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Plant water extracts typically contain organic materials that may cause spectral interference when using isotope ratio infrared spectroscopy (IRIS), resulting in errors in the measured isotope ratios. Manufacturers of IRIS instruments have developed post-processing software to identify the degree of contamination in water samples, and potentially correct the isotope ratios of water with known contaminants. Here, the correction method proposed by an IRIS manufacturer, Los Gatos Research, Inc., was employed and the results were compared with those obtained from isotope ratio mass spectrometry (IRMS). Deionized water was spiked with methanol and ethanol to create correction curves for δ18O and δ2H. The contamination effects of different sample types (leaf, stem, soil) and different species from agricultural fields, grasslands, and forests were compared. The average corrections in leaf samples ranged from 0.35 to 15.73‰ for δ2H and 0.28 to 9.27‰ for δ18O. The average corrections in stem samples ranged from 1.17 to 13.70‰ for δ2H and 0.47 to 7.97‰ for δ18O. There was no contamination observed in soil water. Cleaning plant samples with activated charcoal had minimal effects on the degree of spectral contamination, reducing the corrections, by on average, 0.44‰ for δ2H and 0.25‰ for δ18O. The correction method eliminated the discrepancies between IRMS and IRIS for δ18O, and greatly reduced the discrepancies for δ2H. The mean differences in isotope ratios between IRMS and the corrected IRIS method were 0.18‰ for δ18O, and −3.39‰ for δ2H. The inability to create an ethanol correction curve for δ2H probably caused the larger discrepancies. We conclude that ethanol and methanol are the primary compounds causing interference in IRIS analyzers, and that each individual analyzer will probably require customized correction curves. Copyright © 2011 John Wiley & Sons, Ltd.