The Aktoprak Basin, Turkey, provides important clues regarding regional palaeoclimatic changes which have not so far been elucidated. The purpose of the present study is to fill this gap using mineralogical, geochemical and isotopic characterization of cyclic sedimentation within Neogene sedimentary units. Early Miocene alluvial-fan to cyclic shallow-lacustrine sediments of the Aktoprak Basin consist of conglomerate, sandstone, mudstone, marl, limestone and palaeosol. The increasingly fine upward grain size and bed thicknesses suggest that the alluvial fan was fed by an ephemeral braided river. The cyclic sandflat–mudflat–shallow-lake succession is predominantly composed of small-scale sandstone-mudstone beds. Sandstone intervals in the sedimentary cycles are interpreted to be a result of sedimentation from shallow, ephemeral braided-river channels, the deposits having evolved under water-saturated conditions in response to climate changes. The mudstone intervals are interpreted as having been laid down via sedimentation during distal sheet floods which developed either under sub-aerial exposure or in a water-saturated environment. Palaeocurrent measurements indicate that the general transport direction in the Early Miocene was from east to west. The lacustrine sediments of the Aktoprak Basin consist of calcite + quartz + feldspar + serpentine coexisting mainly with smectite ± palygorskite ± illite ± chlorite. Illite and chlorite are either detrital, having originated from basement units, or the illite formed authigenically from smectite. Calcite and clay appear as cement-building conglomerate, sandstone and mudstone. The clay content decreases with increasing calcite and the presence of an inverse relationship between CaO and other oxides may correspond to an inverse relationship between calcite and other minerals. Furthermore, Al2O3, Fe2O3, TiO2, MgO, Ni, Co, Cu, Sr, Ba and Zr values in the smectite-bearing mudstone and sandstone are consistent with the chemical compositions of rocks in the surrounding area, mainly ophiolitic and volcanogenic associations. Micromorphologically, the development of smectite as a cement on leached feldspar, the occurrence of palygorskite fibres as bridges between crystals and rock fragments, as well as the presence of `edging' smectite flakes suggest an authigenic origin. Field observations, mineralogy, geochemistry and the results of δ18O and δ13C isotopic determinations reveal that periodic palaeoclimatic changes were controlled byalternating wet and dry periods that resulted in a relative upward decrease in precipitation of authigenic smectite ± palygorskite within the sections, under the influence of geochemical and pH fluctuations in meteoric water within the shallow-lake environment.