The Pantanal region of Brazil is the largest seasonally flooded tropical grassland and, according to local chamber measurements, a substantial CH₄ source. CH₄ emissions from wetlands have recently become of heightened interest because global atmospheric ¹³CH₄ data indicate they may contribute to the resumption of atmospheric CH₄ growth since 2007. We have regularly measured vertical atmospheric profiles for 2 years in the center of the Pantanal with the objectives to obtain an estimate of CH₄ emissions using an atmospheric approach, and provide information about flux seasonality and its relation to controlling factors. Boundary layer-free troposphere differences observed in the Pantanal are large compared to other wetlands. Total emissions based on a planetary boundary layer budgeting technique are 2.0-2.8 TgCH₄ yr⁻¹ (maximum flux ∼0.4 gCH₄ m⁻² d⁻¹) while those based on a Bayesian inversion using an atmospheric transport model are ∼3.3 TgCH₄ yr⁻¹. Compared to recent estimates for Amazonia (∼41 ± 3 TgCH₄ yr⁻¹, maximum flux ∼0.3 gCH₄ m⁻² d⁻¹) these emissions are not that large. Our Pantanal data suggest a clear flux seasonality with CH₄ being released in large amounts just after water levels begin to rise again after minimum levels have been reached. CH₄ emissions decline substantially once the maximum water level has been reached. While predictions with prognostic wetland CH₄ emission models agree well with the magnitude of the fluxes, they disagree with the phasing. Our approach shows promise for detecting and understanding longer-term trends in CH₄ emissions and the potential for future wetlands CH₄ emissions climate feedbacks.