We assessed the accuracy and utility of a modified high-performance liquid chromatography/isotope ratio mass spectrometry (HPLC/IRMS) system for measuring the amount and stable carbon isotope signature of dissolved organic matter (DOM) <1 µm. Using a range of standard compounds as well as soil solutions sampled in the field, we compared the results of the HPLC/IRMS analysis with those from other methods for determining carbon and 13C content. The conversion efficiency of the in-line wet oxidation of the HPLC/IRMS averaged 99.3 % for a range of standard compounds. The agreement between HPLC/IRMS and other methods in the amount and isotopic signature of both standard compounds and soil water samples was excellent. For DOM concentrations below 10 mg C L–1 (250 ng C total) pre-concentration or large volume injections are recommended in order to prevent background interferences. We were able to detect large differences in the 13C signatures of soil solution DOM sampled in 10 cm depth of plots with either C3 or C4 vegetation and in two different parent materials. These measurements also demonstrated changes in the 13C signature that demonstrate rapid loss of plant-derived C with depth. Overall the modified HLPC/IRMS system has the advantages of rapid sample preparation, small required sample volume and high sample throughput, while showing comparable performance with other methods for measuring the amount and isotopic signature of DOM. Copyright © 2011 John Wiley & Sons, Ltd.