Freshwaters bring a notable contribution to the global carbon budget by emitting both carbon dioxide (CO2) and methane (CH4) to the atmosphere. Global estimates of freshwater emissions traditionally use a wind-speed-based gas transfer velocity, kCC (introduced by Cole and Caraco, 1998), for calculating diffusive flux with the boundary layer method (BLM). We compared CH4 and CO2 fluxes from BLM with kCC and two other gas transfer velocities (kTE and kHE), which include the effects of water-side cooling to the gas transfer besides shear-induced turbulence, with simultaneous eddy covariance (EC) and floating chamber (FC) fluxes during a 16-day measurement campaign in September 2014 at Lake Kuivajärvi in Finland. The measurements included both lake stratification and water column mixing periods. Results show that BLM fluxes were mainly lower than EC, with the more recent model kTE giving the best fit with EC fluxes, whereas FC measurements resulted in higher fluxes than simultaneous EC measurements. We highly recommend using up-to-date gas transfer models, instead of kCC, for better flux estimates. BLM CO2 flux measurements had clear differences between daytime and night time fluxes with all gas transfer models during both stratified and mixing periods, whereas EC measurements did not show a diurnal behaviour in CO2 flux. CH4 flux had higher values in daytime than night-time during lake mixing period according to EC measurements, with highest fluxes detected just before sunset. In addition, we found clear differences in daytime and night-time concentration difference between the air and surface water for both CH4 and CO2. This might lead to biased flux estimates, if only daytime values are used in BLM upscaling and flux measurements in general. FC measurements did not detect spatial variation in either CH4 or CO2 flux over Lake Kuivajärvi. EC measurements, on the other hand, did not show any spatial variation in CH4 fluxes but did show a clear difference between CO2 fluxes from shallower and deeper areas. We highlight that while all flux measurement methods have their pros and cons, it is important to carefully think about the chosen method and measurement interval, as well as their effects on the resulting flux.