Abstract. The global nitrous oxide (N₂O) budget remains unbalanced. Currently, ~25 % of the global N₂O emission is ascribed to uncultivated tropical soils, but the exact locations and controlling mechanisms are not clear. In this study, we present the first detailed study of the dynamics of soil nitrogen pools and flux of N₂O from the world's largest wetland Pantanal, South America. At three long-term measurement sites we measured porewater pH, NO₃^–, NH₄⁺ , N₂O and O₂ as well as N₂O dynamics in soil slurry, and in situ fluxes of N₂O and CO₂. The pool of inorganic nitrogen changed (7.1–92 μg NH₄⁺-N g dw⁻¹, and 0.1–201 μg NO₃^–-N g dw^–1) with the seasonal flooding and drying cycles, indicating dynamic shifts between ammonification, nitrification and denitrification. In the field, O₂ penetrated to a depth of 60 cm in dry soil, but O₂ was rapidly depleted in response to precipitation. Soil pH fluctuated from pH 7–7.5 in flooded soil to pH 3.5–4.5 in the same drained soil. Microsensor measurements showed rapid N₂O accumulation reaching >500–1000 Pa in soil slurries due to incomplete denitrification. In situ fluxes of N₂O were comparable to heavily fertilized forest or agricultural soils. The dominating parameter affecting N₂O emission rate was precipitation inducing peak emissions of >3 mmol N₂O m⁻² d⁻¹, while the mean daily flux was 0.43 mmol N₂O m⁻² d⁻¹. Single measurement based screening of in situ activity at 10 Pantanal sites during dry conditions averaged 0.39 mmol N₂O m⁻² d⁻¹. The in situ N₂O fluxes were only weakly correlated (r² = 0.177) with NO₃^– and pH value, showing a tendency (p = 0.063) for NO₃^– concentration to be positively correlated with the in situ N₂O flux and a weaker tendency (p = 0.138) for the pH value to be negatively correlated with the in situ N₂O flux. Over 170 days of the drained period we estimated non-wetted drained soil to contribute 70.0 mmol N₂O m⁻², while rain induced peak events contributed 9.2 mmol N₂O m⁻², resulting in a total N₂O emission of 79.2 mmol N₂O m⁻². The total nitrogen loss via emission of NO, N₂O and N₂ was estimated to be 206 mmol N m⁻² over 170 days, representing 0.7–1.6 % of the total nitrogen in the top 6.5 cm soil layer.