From roughly 11 to 5 thousands of calendar years before present (BP), lakes and forests covered the presently hyperarid Saharan desert. This so-called 'African Humid Period' (AHP) is of uppermost interest for the comprehension of climate changes and their impact on the evolution of civilizations. Whether the termination of the AHP was abrupt (occurring within a few hundred years), or not, is still a debated issue. Here, we analyse the variations in diatom fossil assemblages from lake Abiyata (Ethiopia; 7°N) between 6500 and 4500 cal. years BP. Three paleolimnological phases are identified: (1) a phase of stability with diatom characteristic of freshwater conditions, (2) a phase of transition with different, mostly freshwater, species and a high variability of assemblages and (3) a phase with diatoms corresponding to saline conditions and a drier climate. The high variability of diatoms shifting from freshwater to salt-tolerant assemblages in phase 2 may be explained by rapid and intense climate changes and/or by hydrological connection changes, implying large variations in lake conditions and water salinity. Another hypothesis is the existence of a salinity threshold which could generate large variations of diatom communities each time it is crossed, even for minor fluctuations of salinity. The screening of the modern reference African diatom database by gradient forest analysis and the distribution of the species indicator of each paleolimnological phase in the modern salinity gradient, confirm that there might be a salinity threshold between 1500 and 3000 µS.cm-1.