Lake Cuitzeo, within the central sector of the Trans-Mexican Volcanic Belt, forms part of a series of palaeolakes of tectonic origin, limited by E-W or NE-SW trending major faults. The lake basin itself is subdivided into half-grabens, where the blocks are tilted southward; this tectonic disposition results in a series of sedimentary environments such as terrigenous facies (near step faults) that have an influence on the lake hydrology and, therefore, on sedimentary and biogenic facies associations.In outcrops of palaeolake Cuitzeo, the deposits are formed by three members that correspond to three well marked cycles of sedimentation. The basal, predominantly formed by clays, a diatom-rich intermediate one and an upper one, formed by silts and pyroclastic deposits that close the limnic cycle. Two interruptions are observed within the lacustrine development, the first associated with an oxidized horizon and the second with an erosional conglomerate of tectonic origin. A marker diatom species for the Miocene-Pliocene boundary (Thalassiosira cuitzeonensis nov. sp.) was found that enables differentiation of the most ancient sequences from the most recent ones.