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.