Sedimentological, δ13C and δ18O data from stromatolites in a lower and middle Miocene sequence from the Ebro Basin (N Spain) are used to assess the potential of ancient lacustrine stromatolite lamination as an archive of palaeoenvironmental and palaeoclimatic change. The isotopic evolution through the studied sequence supports a general trend toward less saline conditions with time. Stromatolites and muddy-grainy laminated limestones developed in lake water that underwent little renewal, compared with other carbonate facies. The palaeoclimatic value of the stable-isotope changes and concurrent textural variations in calcite stromatolite lamination is studied at different orders of cyclicity. Stromatolite lamination consists of simple laminae (dark dense, light dense and light porous) grouped into alternating composite light and dark laminae. δ13C and δ18O analyses in consecutive composite laminae (bulk sampling) yielded a cyclic pattern that mimics textural variations. Light laminae, with lower δ13C and δ18O values, reflect higher precipitation/evaporation ratio (P/E) and more influence of biogenic 12C. Dark laminae, with higher δ13C and δ18O values, reflect drier conditions, more complete atmospheric CO2 exchange with water and photosynthetic 12CO2 uptake. Textural features of laminae support these results: the dark laminae are related to higher calcite saturation in lake water during drier periods. Isotopic values from high-resolution sampling through a 2.1-cm thick stromatolite reveal palaeoclimate variations at different temporal scales. Isotopic variation in 3rd order cyclicity of alternating light/dark simple laminae is recording seasonal P/E variations. Light and dark composite laminae (2nd order cyclicity) correspond to pluriannual dominantly-humid or -dry conditions, respectively. A gradual succession from light to dark composite laminae forms the 1st order cycles driven by decreasing P/E through longer pluriannual periods, resulting in lake level lowering. The stromatolites are thus recording lake level changes of centennial to millennial scale.