The sedimentological and geochemical properties of a 146 cm long sediment core collected from Sebkha el Melah (Ml core) in south‐eastern Tunisia have been used to infer the genesis and evolution of the Sebkha el Melah over the last 5000 years. Two main sedimentary units have been defined: a huntite [Mg3Ca(CO3)4] unit at the bottom of core Ml is covered by a second unit made up of siliciclastic and evaporitic materials. The huntite level is synchronous with Holocene marine transgression, which was followed by a regression of about 5300 years bp. Geochemical data (major and trace element), magnetic analyses, grain‐size distribution and microtexture of quartz grains were performed to assess the sediment provenance. The upper unit of Ml core is characterized by alternations between fluvial, aeolian and evaporite deposits. Redox proxies displaying marked Fe/Ca and Rb/S peaks, in addition to high magnetic susceptibility (MS) values, polymodal grain‐size frequency curves, as well as sub‐angular grains with V‐shaped percussion cracks, are suggestive of palaeohydrological events. In contrast, a decreasing trend in the low MS values, bi‐modal grain‐size frequency curves as well as well‐rounded quartz grains with crescent percussion marks would indicate enhanced aeolian sand input in the sebkah el Melah sequence. Moreover, geochemical proxies suggest formation of evaporite facies under a strongly warm climate contemporary with marine intrusion.