Dust and sand storms are among the major threats to central Iran. These phenomena pose irreparable risks to natural ecosystems and human societies, including effects on health. In this study, the spatial and temporal pattern of vertical dust flux (VDF) was used to identify dust sources as well as areas with high potential for dust generation. To simulate VDF, two intense dust storms, from 21 February 2015 and 14 February 2018, were selected using synoptic data and Moderate Resolution Imaging Spectroradiometer (MODIS) images. These dust storms were identified as responsible for a reduction of horizontal visibility to less than 1000 m, using remote sensing tools and Ackerman Dust Index. MODIS images show that these two storms covered most of Central Plateau of Iran. The Weather Research and Forecasting model with chemistry (WRF-Chem) was used to simulate the storms, with either the Global Ozone Chemistry Aerosol Radiation and Transport (GOCART) or Air Force Weather Agency (AFWA) scheme to calculate VDF. Modeled vertical dust fluxes in both events indicate that the Arabian deserts in Saudi Arabia and in southwestern Iran can be identified as main sources of the dust in the central Iranian plateau. The other source of dust is the Hirmand Basin, located in the country of Afghanistan and in the southeast of Iran. The results of VDF simulations indicate that central southeast Iran could be the main dust source of internal origin. Additionally, over seasonal wetlands in Iran, the amount of VDF was simulated to be sometimes over 4000 μg/(m2s), an indication that these areas are sensitive to wind erosion in dry conditions and can be a source of dust. The WRF-Chem results were compared with the horizontal visibility measured in synoptic stations in the area. The results showed that the coefficients of determination of GOCART results with the measured horizontal visibility on 21 February 2015 and 14 February 2018 were 0.72 and 0.76, respectively, while the coefficient values from the simulations with AFWA scheme on 21 February 2015 and 14 February 2018 with the measured horizontal visibility were lower, 0.44 and 0.50, respectively. Modern-Era Retrospective analysis for Research and Applications, version 2 (MERRA2) re-analysis data also showed timing of peak dust levels consistent with the GOCART scheme.