Abstract The lacustrine carbonate facies from three allostratigraphic units (N 1, N 2 and N 3) of Miocene age in the Los Monegros region (Ebro Basin) are characterized isotopically. The dominant facies are marls, laminated limestones, stromatolitic limestones, massive limestones and bioturbated limestones. These are associated with lacustrine sulphate deposits and distal alluvial facies. Palaeohydrological reconstructions of the study area are supported by the isotopic and the mineralogical composition of the carbonates. Massive and bioturbated limestones occupy a very similar compositional domain and have the lowest isotopic compositions of all the facies ( −9‰ < δ 18 O PDB < −4.5‰ and −6.4‰ < δ 13 C PDB < −0.4‰ ), reflecting a short residence time of the water and variable, commonly high influence of biogenic CO 2. Laminated limestones and stromatolites define a comparatively enriched domain with δ 18O values ranging from −6 to 0‰ and δ 13C values ranging from −3.5 to 0‰ These values indicate stronger evaporation and enhanced 12C assimilation due to intense biological activity during periods of longer water residence time. Marls have isotopic values intermediate between these two domains and correspond to periods of lacustrine dilution. Dolomite-bearing samples, mainly laminated and stromatolitic facies, show a Δ 18 O DOL-CAL = 7.5‰ with respect to calcite from the same facies, while δ 13C values show very little enrichment (up to 1‰). The positive correlation ( r = 0.85) between 18O and dolomite contents suggests that dolomite resulted from the progressive evaporative concentration of a single water mass and not from the mixing of waters of different compositions. The dolomite is thought to be primary or, at most, the product of very early diagenetic processes. The isotopic composition of the facies and their spatial and temporal variations depend on the depositional environment and were constrained by changing regional paleogeography. Isotopic trends from units N 1 to N 3 (Upper Agenian-Vallesian period) display a regular depletion in heavy isotopes that indicates a climatic change towards wetter conditions.