The processes that determine which areas are strong sources of mineral aerosols are not well known. In this study we consider the role of ephemeral lakes in modulating emissions of atmospheric mineral aerosols. We focus on two ephemeral lake regions that have been identified as source regions: the zone of Chotts in Tunisia and Algeria, and Etosha Pan in Namibia. Comparisons of satellite retrieved inundation data and the TOMS absorbing aerosol index suggest that during some periods of inundation, desert dust loadings are reduced. There is some indication that after flooded areas have dried there is increased dust loading. However, the role of the inundated ephemeral lake compared with nearby regions in modulating desert dust sources is unclear, in addition, problems with interpreting the TOMS AI make conclusions difficult. More research is required to understand the small-scale sources of atmospheric desert dust in dry, unvegetated, topographic lows.