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<p>The determination of dissolved gases (<span class="inline-formula">O₂</span>, <span class="inline-formula">CO₂</span>, <span class="inline-formula">CH₄</span>, <span class="inline-formula">N₂O</span>, <span class="inline-formula">N₂</span>) in surface waters allows the estimation of biological processes and greenhouse gas fluxes in aquatic ecosystems. Mercuric chloride (<span class="inline-formula">HgCl₂</span>) has been widely used to preserve water samples prior to gas analysis. However, alternates are needed because of the environmental impacts and prohibition of mercury. <span class="inline-formula">HgCl₂</span> is a weak acid and interferes with dissolved organic carbon (DOC). Hence, we tested the effect of <span class="inline-formula">HgCl₂</span> and two substitutes (copper(II) chloride – <span class="inline-formula">CuCl₂</span> – and silver nitrate – <span class="inline-formula">AgNO₃</span>), as well as storage time (24 h to 3 months) on the determination of dissolved gases in low-ionic-strength and high-DOC water from a typical boreal lake. Furthermore, we investigated and predicted the effect of <span class="inline-formula">HgCl₂</span> on <span class="inline-formula">CO₂</span> concentrations in periodic samples from another lake experiencing pH variations (5.4–7.3) related to in situ photosynthesis. Samples fixed with inhibitors generally showed negligible <span class="inline-formula">O₂</span> consumption. However, effective preservation of dissolved <span class="inline-formula">CO₂</span>, <span class="inline-formula">CH₄</span> and <span class="inline-formula">N₂O</span> for up to 3 months prior to dissolved gas analysis was only achieved with <span class="inline-formula">AgNO₃</span>. In contrast, <span class="inline-formula">HgCl₂</span> and <span class="inline-formula">CuCl₂</span> caused an initial increase in <span class="inline-formula">CO₂</span> and <span class="inline-formula">N₂O</span> from 24 h to 3 weeks followed by a decrease from 3 weeks to 3 months. The <span class="inline-formula">CO₂</span> overestimation, caused by <span class="inline-formula">HgCl₂</span> acidification and a shift in the carbonate equilibrium, can be calculated from predictions of chemical speciation. Errors due to <span class="inline-formula">CO₂</span> overestimation in <span class="inline-formula">HgCl₂</span>-preserved water, sampled from low-ionic-strength and high-DOC freshwater, which is common in the Northern Hemisphere, could lead to an overestimation of the <span class="inline-formula">CO₂</span> diffusion efflux by a factor of <span class="inline-formula">&gt;</span> 20 over a month or a factor of 2 over the ice-free season. The use of <span class="inline-formula">HgCl₂</span> and <span class="inline-formula">CuCl₂</span> for freshwater preservation should therefore be discontinued. Further testing of <span class="inline-formula">AgNO₃</span> preservation should be performed under a large range of freshwater chemical conditions.</p>