An evaluation of the flux-gradient and the eddy covariance method to measure CH4, CO2, and H2O fluxes from small ponds

•Of the three gaseous fluxes, the CH4 flux suffered the largest high frequency loss.•The aerodynamic model yielded the best results for the CO2 and CH4 fluxes.•The footprint with flux-gradient method was smaller than that of the eddy covariance.•A hybrid scheme is the most appropriate flux observation method for small ponds.