Abstract Strongly increasing trends in global methane in recent decades highlight the importance of understanding source‐sink attributions and climate feedback mechanisms, especially for large natural sources like wetlands. Here, we present an analysis of airborne methane observations above the Amazon Basin conducted from December 2022 through January 2023 that reveal enhanced methane concentrations, especially below 6 km. Using Bayesian inversion with the atmospheric transport model STILT, we optimize surface fluxes to match our observations, starting from prior bottom‐up flux estimates by WetCHARTs. The posterior suggests underestimated emissions across the Amazon Basin. The largest underestimates occur along rivers and tributaries, where emissions exceeded model values by up to a factor of four. River deltas make up 26% of the underestimated fluxes with reservoirs, and regularly flooded riverine areas contribute 19% and 13%, respectively. This highlights the need for improved understanding of the continuum across wetlands and freshwaters for tropical methane emissions.