The Amazon River basin (ARB) in Sud-America contains the world largest rainforest and biodiversity and plays an important role in the regional and global hydrological cycle. It consist of several sub-basins as the Negro River basin (NRB) in the north and the Madeira River basin (MRB) to the south, both considered of utmost importance in the Amazonia for the Amazon River. The precipitation annual cycle in both basins experiences an opposite annual cycle and as a consequence their contributions to the Amazon River are lagged in time. Here we utilized the Standardized Precipitation Index (SPEI) to identify drought and wet conditions in the NRB and MRB along the period 1980-2016. This index has the advantages over other index because considers the effect of the Atmospheric Evaporation Demand (AED) on drought severity. Besides, the Lagrangian dispersion model FLEXPART v9.0 was used to track backward in time air masses residing over the basins and to calculate along the trajectories the budget of (E-P). This permitted to identify those regions from where air masses gain humidity (E-P>0) before arriving at the basins, what we consider as moisture sources. FLEXPART has been successfully utilized for the same goal in several studies. This allowed investigating the hydrological budget of (E-P) over the NRB and MRB as well as their role as sources of moisture for surrounded continental regions. This study examines the variability of moisture uptake by the basins from these sources during drought and wet episodes in the basins. We consider this a new approach to be a useful method for understanding the causes and variability of drought and wet events in other regions worldwide.