Several outcrops with diatoms have been identified in the Neogene-Quaternary Baza basin. The most relevant two are located in the NE margin, in different lithostratigraphic units. Their diatom flora is dominated by Epithemia adnata and Epithemia turgida, a littoral epiphytic aquatic plants. These diatom assemblages are typical of fresh to slightly brackish waters in shallow and alkaline lakes. Those two diatomitic deposits are interstratified between alluvial sediments and represent permanent shallow lakes developed during two wet periods of time. Barranco de las Lumbres is the oldest of these lake events and is dated by fauna and paleomagnetism as late Miocene (Turolian). The upper beds of the younger lake episode (Rincon de la Losa) is dated by paleomagnetism and mammals at 1.9 Ma. In addition to these marginal diatomitic deposits, other outcrops with diatoms have been identified in more central areas of the Basin in Galera village, the lower part of Barranco del Agua section is composed of gypsum, carbonates and dark-brown clays and marls. Here epiphytic shallow-water diatoms Epithemia adnata, Epithemia turgida and some planktonic littoral forms (Fragilaria sp.) suggest a shallow fresh to oligosaline water environment. Additional diatomaceous deposits were located in a more evaporitic zone of the basin near the town of Castillejar. This outcrop presents species (Navicula digitoradiata and Surirella ovalis), which indicate distinctive more saline waters and environment. The distribution of the diatom flora in the Baza basin is consistent with stratigraphic data, which indicates an increase of evaporitic facies towards the center of the basin and the occurrence of different kinds of waters within the lake system. The isotopic composition (δ34S, δ18O) of the gypsum samples of Baza basin (Gibert et al., 2007a) is consistent with a Triassic origin of the sulphate as a result of chemical recycling. These data also suggest that a similar recycling mechanism operated in the saline lake system, where the gypsum sediments from the margins were coevally recycled towards the inner part.