An increasing number of rivers is being dammed, particularly in the tropics, and reservoir water surfaces can be a substantial anthropogenic source of greenhouse gases. On average, 80% of the CO2-equivalent emission of reservoirs globally has been attributed to CH4, which is predominantly emitted via ebullition. Since ebullition is highly variable across space and time, both measuring and upscaling to an entire reservoir is challenging, and estimates of reservoir CH4 emission are therefore not well constrained. We measured CH4 ebullition at high spatial resolution with an echosounder and bubble traps in two reservoirs of different use (water storage and hydropower), size and productivity in the tropical Brazilian Atlantic Rainforest biome. Based on the spatially most well-resolved whole-reservoir ebullition measurements in the tropics so far, we found that mean CH4 ebullition was twice as high in river inflow areas as in other parts of the reservoirs, and more than 4 times higher in the eutrophic compared to the oligotrophic reservoir. Using different upscaling approaches rendered similar whole-reservoir CH4 ebullition estimates, suggesting that highly spatially-resolved measurements may be more important for constraining reservoir-wide CH4 estimates than choice of upscaling approach. The minimum sampling effort was high (>250 and >1,700 thirty-meter segments of hydroacoustic survey to reach within 50% or 80% accuracy, respectively). This suggests that traditional manual bubble-trap measurements should be abandoned in favor of highly resolved measurements in order to get spatially representative estimates of CH4 ebullition, which accounted for 60% and 99% of total C emission in the two studied reservoirs.