Ebullition (bubbling) is an important mechanism for the transfer of methane (CH4) from shallow waters to the atmosphere. Because of their stochastic nature, however, ebullition fluxes are difficult to accurately resolve. Hydroacoustic surveys have the potential to significantly improve the spatiotemporal observation of emission fluxes, but knowledge of bubble size distribution is also necessary to accurately assess local, regional, and global water body CH4 emission estimates. Therefore, we explore the importance of bubble size and small-scale flux variability on CH4 transport in and emissions from a reservoir with a bubble-size-calibrated echosounder that can efficiently and economically survey greater areas while still resolving individual bubbles. Using a postprocessing method that resolves bubble density, we found that the largest 10% of the >6700 observed bubbles were responsible for more than 65% of the total CH4 transport. Furthermore, the asymmetry of CH4 ebullition flux distribution and the high spatial heterogeneity of those fluxes suggests that inadvertently omitting emission hot spots (i.e., areas of high flux) could lead to significant underestimations of CH4 emissions from localized areas and potentially from entire water bodies. While the bubble sizes resolved by the hydroacoustic method may provide insight into the factors controlling ebullition (e.g., sediment type, carbon sedimentation), the better resolution of small-scale CH4 emission hot spots afforded by hydroacoustics will bring us closer to the true CH4 emission estimates from all shallow waters, be them lakes, reservoirs, or coastal oceans and seas.