Abstract Repetitive sequences of carbonate deposits, occurrence include in the lower part of the Paleogene Carbonate Unit (northeast border of the Madrid Basin), have been studied, defining regressive lacustrine sequences and early diagenetic processes. Binocular microscopic examination, scanning electron microscopic/energy dispersive X-ray observations, and X-ray diffraction analyses joint to isotopic studies ( δ 18O and δ 13C) have been used to characterise the facies and environments. The sequences consist of a lower uncemented carbonate mud unit, calcitic or dolomitic in composition, and an upper carbonate unit (arenites, bioclastic limestones, and microbial laminated limestones with cherts). Visual features (vertical prismatic structures, fissures, massive nodulization, rhizoliths, brecciation) and microscopic features (micrite micronodules, vug porosity, circumgranular cementation, gypsum lenticular crystals) outline pedogenic processes. These features, found locally in bioclastic and microbial laminated limestones or in dolomite uncemented muds, define, respectively, palustrine limestones or dolocretes. Facies analysis allows us to define several lacustrine sub-environments (basinal, littoral, eulittoral and supralittoral) and characterises different types of shallowing upward lacustrine sequences, either with or without subaerial exposure. The isotopic values of the bioclastic and microbial laminated limestone (from −5.77‰ to −6.78‰ for δ 13C, and from −5.25‰ to −5.53‰ for δ 18O) and those of uncemented calcitic muds (from −5.80‰ to −7.01‰ for δ 13C, and from −4.98‰ to −5.58‰ for δ 18O) establish that both types of carbonates precipitated in equilibrium with meteoric waters. In the palustrine carbonate deposits, the δ 13C values suggest a strong organic contribution. The dolomitization that only affected the uncemented carbonate muds is early interpreted because of the structural and compositional characteristics of the dolomite (micro-rhombic dolomicrite, nearly stoichiometric and poorly ordered), and because the calculated average Δ 18O dol–cal for calcitic and dolomitic uncemented muds is about 6‰. The δ 18O isotopic values indicate that the dolomite precipitated from water that was slightly more enriched in heavy isotopes than the calcite, because of an increase in evaporation rates. Nodules and nodular levels of cherts occur in the upper units of littoral and eulittoral sequences, probably as a consequence of the existence of microbial mats that could include the silica source. According to their mineralogy (Opal CT and quartz/moganite) and structures (double nodules, lamination and bioturbation), three types of chert are described (TB, MB and WO). These types define three general stages of silicification during the early diagenesis, from the recently buried to the postcompactation of carbonate deposits. The δ 18O values of quartz show that the silicification and ageing of opaline phases occurred from meteoric waters, which were lighter than the calcite or dolomite precipitating waters. The cherts included in palustrine limestones show δ 18O values of quartz that record more evaporated waters than those of the general stages of silicification.