A geoarchaeological study of sediments in the Azraq Oasis, in the Eastern Desert of Jordan, provides information on the fluctuations of the geomorphic and hydrologic systems in this region in relation to the local Middle Paleolithic and Upper Paleolithic occupations. The study shows that local geomorphic and hydrological environments fluctuated between marsh, lake and playa (dry lake bed with eolian activity and/or carbonate accumulation). In some instances, local wet conditions correlate with those registered in other regional paleoclimatic records, as is the case of the period comprising MIS 5a and probably early MIS 4. In other cases, however, local wet conditions represented by marsh deposits with hominin occupations are asynchronous with regional wet conditions. This suggests that the Azraq oases may have acted as desert refugia at times of regional adverse climatic conditions. The fact that Azraq represents a potential desert refugia has important consequences for understanding major issues in the Middle Paleolithic of Southwest Asia, namely (1) the arrival, survival, and extinction of populations of both Neanderthals and early modern humans. The location of Azraq at a crossroads between the Levant, the Arabian Peninsula and other regions of the Middle East, is also an important geographic aspect of desert refugia during the critical period of hominin dynamics in the Middle Paleolithic.