<p>Estimations of methane (CH<sub>4</sub>) emissions are often based on point measurements using either flux chambers or a transfer coefficient method which may lead to strong underestimation of the total CH<sub>4</sub> fluxes. In order to demonstrate more precise measurements of the CH<sub>4</sub> fluxes from an aquaculture pond, using higher resolution sampling approach we examined the spatiotemporal variability of CH<sub>4</sub> concentration in the water, related fluxes (diffusive and ebullitive) and relevant environmental conditions (temperature, oxygen, chlorophyll-a) during three diurnal campaigns in a hyper-eutrophic fishpond. Our data show remarkable variance spanning several orders of magnitude while diffusive fluxes accounted for only a minor fraction of total CH<sub>4</sub> fluxes (4.1–18.5 %). Linear mixed-effects models identified water depth as the only significant predictor of CH<sub>4</sub> fluxes. Our findings necessitate complex sampling strategies involving temporal and spatial variability for reliable estimates of the role of fishponds in a global methane budget.</p>