Facies analysis and 230Th/U dating was performed to clarify if Neogene limestones, which belong to the Brak Member of the Al Maharuqah Formation in the Murzuq Basin, are reliable tracers for the occurrence and extension of large northern Sahara lakes in the Pleistocene, previously described as Lake Megafezzan. The Brak Member is an up to 12 m thick limestone sequence, which crops out at the northern flank of the Wadi ash Shati Valley in the northern Murzuq Basin and unconformably overlies Carboniferous sandstones and claystones. Based on textural and compositional changes, the Brak Mb. can be subdivided into four intervals. A lower interval is transitional between the Carboniferous siliciclastics and the carbonates, and consists of in situ brecciated deposits with a carbonate matrix. A second interval consists of a calcareous matrix-supported conglomerate, which contains pisoids. It is overlain by an evaporate-carbonate interval with gypsum, halite and dolomite. The upper interval of the Brak Mb. is a partly chertified massive limestone with in-situ brecciation, circumgranular cracks, fenestral structures, and gravitational cements. Based on these characteristics, the limestones are interpreted as calcrete deposits, i.e. groundwater calcretes. This is contrary to previous interpretation of the Brak Mb. as a lacustrine limestone. The results of the230Th/U radiometric age dating scatter from indefinite ages to about 240 ka, which could indicate pre-Pleistocene to middle Pleistocene periods of diagenesis in densely cemented carbonates. The facies analysis and age dating results should be taken into account for further reconstructions of the palaeohydrological regime in the northern Sahara, and especially has a repercussion for the assumption that a pronounced phase of humidity occurred north of the central Saharan watershed during the Pleistocene.