Determination of dissolved greenhouse gas (GHG) in freshwater allows us to estimate GHG fluxes. Mercuric chloride (HgCl₂) is used to preserve water samples prior to GHG analysis despite its environmental and health impacts and interferences with water chemistry in freshwater. Here, we tested the effects of HgCl₂, two substitutes and storage time on GHG in water from two boreal lakes. Preservation with HgCl₂ caused overestimation of CO₂ concentration with consequences for GHG flux estimation.