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<p>Headspace analysis of CO<span class="inline-formula">₂</span> frequently has been used to quantify the concentration of CO<span class="inline-formula">₂</span> in fresh water. According to basic chemical theory, not considering chemical equilibration of the carbonate system in the sample vials will result in a systematic error. By analysing the potential error for different types of water and experimental conditions, we show that the error incurred by headspace analysis of CO<span class="inline-formula">₂</span> is less than 5 % for typical samples from boreal systems which have low alkalinity (<span class="inline-formula">&lt;</span> 900 <span class="inline-formula">µ</span>mol L<span class="inline-formula">⁻¹</span>), with pH <span class="inline-formula">&lt;</span> 7.5, and high <span class="inline-formula"><i>p</i></span>CO<span class="inline-formula">₂</span> (<span class="inline-formula">&gt;</span> 1000 <span class="inline-formula">µ</span>atm). However, the simple headspace calculation can lead to high error (up to <span class="inline-formula">−</span>300 %) or even impossibly negative values in highly undersaturated samples equilibrated with ambient air, unless the shift in carbonate equilibrium is explicitly considered. The precision of the method can be improved by lowering the headspace ratio and/or the equilibration temperature. We provide a convenient and direct method implemented in an R script or a JMP add-in to correct CO<span class="inline-formula">₂</span> headspace results using separately measured alkalinity.</p>