Abstract. The Regional Carbon Balance in Amazonia (BARCA) campaign provided the first Amazon Basin-wide aircraft measurements of ozone (O₃) during both the dry-to-wet (November and December 2008) and wet-to-dry (May 2009) transition seasons. Extremely low background values (< 20 ppb) were observed to the west and north of Manaus in both seasons and in all regions during the wet-to-dry transition. On the other hand, elevated O₃ levels (40–60 ppb) were seen during the dry-to-wet transition to the east and south of Manaus, where biomass burning emissions of O₃ precursors were present. Chemistry simulations with the CCATT-BRAMS and WRF-Chem models are within the error bars of the observed O₃ profiles in the boundary layer (0–3 km a.s.l.) in polluted conditions. However, the models overestimate O₃ in the boundary layer in clean conditions, despite lacking the predominant NO source from soil. In addition, O₃ simulated by the models was either within the error bars or lower than BARCA observations in mid-levels (3–5 km a.s.l.), and lower than total tropospheric O₃ retrieved from the OMI/MLS instruments, which is primarily comprised of middle troposphere O₃ and thus reflects long-range transport processes. Therefore, the models do a relatively poor job of representing the free troposphere-boundary layer gradient in O₃ compared with aircraft and satellite observations, which could be due to missing long-range and convective transport of O₃ at mid-levels. Additional simulations with WRF-Chem showed that the model O₃ production is very sensitive to both the O₃ deposition velocities and the NO_x emissions, which were both about one-half of observed values. These results indicate the necessity of more realistic model representations of emissions, deposition, and convective processes for accurate monitoring and prediction of increases in O₃ production in the Amazon Basin as the regional population grows.