This study examines the influence of changes in the water coverage in the Hamoun dry-bed lakes on visibility, dust outbreaks, aerosol loading and land-atmospheric fluxes over the region covering the period 1985-2005. The Hamoun basin, located on the southeastern Iran and western Afghanistan borders, has been recognized as one of the major dust source regions in south Asia and is covered by shallow, marshy lakes that are fed by the Helmand and Farahrood rivers. When the water in watersheds that support the lakes is drawn down for natural or human-induced reasons, the end result is a decrease in the water coverage in the basin, or even complete dryness as occurred in 2001. Then, strong seasonal winds, mainly in summer, blow fine sand and silt off the exposed lakebed, enhancing dust activity and aerosol loading over the region. Satellite (Landsat) and meteorological observations reveal that the water levels in the Hamoun lakes exhibit considerable inter-annual variability during the period 1985-2005 strongly related to anomalies in precipitation. This is the trigger for concurrent changes in the frequency of the dusty days, aerosol loading and deterioration of visibility over the region, as satellite (TOMS, MODIS, MISR) observations reveal. On the other hand, soil moisture and latent heat, obtained via model (GLDAS_noah-10) simulations are directly linked with water levels and precipitation over the region. The desiccation of the Hamoun lakes in certain years and the consequent increase in frequency and intensity of dust storms are serious concerns for the regional climate, ecosystems and human health. © 2013 Elsevier B.V.