The importance of water vapor in arid and hyperarid regions motivates a comparative study in the Atacama and Namib deserts, a natural laboratory to test the role of topography in present-day climate. Based on ERA5 reanalysis evaluated by satellite and ground-based instruments, we focus on the climatological water vapor seasonal cycle and interannual variability offshore the deserts, distinguishing between the free troposphere (FT) and the marine boundary layer (MBL) moisture. In the Namib, moisture variability is strongly controlled by air mass transport. For example, between austral fall and winter, an easterly continental warm and cloud-free air mass settles over the coast, reducing the MBL height to a few hundred meters and decreasing humidity. In summer, the easterly winds are also present, bringing moisture from the center of the continent to the FT of the Namib, along with clouds and rainfall. This feature is intensified during the cold phase of ENSO (La Niña). In contrast, the Andean Cordillera blocks any air mass exchange between the continent and the MBL in the Atacama, allowing the development of stable southerly winds along the coast that transport cold air over warmer waters due to the early westward turn of the Humboldt Current. This induces a strong coupling between SST and MBL moisture, which is enhanced by a permanent stratocumulus cloud cover. In addition, the FT remains drier than the Namib for most of the year due to the predominance of westerly dry air in the region. ENSO is not correlated with the MBL moisture offshore Atacama, and it is the local SST that plays a major role in modulating interannual moisture variability. Only in winter, ENSO seems to impact the FT by increasing the moisture transport from the mid-latitudes during the warm phase (El Niño). We hypothesize that the differences in moisture seasonality and its controlling mechanisms are strongly related to differences in topography and the resulting circulation patterns. Furthermore, similar moisture transport and variability may have been part of a Paleo-Atacama when its topography was similar to the present-day Namib Desert.