The static floating chamber technique and the diffusion model approach are the two methods most commonly used for quantifying methane (CH₄) and nitrous oxide (N₂O) fluxes from water bodies. However, the comparability of these two methods for measuring gas fluxes remains unclear. In this study, the water-atmosphere exchange fluxes of CH₄ and N₂O were simultaneously determined using both methods under variable conditions to investigate their comparability. The results showed that most of the CH₄ fluxes determined by either method negatively and linearly correlation with the dissolved oxygen content in the water (significance coefficient P<0.001). Meanwhile, the N₂O flux results from either method could be expressed as a compound function of water temperature, ammonia, nitrate, dissolved carbon, and oxygen following Arrhenius kinetics, by which 86%-90% of the variances in the N₂O fluxes can be jointly explained by these five factors (P<0.0001). The fitting functions provided an apparent activation energy and a temperature sensitivity coefficient (Q₁₀) of 47-59 kJ mol^-1 and 1.92-2.27, respectively. The CH₄ and N₂O fluxes measured using the diffusion model method went from 13% to 1.75 times and from 15% to 2.4 times the results from the chamber method, respectively. The magnitudes of the differences varied between the adopted methods. The differences in the gas fluxes between the two methods ranged from 20% to a 12-fold increase, with a mean of a 2.3-fold increase. Our results suggest that applying a single method exclusively to estimate the CH₄or N₂O fluxes may inevitably yield huge errors, although the flux results from both methods can consistently reflect the processes of gas production kinetics. Our results also suggest that further studies are still needed to verify and quantify the systematic errors which are likely being caused by either the chamber technique or the diffusion model approach.