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 offshore the deserts by distinguishing the free-troposphere (FT) and marine boundary layer (MBL) humidity. We found that the sea surface temperature (SST) drives the MBL water vapor seasonal variability in both oceanic regions. However, its effect is less marked in the Namib than in the Atacama. Between fall and winter, easterly continental warm and cloud-free air mass settles over the Namib's coast, reducing the MBL height to a hundred of meters. Additionally, the coastal MBL warms up more than the Benguela current SST, reducing vertical motions, inducing clear-sky conditions and further drying the MBL. On the contrary, year round southerly winds in Atacama's MBL transport cold air over warmer waters due to the Benguela current early turn to the west. This vertical temperature gradient induces a strong coupling between the SST and the MBL humidity, enhanced by a permanent stratocumulus cloud cover. Seasonal differences are also found in the FT. The Namib experiences wetter conditions in summer and spring thanks to moist easterlies and northerlies, respectively. This contrasts with the Atacama where the moisture transport is weaker, maintaining a drier FT year round. We hypothesize that the differences in the humidity seasonality and its controlling mechanisms are strongly associated with differences in topography and the resulting circulation patterns. Furthermore, similar moisture transport and variability could have been part of a paleo-Atacama when its topography resembled the nowadays Namib Desert. Keywords: water vapor, reanalysis, atacama, namib, desert, free troposphere, boundary layer, hyperaridity.