At the Azraq Oasis, located in the Eastern Desert of Jordan, late Middle to early Late Pleistocene wetland deposits contain abundant Lower Palaeolithic stone tools and faunal remains. Focusing on the southern portion of the Azraq Oasis, known as the Shishan Marsh, this study aims to establish the palaeoecological context of this palaeowetland and associated hominin occupations (c. 300–120 ka) using phytoliths and other biogenic silica microfossils. Phytoliths, diatoms, and sponge spicules were extracted from 24 bulk sediment samples from seven stratigraphic profiles across the Shishan Marsh, as well as from three surface sediment samples collected from the Azraq Wetland Reserve and Shaumari Wildlife Reserve. The results indicate that a shallow waterbody existed across the Shishan Marsh during the late Middle Pleistocene, which underwent drying and marsh development due to increasing regional aridity across Marine Isotope Stages (MIS) 8–6. The extensive marsh and associated grassland environment that existed across the Middle to Late Pleistocene transition represented an attractive and resource-rich habitat for fauna and hominins in an otherwise desert region, seemingly acting as a desert refugium during this time.