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This paper describes and interprets the mineral and facies assemblages that occur in carbonate–evaporite shallow lacustrine deposits, considering the importance of the processes pathway (i.e. dolomitization, gypsum calcitization and silicification). The Palaeogene deposits of the Deza Formation (Almazán Basin, central‐northern Spain) are selected as a case study to determine the variety of physicochemical processes taking place in carbonate–evaporite shallow lakes and their resulting diagenetic features. Dolostones are the predominant lithology and are composed mainly of dolomite with variable amounts of secondary calcite (5 to 50%), which mainly mimic lenticular gypsum (pseudomorphs). Five morphological types of dolomite crystal were identified as follows: dolomite tubes, dolomite cylinders, rhombohedral dolomite, spheroidal and quasi‐rhombohedral dolomite, and cocoon‐shaped dolomite. The dolomite cylinders and tubes are interpreted as the dolomitized cells of a widespread microbial community. The sequence of diagenetic processes started with growth of microlenticular interstitial gypsum in a calcareous mud deposited on the playa margin mudflats, and that sometimes included microbial sediments. Immediately following growth of gypsum, dolomite replaced the original calcite (or possibly aragonite) muds, the microbial community and the gypsum. Partial or total replacement of gypsum by dolomite was related mainly to the biomineralization of endolithic microbial communities on gypsum crystals. Later calcitization took place under vadose, subaerial exposure conditions. The development of calcrete in distal alluvial settings favoured the release of silica and subsequent silicification on the playa margin mudflats. Stable isotope compositions of calcite range from −9·02 to −5·83‰ δ13CPDB and −7·10 to 1·22‰ δ18OPDB; for the dolomite, these values vary from −8·93 to −3·96‰ δ13CPDB and −5·53 to 2·4‰ δ18OPDB. Quartz from the cherts has δ18OSMOW values ranging from 27·1 to 31·1‰. Wide variation and relatively high δ18OSMOW values for dolomite indicate evaporitic and closed hydrological conditions; increased influx of meteoric waters reigned during the formation of secondary calcite spar., This research was funded by the Spanish Ministry of Economy and Competitiveness, projects CGL2011‐27826‐CO2‐02 and CGL2014‐54818‐P.

Four regressive sequences are present in the opaline rocks and related deposits of the Miocene Intermediate Unit of the Madrid Basin. The sequences consist of silty mudstones and argillaceous opals, separated by transitional facies. The silty mudstone consists mainly of dioctahedral smectites, whereas the argillaceous opal is principally opal-CT and variable amounts of sepiolite. In the transitional facies, lamina of dioctahedral smectite co-exist with neoformed opal-CT and sepiolite. Petrological and geochemical features (major, trace and REE elements) indicate that the opaline levels and the transitional facies are related and are a consequence of silcrete formation in an argillaceous playa deposit. The isocon method was used to calculate changes in element concentration associated with silcrete formation. The geochemical data suggest silicification in an arid environment. The silcrete profile occurs four times, possibly as a result of highstand–lowstand fluctuations of the lake level caused by climatic changes. Structures and cements in the silcretes indicate that, although silicification may have commenced at the top of a groundwater table, it continued in the unsaturated zone above the water table.

In Upper Jurassic carbonate turbidites of the Betic mountains (southern Spain), chert occurs in three morphologies: bedded chert, nodular chert and mottled chert. The last refers to a weak dispersed and selective silification which gives a speckled appearance to the rock. The three types of chert are formed by replacement of limestones and are associated with different calcareous facies. Turbidite packstones of Saccocoma and peloids, and turbidite lime mudstones of pelagic material contain bedded and nodular cherts. The silicification textures are mainly micro- and cryptocrystalline quartz, with local chalcedonic quartz (both length-fast and length-slow) which is more common in the packstones. Only mottled chert is produced where calcareous breccia beds are silicified. Mottled chert consists of micro- and cryptocrystalline quartz, length-slow chalcedonic quartz and mosaics or individual crystals of euhedral megaquartz. Beds and nodules are the result of early diagenetic silicification, with silica derived from the calcitization and dissolution of radiolarians and, subordinately, sponge spicules, whereas mottled chert is the consequence of later silicification in a probably Mg-rich environment. Early silicification is mainly confined to turbidite beds and only rarely occurs in the interbedded pelagic limestones. Turbidite sedimentation favours silicification because rapid burial of the transported siliceous tests prevents silica from the dissolution of tests passing into overlying sea water. A silica-rich interstitial fluid develops in the turbidite layer and this migrates to more permeable zones giving rise to bedded and nodular chert.