Mg clay minerals are usually associated with carbonates in alkaline-saline environments, precipitated from solution and/or transformation from other minerals. The aim of this research is to identify the mineralogy and geochemistry of clay minerals in different alkaline lakes in the Nhecolândia region, the southernmost region of the Pantanal wetland (Brazil). Sediment samples were analyzed by X-ray diffraction, X-ray fluorescence, scanning electron microscopy and transmission electron microscopy. Water samples were analyzed, determining their main cations and anions, in order to understand their relationship with the clays. The analyses allowed classifying the water bodies as saline, oligosaline and freshwater lakes. The sediments are composed mainly of quartz and a fine-clay fraction, dominated by illite, kaolinite and smectite. The XRD results showed illite and smectite mixed-layered in the saline lakes at Barranco Alto farm, whereas at Nhumirim farm, trioctahedral smectite was only observed in one lake. The smectite minerals were normally identified coupled with calcite at the top of the sequences, associated with exopolymeric substances (EPS) in the lakes, suggesting that these minerals are precipitating due to the physical-chemical and biological conditions of the water bodies.