Interdune deposits are sensitive to climatic fluctuations and ancient interdune lacustrine systems can reveal the drivers of erg dynamics through time and space. This southern African study details the dynamics of interdune deposition in a vast ancient desert system that was active over Pangaea in the Middle Mesozoic and formed part of one of the largest known sand seas in Earth's history. Focusing on the Sinemurian to Pliensbachian Clarens Formation in the main Karoo Basin (south-west Gondwana), three facies associations were identified that formed in meso-scale and macro-scale lakes amongst aeolian dunes and sand sheets of the Clarens erg system. The northern facies association is restricted to interdune hollows within an actively climbing dune system. High-sediment availability and high-wind speeds limited the space available for these meso-scale lakes to expand. Here, migrating dunes outpaced the water table rise promoting the formation of discontinuous lenses of lake deposits, as is typical in erg centres. The southern facies associations developed both in spatially isolated meso-scale lakes, where flooding was controlled by groundwater inundation (water table rise), as well as in macro-scale lakes, where flooding was related to groundwater inundation and floods (surface runoff) that induced terminal splays. Relative to the north, the southern facies associations, with their more significant thickness and lateral extent, show that, here, the basin was characterized by a higher rate of relative subsidence. Moreover, the southern lake systems were established along the erg's margin, where the interdunes expanded during pluvial phases. Ultimately, the facies associations in the Clarens Formation show that the widespread arid conditions in the Early Jurassic of south-west Gondwana were subjected to prolonged and repeated pluvial phases in an otherwise harsh environment. Given the prominence of Jurassic aeolianites across Pangea, this study provides a southern African perspective on global palaeoerg dynamics and Early Jurassic climatic shifts.