Late Miocene clayey sediments were deposited in lake-margin and shallow-lake environments of the southeastern Central Anatolian Volcanic Province (CAVP). Yellow to red mudstone, alternating with thin beds of conglomerate and sandstone in the Mustafapaşa Formation, is overlain by altered white Cemilköy ignimbrite. Grain size fines upward in each sequence (conglomerate, sandstone, and mudstone). The occurrence of reddish coloration upward, ripple marks, desiccation cracks, plant rootlets and remnants, and the development of initial-stage paleosols in association with smectite reveal that the area underwent alternating periods of siliciclastic and volcaniclastic sediment supply (wet) and drying. Micromorphologically, the development of spongy smectite in mudstone of the Mustafapaşa Formation and vermiform kaolinite in the Cemilköy ignimbrite on resorbed detrital feldspar and devitrified glass reveals in situ precipitation driven by dissolution and precipitation mechanisms. In addition, alteration of these sediments may have resulted in the depletion of soluble alkaline elements, such as Ca, Na, and K, from the ignimbrite downward into the Mustafapaşa Formation. Alternatively, the leaching of these elements – due to the hydrologically open system of the lake environment – may have resulted in the enhancement of Al+Fe/Si-favored precipitation of kaolinite in an acidic environmental condition, namely, of the altered Cemilköy ignimbrite at the top of the profile of the Mustafapaşa Formation, and of smectite in an alkaline setting within lower-level sediments where carbonate minerals were lacking. The coexistence of smectite with accessory illite indicates that illitization occurred via release of K and Al during excess desorption of feldspar. Large Ni and Co values in mudstone samples, and Fe oxidized and partly chloritized pyroxene and hornblende, indicate that the basin was also affected by ophiolite-related supply.