The stable isotopes of organic matter can provide valuable information on carbon cycling dynamics, microbial metabolisms, and past climates. Since bulk measurements may mask dynamic changes to critical portions of the organic pool, researchers are increasingly isolating individual compounds for isotopic analysis. The amount of carbon isolated is frequently small, requiring specialized equipment for its analysis. We present a simple and accurate method to measure the δ13C values of µg-amounts of organic compounds and dissolved organic matter in freshwaters using wet oxidation and a GasBench II preparation device. Samples containing 3 µg C can be analyzed with a precision of <0.4‰. For samples containing 1.2 µg C, the precision is <0.8‰. The blank is estimated to be ~0.2 µg C. The accuracy of the method is demonstrated for a wide range of compounds including those that are difficult to oxidize such as humic acid and phthalic acid. The δ13C values of DOC from river and riparian ground water determined by this method are comparable with those determined with an elemental analyzer on freeze-dried samples of DOC. The low detection limit and the ease with which it can be combined with isolation techniques such as liquid chromatography make this technique attractive for the off-line analysis of organic compounds, and open new possibilities for the development of methodologies for compound-specific carbon isotope analysis of complex mixtures separated by HPLC. Copyright © 2011 John Wiley & Sons, Ltd.