Minerals in stratigraphic sections are valuable tools for reconstructing past environmental conditions. Given the state of preservation of clay minerals, it is possible to determine under what conditions they formed, which provides clues about continental weathering (inherited minerals) and geochemical conditions in the water column or pore waters (neoformed or transformed) of the sedimentary environment. This study presents new mineralogical and chemical data from the Baskil section, a well-preserved middle Eocene Neo-Tethys sequence from eastern Turkey. Greater terrigenous input is marked by the increase of silicate minerals (e.g. phyllosilicates, quartz, and albite) in the section from 40.5 to 40 Ma, which diluted the marine carbonate content. This period is correlative with the global Middle Eocene Climatic Optimum (MECO) event. Authigenic palygorskite increased from the middle to the uppermost portion (similar to 40 to 37.3 Ma) of the section, indicating dryer conditions in the continent and availability of Si and Mg in the water column and pore waters favorable for its formation. Additionally, we suggest a stratified water column with warmer and more saline conditions at greater depths (e.g. > 200 m) after similar to 40 Ma favoring palygorskite and possibly authigenic dolomite precipitation. The mineralogical variations and element chemistry of rocks in the Baskil section reflect how detrital sources and weathering regimes changed in this area during the middle Eocene, and how these changes can be related to global, regional, and local processes.