–2555 mg/kg), indicating that 20%–80% of the phosphonates are present in the adsorbed state. The removal of total dissolved phosphonate by secondary clarification was between 69.7% and 92.4% (medians: 90.7% and 87.7%). In both WWTPs, HEDP (medians: 89.2% and 86.4%) was slightly better eliminated than PBTC (medians: 87.2% and 82.5%). In the sand filtration stage of a WWTP, the average removal was not further improved. In contrast, an additional removal of dissolved phosphonates could be achieved by activated carbon treatment (median: 96.4%). The proportion of phosphonate-P in the dissolved unreactive phosphorus fraction was consistently between 10% and 40% throughout all treatment stages.