The Lake Qarun (Faiyum Oasis, northern Egypt) is a relic of the much larger Holocene lake. Past lake levels and extensions were reconstructed, based on setting of archaeological sites scattered along northern paleoshores of the ancient lake. However, geoarcheological works did not yield enough data to establish continuous environmental history of the lake. A deep drilling FA-1 on the southeastern shore of the lake, performed in 2014, supplied with a core, 26 m long that is the one of the longest lake sediment cores in northeastern Africa. The basal section of the core consisted of thin-laminated diatom marly deposits, underlain at the Late Pleistocene/Holocene boundary by coarse-grained sands. The sediment lamine were quite well developed, especially in the lower part of the core. Preliminary results indicated annually deposited sediment sequence with seasonality signals provided by microlamine of diatoms, calcite, organic matter and clastic material. Early Holocene varved sediments from the Faiyum Oasis supplied with exceptional paleoenvironmental data for northeastern Africa, which enriched a record from previous logs drilled at the southwestern margin of the Qarun Lake.