The Urrea de Jalón tufa deposits constitute the 20- to 50-m-thick caprock (0·3 km2) of an isolated mesa. They disconformably overlie horizontal strata of the Tertiary Ebro Basin (NE Spain), which contains a thick succession of lacustrine gypsum and marls, followed by limestones, marls and, locally, fluvial sandstones and mudstones. The tufa deposits show a complex, large-scale framework of basin-like structures with centripetal dips that decrease progressively from the base to the top of the tufa succession, and beds that thicken towards the centre of the structure (cumulative wedge-out systems). These geometries reveal that the tufa deposits were affected by differential synsedimentary subsidence. Distinct onlapping depressions reflect time migration of the subsiding areas. The studied carbonates are composed mostly of low-Mg calcite, with minor quartz. Some samples have anomalously high contents of Fe, Mn and Ba that may exceed 1% (goethite, haematite and barite are present). Carbonate facies are: (a) macrophyte encrustation deposits; (b) bryophyte build-ups; (c) oncolite and coated grain rudstones; (d) non-concentric stromatolite-like structures; (e) massive or bioturbated biomicrites; and (f) green and grey marls. Facies a and c show a great variety of microbial-related forms. These facies can be arranged in dm- to 2-m-thick vertical associations representing: (i) fluvial–paludal sequences with bryophyte growths; (ii) pond-influenced fluvial sequences; and (iii) lacustrine–palustrine sequences. The Urrea de Jalón tufa deposits formed in a fluvio-lacustrine environment that received little alluvial sediment supply. Isotope compositions (δ13C and δ18O) reveal meteoric signatures and accord with such a hydrologically open system of fresh waters. The Fe, Mn and Ba contents suggest an additional supply of mineralized waters that could be related to springs. These would have been discharge points in the Ebro Depression of a regional aquifer of the Iberian Ranges. Rising groundwater caused the solution of the underlying evaporites and the synsedimentary subsidence of the tufa deposits.