The relationships between human modification of the environment and natural events in the Roman city of Lepti Magna (UNESCO world heritage), western Libya, are analyzed. For the first time, the history of Leptis Magna is tested against a geomorphological and stratigraphical reconstruction and radiocarbon dating. Historical and archaeological interpretations or analyses indicate the occurrence of different extreme natural events as the cause of the town’s decline: earthquakes, flooding and tsunami. Geological and geomorphological surveys investigated the dynamics of the nearby Wadi Lebda, a major dryland stream that forms the depositional and erosional systems of the settlement area. Alluvial phases were studied by applying traditional stratigraphic analyses of outcrops and hand-cores. Additionally, the mapped flights of inset terrace surfaces provided insights into the human modifications of the natural depositional/erosional environment during historical times and the following alluvial phases affecting the Leptis Magna harbor. The results integrate the archaeological knowledge by providing some independent chronological constraints, and indicate that Leptis Magna history was tightly linked to the Wadi Lebda. Aware of the hazards related to devastating flooding, the Romans were able to cope with the threat posed by the wadi by performing engineering defensive hydraulic works around the town (dam and artificial channels). Once the economic decay began and the society could no longer guarantee the ongoing maintenance of these structures, the decline of the settlement started and the occurrence of destructive floods reclaimed the populated areas. Conversely, the occurrence of a large earthquake (365 CE), or of a tsunami that caused the disruption of the hydraulic systems and the infill of the harbor, has been discarded as primary cause of the decline of Leptis Magna.