The potent greenhouse gas methane (CH4) is readily emitted from tropical reservoirs, often via ebullition (bubbles). This highly stochastic emission pathway varies in space and time, however, hampering efforts to accurately assess total CH4emissions from water bodies. We systematically studied both the spatial and temporal scales of ebullition variability in a river inflow bay of a tropical Brazilian reservoir. We conducted multiple highly resolved spatial surveys of CH4 ebullition using a hydroacoustic approach supplemented with bubble traps over a 12‐month and a 2‐week timescale to evaluate which scale of variation was more important. To quantify the spatial and temporal variability of CH4 ebullition, we used the quartile coefficients of dispersion at each point in space and time and compared their frequency distributions across the various temporal and spatial scales. We found that CH4 ebullition varied more temporally than spatially and that the intra‐annual variability was stronger than daily variability within 2 weeks. We also found that CH4 ebullition was positively related to water temperature increase and pressure decrease, but no consistent relationship with water column depth or sediment characteristics was found, further highlighting that temporal drivers of emissions were stronger than spatial drivers. Annual estimates of CH4ebullition from our study area may vary by 75–174% if ebullition is not resolved in time and space, but at a minimum we recommend conducting spatially resolved measurements at least once during each major hydrologic season in tropical regions (i.e., in dry and rainy season when water levels are falling and rising, respectively).