The Bursa-Orhaneli and Keles-Harmanalan coal deposits were developed in swampy and fluvial-lacustrine environments in western Anatolia under the E–W-trending graben zone during the Neogene. The present study aimed to determine the mineralogical and geochemical properties of clays interlayering the coal seams to define the origin of clay minerals, in particular, smectite. These deposits, comprising argillaceous sediment, marl, coal seam, mudstone, organic-rich shale, and sandstone, were deposited in a lacustrine environment accompanied by volcanogenic materials. The characteristics of sediments and their parent rocks were examined using X-ray diffraction, scanning electron microscopy, energy dispersive spectroscopy, palynology, and chemical analyses. The association of abundant smectite with quartz, amphibole, accessory chlorite, and a decrease in feldspar in fluvial-lacustrine sediments compared to those in the smectite accompanied by feldspar and volcanic glass and the absence of quartz and amphibole in the pyroclastic units suggest that smectite had detrital and authigenic origins. Flaky smectite shows either detrital, irregularly outlined coating and filling pores of terrigenous sediments or in situ precipitation edging resorbed feldspar and devitrified volcanic glass. Chemical analyses of the smectite-rich fraction show montmorillonite compositions with an average structural formula of: (Ca0.42Na0.25K0.08)(Al2.76Fe0.47Mg0.59Ti0.07Mn0.002)(Si7.65Al0.35)O20(OH)4.The positive correlation of Al2O3 vs. TiO2 and K2O vs. Rb may be related to the abundant detrital input. Feldspar and biotite were replaced by illite during diagenesis.An increase in the Ni/Co and V/(V + Ni) ratios in the altered units also suggest oxic, suboxic to anoxic conditions, under the control of a dry, warm to subtropical climate in fresh water and lakes during the Late Eocene to Middle Miocene. The slight enrichment of light rare earth elements (LREE) compared to heavy rare earth elements (HREE) with positive Eu and positive/negative Ce anomalies reflect fractional crystallization of feldspar. The δ18O and δD values of smectite and illite fractions and the wide range of δ34S isotope values (–1.5 to 15‰) for pyrite and chalcopyrite associated with coal indicate a signature of both diagenetic and partial hydrothermal origin.