The Atlas Mountains are classically regarded as a failed Mesozoic rift arm subject to Alpine inversion, folding and thrusting. Here, we present new integrated structural and sedimentological studies that have revealed numerous Early–Middle Jurassic diapiric ridges and minibasins, characterized by distinctive halokinetic structures. Diachroneity in halokinesis is observed across the Central High Atlas, waning first in the SW during the Early–Middle Jurassic (Jbel Azourki and Tazoult ridges) and continuing to late Middle Jurassic towards the NE (Imilchil region). The halokinetic structures are readily differentiated from the effects of later Alpine deformation, allowing a new picture of the Central High Atlas to emerge. The most pervasive deformation in the Central High Atlas is associated with Early–Middle Jurassic diapirism, whereas the impact of Alpine inversion is mostly focused at the basin margins. This new understanding helps explain previously problematic aspects of the Atlas Mountains, which we now recognize as an exceptionally well exposed natural laboratory for understanding the interactions between halokinesis, tectonics and sedimentation.