This article focuses on the molecular geochemistry of previously unreported carbonate- and siliceous-mat assemblages at two adjacent lake-shore environments. The first study area, on the Lake Van shore, is an intersection of hyper-alkaline lake water and seep water discharge, both of which represent an acid-base geochemical barrier. Comparing alkaline lake water with seep water samples collected from a biomineralization site reveals that seep water has an acidic character and is rich in Ca and Si cations. The second study area, Mt. Nemrut, is the largest volcanic caldera located west of Lake Van in eastern Anatolia, and is the only volcano that has erupted in historical time. While the main lithified-mat components of Lake Van's shore environments are Ca-carbonate and diatoms, Na-carbonate and diatom assemblages represent recent biomineralization in the Mt. Nemrut Souk Lake shores. In particular, the normal habitat for the development of these unique microbial mat assemblages can be changed in a short time by the decreasing seep water discharge into the Lake Van shore environment. A detailed study on these lake shore microbialites, before they are lost, would provide a great opportunity to understand the biogeochemical interactions that produce unique sediment fabrics.