Proximity to large desert areas, 120-day winds in Sistan, runs of severe drought periods, and control of the inflowing upstream waters have led to the drying up of Hamoun Lakes. These factors have transformed the Sistan plain into one of the most active sources of dust emission in southwestern Asia. Accordingly, the present study relied on a framework of spatio-temporal modeling to evaluate the effects of water body changes on dust emission and its climatic feedback across the Sistan plain. The research used remote sensing indices based on the long-term archive of Landsat 5, 7, and 8 data in the 1990–2021 period. The WRF-Chem model was applied under three scenarios including unchanged, 50%, and 100% drying of water bodies in two modes of with and without dust aerosol simulation and their atmospheric radiative feedbacks. The results show that with the drying of water bodies, dust emission increases by an average of about 40% (up to 80%). These conditions affect the radiative forcing of dust aerosol, including intensification of cooling/heating due to the reduction/increasing of shortwave (SW) radiation perturbation on average from −14 to −34 W/m2 at the bottom of the atmosphere (BOA) and from 0.9 to 2.1 W/m2 at top of the atmosphere (TOA). Additionally, these condition leads to the intensification of heating due to the increase in longwave (LW) radiation at BOA and TOA from 8.9 to 15 W/m2 and from 4.3 to 7.7 W/m2, respectively. Therefore, it can be acknowledged that in the 1990–2021 period, the drying of Hamoun Lakes has intensified the surface cooling by reducing net radiation (SW + LW) at the surface.