This paper focuses on the clay mineralogy (using XRD, SEM and TEM methods) of the lacustrine “Calizas de Torrente de Cinca” unit that represents the Oligocene-Miocene transition in the central part of the Ebro Basin (NE Spain). Phyllosilicates are mainly detrital although Mg-smectites could have been generated in the lake. Although a temperate, relatively humid climate dominated the source area during the Oligocene-Miocene transition (Chattian-Aquitanian), as deduced by detrital phyllosilicates assemblage, mineralogical vertical trends along with sedimentological studies indicate some changes. Relatively warmer and more humid conditions during the late Chattian, that favoured increasing chemical weathering, were replaced during the early Aquitanian by drier conditions coinciding with the Mi-1 glaciation effects; this change is coeval with a transition from deeper to shallower lacustrine facies. Phyllosilicate association analysis has also permitted an improvement in the palaeogeographical sketch and infers that the Pyrenees are the main source area for the lacustrine system.