<p>Karst lakes, often sustained by groundwater, feature unique opportunities to investigate lake formation and depositional processes reflecting their dynamic hydrological and geological settings. Located in an arid environment in the centre of the Arabian Peninsula, the recently dried out Layla Lakes reveal a unique history of their formation and contain sediments resulting from complex interlinked depositional processes controlled by seasonal climatic, biological and chemical processes. The region’s gypsum-anhydrite karst formation is interacting with carbonate and sulfate (co-)precipitation processes and is accompanied by caves and sinkhole development. This study employs a combined approach of fieldwork, lithofacies analysis, digital elevation analysis, and digital photogrammetry as well as radiocarbon dating to explore lake-forming processes and the combination of depositional environments that define a distinct evaporitic and biotic sediment inventory. The findings reveal that the collapse of the karst features leading to the formation of groundwater-filled sinkholes within the Layla Lakes could be explained by swelling of anhydrite and the aggradation of a sabkha environment at the surface. Within these sinkholes, laminated lake sediments developed, recording diverse lithofacies produced by subaqueous deposition of biogenic and biotically induced components, together with carbonate–sulfate co-precipitation controlled by water chemistry. Continuous evaporative pumping promoted progressive accumulation of haloturbated and crystalline precipitates within and around the lakes. This study provides a detailed characterization of mixed evaporative sediment associations composed of sulfates, carbonates, and microbial structures, and presents a semi-quantitative facies model over time that may serve as a pilot study for further investigations in similar locations.</p>