Pre‐evacuated Exetainers are commonly used as measurement vials for the determination of methane (CH₄) and nitrous oxide (N₂O) concentrations in liquid and gaseous samples from aquatic environments. The impact of residual air in these Exetainers on measurement accuracy is assessed. Residual air pressure in commercially available, pre‐evacuated Exetainers varied between 0.071 ± 0.008 atm and 0.180 ± 0.031 atm in examined batches. This background contamination can lead to large errors when determining dissolved and gaseous CH₄ and N₂O concentrations particularly at low concentrations. A method for Exetainer pretreatment is suggested and verified, to reduce the residual CH₄ and N₂O. Vials are flushed (needle 30 G × 0.5″, 0.3 mm) with nitrogen gas (N₂) for 5 min, which reduces the background CH₄ and N₂O concentrations to 0.092 ± 0.008 ppm and 0.016 ± 0.001 ppm, respectively, approximately 3–4% of their respective concentrations in air. To avoid an alteration of sample concentration by variable residual gas levels left during a pre‐evacuation step, liquid and gaseous samples are injected into the N₂ filled Exetainers. For gaseous samples where large volumes of gas are available, Exetainers can alternatively be flushed with 100 mL of sampling gas. For gaseous samples, measured CH₄ and N₂O concentrations of standard gases were statistically identical to their known concentrations. For liquid samples, measured CH₄ and N₂O concentrations of liquid standard dilution series showed strong linear correlations with theoretically calculated concentrations (slope CH₄: 1.04, slope N₂O: 1.12). Sample concentrations remained constant over a minimum storage period of 6 weeks.