The spatiotemporal evolution of droughts in the Congo River Basin (CRB) from 1981–2018 was investigated using the Standardised Precipitation Index (SPI) and Standardised Precipitation–Evapotranspiration Index (SPEI) to assess the roles of precipitation and potential evapotranspiration. The results confirmed a notable trend toward drier conditions, particularly in parts of the northern and central basin, as well as in the south of the CRB, which was associated with increases in potential evapotranspiration and declining rainfall. Global outputs of the Lagrangian model FLEXPART were used to model air masses over four important climatological regions considered to be the main sources of precipitation in the CRB, and their contributions to precipitation over the basin were computed. These analyses confirmed that moisture in the CRB is ~60% self-sourced; African lands were the next greatest contributor, followed by the Indian and Atlantic Oceans. It was found that a reduction in contributions of the sources prevailed during 53 meteorological drought episodes that affected the CRB during the study period and it could be inferred that a reduction in moisture supplied from the Atlantic and Indian Oceans played an important role in the onset of drought episodes. It was also observed that the contribution of moisture from all sources to the CRB decreased during the study period, especially over the northern half of the basin, where the main humid forest of the CRB is located, confirming the importance of water transport and local hydroclimatological dynamics on the hydrological conditions, ecosystems, and local communities of the CRB.