Lake Pavin, a maar lake was formed approximately 7000 years ago by a phreatomagmatic explosion, leaving a deep central crater with shallow steep side slopes. PAV12 core, collected from the center of the lake, displayed two diatomite layers, separated by a 4-m thick unit of reworked sediments. Diatom diversity and zonation analyses registered six zones documenting the lake evolution. Asterionella formosa, Pantocsekiella ocellata and Discostella pseudostelligera (including f. diminuta) along with fragilariod taxa composed the basal unit (L-1, ~ 6900 to 6570 cal a BP). With increased mineralization of the lake waters, Stephanodiscus taxa became the major species (L-2, 6190-3800 cal a BP). A transition zone was noted between Zone L-2 and L-3 (3950-3700 BP) and related to a major change in diatom composition. Asterionella formosa and Nitzschia paleacea dominated Zone L-3 (3760-1470 cal a BP) with a large decrease in Stephanodiscus taxa. This major change has been related to soil erosion and the possible development of meromixis. Stephanodiscus parvus and Asterionella formosa dominated the upper diatomite zone L-4 (640-400 cal a BP) while zone L-5 (290-160 cal a BP) is dominated by Aulacoseira subarctica (including f. recta) and may be caused by the Little Ice Age. Zone L-6 (subrecent) saw a return to similar conditions as in zone L-4. The gradual opening of the diversified forest and appearance of regional agriculture appears to be related to the development of meromixis. Changes in the upper diatomite zone are related to agricultural activity, changes in incomplete overturn and climate. This study examines relationships between diatom changes and pollen and geochemical changes observed within the lake.