Atmospheric processes and climate are closely linked to the carbon cycle in the Amazon region as a consequence of the strong biosphere-atmosphere coupling. The radiative effects of aerosols and clouds are still unknown for a wide variety of species and types of vegetation present in Amazonian biomes. This study examines the effects of atmospheric aerosols on solar radiation and their effects on Net Ecosystem Exchange (NEE) in an area of semideciduous tropical forest in the North of Mato Grosso State. Our results show a reduction of assimilation in the NEE with a considerable loss with the decrease of incident solar radiation of 40% and relative irradiance between 1.10-0.67. An average increase of 35-70% in net CO2 assimilation was observed for pollution levels (Aerosol Optical Depth) above 1.25. The increase of 35-70% in the NEE was attributed to the increase of up to 60% in the diffuse fraction of Photosynthetically Active Radiation, concerning its direct fraction. These results were mainly attributable to the Biomass Burning Organic Aerosols from fires over the area studied. Important influences on temperature and relative humidity of air, induced by the interaction between solar radiation and high aerosol load in the observation area, were also observed; an average cooling of 3.0 °C and 10%, respectively. Given the long-distance transport of aerosols emitted by burning biomass, significant changes in CO2 flux can be occurring over large areas of the Amazon, with important effects on the potential for CO2 absorption on ecosystems of semideciduous forests distributed in the region.