Determination of compound-specific carbon isotope values by continuous flow isotope ratio mass spectrometry is impacted by variation in several routine operating parameters of which one of the most important is signal size, or linearity. Experiments were carried out to evaluate the implications of these operating parameters on both reproducibility and accuracy of delta13C measurements. A new method is described for assessing total instrumental uncertainty of routine compound-specific delta13C analysis, incorporating both accuracy and reproducibility. These findings have important implications for application of compound-specific isotope analysis in environmental geochemistry and in particular for the rapidly developing field of isotopic investigation of biodegradation and remediation of organic chemicals in contaminant hydrogeology.