The water cycle over the Amazon basin is a regulatory mechanism for regional and global climate. The atmospheric moisture evaporated from this basin represents an important source of humidity for itself and for other remote regions. The deforestation rates that this basin has experienced in the past decades have implications for regional atmospheric circulation and water vapor transport. In this study, we analyzed the changes in atmospheric moisture transport towards tropical South America during the period 1961–2010, according to two deforestation scenarios of the Amazon defined by Alves et al. (Theor Appl Climatol 100(3-4):337–350, 2017). These scenarios consider deforested areas of approximately 28% and 38% of the Amazon basin, respectively. The Dynamic Recycling Model is used to track the transport of water vapor from different sources in tropical South America and the surrounding oceans. Our results indicate that under deforestation scenarios in the Amazon basin, continental sources reduce their contributions to northern South America at an annual scale by an average of between 40 and 43% with respect to the baseline state. Our analyses suggest that these changes may be related to alterations in the regional Hadley and Walker cells. Amazon deforestation also induces a strengthening of the cross-equatorial flow that transports atmospheric moisture from the Tropical North Atlantic and the Caribbean Sea to tropical South America during the austral summer. A weakening of the cross-equatorial flow is observed during the boreal summer, reducing moisture transport from the Amazon to latitudes further north. These changes alter the patterns of precipitable water contributions to tropical South America from both continental and oceanic sources. Finally, we observed that deforestation over the Amazon basin increases the frequency of occurrence of longer dry seasons in the central-southern Amazon (by between 29 and 57%), depending on the deforestation scenario considered, as previous studies suggest.