We developed analytic methods to enable Compound Specific Isotope Analysis (CSIA) of two frequently detected pesticides, bentazone and MCPA. Both occur in negatively charged form at circum neutral pH and are not easily analysed by GC/IRMS. We therefore pursued two strategies, (i) derivatization by trimethylsulfonium hydroxide (TMSH), followed by GC-IRMS, and (ii) analysis by liquid chromatography-isotope ratio mass spectrometry (LC-IRMS). In the tested concentration range (4000-5000 ppm), accurate and precise δ 15N values of -0.63‰ ± 0.3‰ (n = 33) were observed for the bentazone derivative when TMSH was used in a small excess. This value was in perfect agreement with results from elemental analyser-IRMS (EA-IRMS) (δ 15N = -0.62‰ ± 0.03‰). In contrast, carbon isotope values δ 18C of methylated bentazone and MCPA showed a bias towards negative values becoming more positive with increasing excess of TMSH. With an excess of 250 or more, constant and reproducible δ 13C values (SD < 0.3‰) were obtained for bentazone concentrations between 3 and 300 ppm and a MCPA concentration of 200 ppm. In both cases values showed an offset of 1‰ compared to EA-IRMS values, likely because of the addition of a carbon atom during derivatization. In comparison, LC-IRMS results for δ 13C of bentazone (60-200 ppm) also resulted in reproducible values, but surprisingly also showed an offset of 1‰ compared to EA-IRMS values. Our study showed that both methods (derivatization with GC-IRMS and LC-IRMS) are feasible approaches for isotope analysis of ionic pesticides, allowing a novel way to assess their fate in the environment.