Lakes are sources of nitrous oxide (N2O). However, labor-intensive gas analysis has confined evaluations of temporal variability in lakes to the seasonal time scale. We used a state-of-the-art laser-based N2O analyzer combined with a floating chamber to examine sub-daily variations in N2O emissions from a shallow eutrophic lake in Japan. We conducted intense daytime field campaigns during different seasons to reveal differences in sub-daily variations in N2O emissions from the water surface in conjunction with the dynamics of dissolved N2O concentrations in the lake water. The study revealed that N2O fluxes varied within a day: emissions increased in response to increased wind speeds. Variations in surface dissolved N2O concentrations caused by water mixing were also important during the summer, when accumulation of N2O initially occurred in the lake bottom layer during stably stratified conditions. During winter, the lake water was well mixed and dissolved N2O concentrations were uniform throughout the water column; thus, wind speed was the only factor controlling the diurnal variations in N2O emissions. These findings demonstrate the need to consider diurnal variability when estimating cumulative N2O emissions accurately over long periods.