Relations between climate change and landscape evolution during the last two millennia in southeastern coastal Tunisia have been documented using high-resolution reconstruction of flood history and fire activity in the Sebkha Mhabeul core. The age model, based on tephrochronology, indicates that the core extends from Roman to modern times and encompasses the well-defined climatic periods of the last two millennia. This record provides a first palaeoecological/palaeoclimatic high resolution reconstruction in North Africa using a cross-disciplinary approach with both physical (grey-scale intensity, quartz particles) and biological (charcoal and pollen) indicators. The flood history shows four wet/dry cycles (ca. AD 550–950, 950–1300, 1300–1570 and 1570–1870) of different duration. Major hydrological instabilities are concentrated during the Medieval Climate Anomalies and the early Little Ice Age, between AD 1000 and 1550. Direct correlation between climate and fire cannot be established suggesting that the fire history of the Sebkha environment is mainly influenced by human activity. This study demonstrates the great value of sebkhas as palaeoenvironmental archives.