In the present study, we used the FORTH deterministic spectral Radiation Transfer Model (RTM) to estimate detailed three-dimensional distributions of the Direct Radiative Effects (DREs) and their consequent modification of the thermal structure of the regional atmosphere during an intense dust episode that took place from 16 to 18 June 2016 over the Mediterranean Basin (MB). The RTM operated on a 3-hourly temporal and 0.5 × 0.625° spatial resolution, using 3-D aerosol optical properties (i.e., aerosol optical depth, single scattering albedo, and asymmetry parameter) and other surface and atmospheric properties from the MERRA-2 reanalysis and cloud properties (i.e., cloud amount, cloud optical depth, and cloud top height) from the ISCCP-H dataset. The model ran with and without dust aerosols, yielding the upwelling and downwelling solar fluxes at the top of the atmosphere, in the atmosphere, and at the Earth’s surface as well as at 50 levels in the atmosphere. The dust direct radiative effect (DDRE) was estimated as the difference between the two (one taking into account all aerosol types and one taking into account all except for dust aerosols) flux outputs. The atmospheric heating rates and subsequent convection induced by dust radiative absorption were calculated at 50 levels to determine how the DDRE affects the thermal structure and dynamics of the atmosphere. The results showed that such a great and intense dust transport event significantly reduces the net surface solar radiation over the MB (by up to 62 W/m2 on a daily mean basis, and up to 200 W/m2 on an hourly basis, at 12:00 UTC) while increasing the atmospheric solar absorption (by up to 72 W/m2 daily and 187 W/m2 hourly, at 12:00 UTC). At the top of the atmosphere, both heating (over desert areas) and cooling (over oceanic and other continental areas) are observed due to the significantly different surface albedos. Transported dust causes considerable heating of the region’s atmosphere, which becomes maximum at altitudes where the dust loadings are highest (0.14 K/3 h on 17 June 2016, 12:00 UTC, at 3–5 km above sea level). The dust solar absorption and heating induce a buoyancy as strong as 0.014 m/s2, resulting in considerable changes in vertical air motions and possibly contributing to the formation of middle- and high-level clouds over the Mediterranean Basin.