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In vegetation canopies with complex architectures, diffuse solar radiation can enhance carbon assimilation through photosynthesis because isotropic light is able to reach deeper layers of the canopy. Although this effect has been studied in the past decade, the mechanisms and impacts of this enhancement over South America remain poorly understood. Over the Amazon deforestation arch large amounts of aerosols are released into the atmosphere due to biomass burning, which provides an ideal scenario for further investigation of this phenomenon in the presence of canopies with complex architecture. In this paper, the relation of aerosol optical depth and surface fluxes of mass and energy are evaluated over three study sites with artificial neural networks and radiative transfer modeling. Results indicate a significant effect of the aerosol on the flux of carbon dioxide between the vegetation and the atmosphere, as well as on energy exchange, including that surface fluxes are sensitive to second order radiative impacts of aerosols on temperature, humidity, and friction velocity. CO2 exchanges increased in the presence of aerosol in up to 55% in sites with complex canopy architecture. A decrease of approximately 12% was observed for a site with shorter vegetation. Energy fluxes were negatively impacted by aerosols over all study sites.