Phosphonates are increasingly used as water-softening agents in detergents, care products, and industrial processes. Despite poor biodegradability, high removal rates during wastewater treatment (WWT) have been observed, owing to strong adsorption affinity to activated sludge and mineral surfaces. Due to phosphonates representing challenging analytes, no method for the compound-specific quantification of phosphonates from solid samples has hitherto been published. In order to improve the data foundation on the environmental fate of phosphonates, an analytical method based on anion exchange chromatography and detection by electrospray ionization coupled to tandem mass spectrometry (IC-ESI-MS/MS) was developed, allowing the trace quantification of phosphonates from surface water (LOQs between 0.04 and 0.16 μg/L), wastewater (LOQs between 0.6 and 2.3 μg/L), sediment and suspended matter of rivers (LOQ < 0.1 mg/kg), and suspended matter of wastewater (LOQ < 1 mg/kg). Specificity and selectivity were enhanced by the implementation of isotope-labeled internal phosphonate standards derived through synthesis. This study describes the development of a comprehensive tool set for the determination of aminotris(methylenephosphonic acid) (ATMP), diethylenetriaminepenta(methylenephosphonic acid) (DTPMP), ethylenediaminetetra(methylenephosphonic acid) (EDTMP), 1-hydroxyethanediphosphonic acid (HEDP), and 2phosphonobutane-1,2,4-tricarboxylic acid (PBTC) during WWT and in the aqueous environment. In the investigated matrices, HEDP and PBTC were generally present in highest and EDTMP in lowest abundance. The phosphonate contents detected in river water were in the sub to low μg/L range, depending on the wastewater burden, whereas contents in the low to medium μg/L range were found in untreated wastewater. The loads of the solid phases exceeded the contents of the corresponding liquid phases by roughly three orders of magnitude. Current data imply that phosphonates undergo significant partitioning to the solid phase during WWT and in natural water bodies.