AbstractThe 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.