Ensemble simulations of a regional climate model assuming smoke aerosol in the Amazon suggest that dynamic changes of cloud cover contributes to the radiative effect of the smoke on the diurnal cycles of surface fluxes and the depth and structure of planetary boundary layer (PBL). In addition to their local effects, the aerosol radiative forcing also appears to weaken or delay the circulation transition from dry to wet season, leading to a weaker moisture transport into the smoke area where the aerosols optical depth, AOD, exceeds 0.3 and a stronger moisture transport and increase of cloudiness in the region upwind to the smoke area. The land surface scheme is modified to improve the regional climate model simulation of the daily mean and diurnal cycle of the surface sensible and latent heat fluxes over the Amazon rain forest. The aerosol radiative forcing is applied to the model during a dry to wet transition season (August–October) in that region. Cloudiness decreases in early afternoon due to the absorption of solar radiation by smoke aerosols partially compensate for the reduction of surface solar flux by aerosol scattering, shifting the strongest changes of surface flux and the PBL to late morning. The reduction of net solar radiation at the surface by smoke is locally largely compensated by reduction of surface sensible flux, with reduction of latent flux only about 30% as large. The strong aerosol absorption in the top 1 km of the aerosol layer stabilizes the 2 to 3 km layer immediately above the daytime PBL and consequently cloudiness decreases. This reduced surface solar flux and more stable lapse rate at the top of the PBL stabilize the lower troposphere. These changes lead to anomalous wind divergence in the southern Amazon and anomalous wind convergence over the equatorial western Amazon in the upwind direction of the smoke area.