Rationale: Ion chromatography combined with inductively-coupled plasma mass spectrometry is an ideal tool for measuring low concentrations of anionic species such as phosphite; however, the high concentration of chloride and other anions in natural solutions may negatively impact chromatographic separation and data quality. Method: We developed an on-line mechanism of removing chloride from the sample within the ion chromatograph, using an additional valve and a separation column that transfers chloride to waste while phosphite and most other anions are retained. We installed this system in a coupled IC-ICPMS system (ICS6000 and Element 2 in medium resolution mode) and determined linearity and detection limits. In addition, we measured phosphorous species by NMR for comparison as an alternative method for phosphite determination. Results: Chloride was fully removed from the samples while phosphite was retained and could be analysed by IC-ICPMS. Concentrations could be measured down to 0.003 µmol/L and possibly less with good linearity over the explored range (up to 1.615 µmol/L; r ² = 0.999). In contrast, the detection limit by NMR was 6.46 µmol/L. Conclusions: The on-line removal mechanism works well for simplifying sample matrices. It removes the need for costly pre-analytical sample treatment with OnGuard columns. We confirm that IC-ICPMS is the most powerful technique for quantifying phosphite in natural solutions. The new Cl-removal method may also be applicable to analyses of other anions.