River flooding triggered by extreme rainfall events is a major natural hazard that frequently causes fatalities and damages in southeastern France. A 2000-year record of flooding from the Hérault River basin was reconstructed using magnetic susceptibility data from lagoon deposits, supported by documentary databases of floods in coastal river basins from Languedoc over the last centuries. Flooding was particularly important between 800 and 1350 cal CE, i.e. during the warm climatic conditions of the Medieval Climate Anomaly. Moreover, several periods of increased flooding occurred in the 2nd, 6th-7th, 16th, 18th and 20th centuries. Increased flooding was significantly correlated with higher air temperature in the northwestern Mediterranean and with higher sea surface temperature in the Gulf of Lions. The analysis of relationships between river flooding and atmospheric conditions shows that autumn flood events in Languedoc were generally more frequent during the positive phase of the East Atlantic pattern, which is associated with southerly to southeasterly winds in the Gulf of Lions. Besides, increased flooding could also have been controlled by forest decline and human activities after 500 cal CE. Between 1400 and 1800 cal CE, palaeobotanical data show an intensification of land use characterized by an expansion of grasslands and cultivated areas in the coastal lowlands east of the Hérault River. Forest clearings and the development of agriculture seem to have led to a relative increase in river flooding, especially in the late Middle Ages and early modern period.