Joint pedological, geochemical, hydrological and geophysical investigations were performed to study the coexistence of saline and freshwater lakes in close proximity and similar climatic conditions in the Nhecolândia region, Pantanal wetlands in Brazil. The saline lakes are concentrically surrounded by green sandy loam horizons, which cause differential hydrological regimes. Mg-calcite, K-silicates, and amorphous silica precipitate in the soil cover, whereas Mg-silicates and more soluble Na-carbonates are concentrated in the topsoil along the shore of the saline lake. In saline solutions, some minor elements (As, Se) reach values above the water quality recommendations, whereas others are controlled and incorporated in solid phases (Ba, Sr). Locally, the destruction of the sandy loam horizons generates very acidic soil solution (pH ~ 3.5) through a process not yet understood. The soil distributions indicate that some freshwater lakes are former saline lakes. They are invaded by freshwater after destruction of the sandy loam green horizons, then the freshwater becomes enriched in K+, SO42-, Fe, Al, and a stream of minor and trace elements. The formation of these green sandy loam horizons in the saline environment and their destruction in the non-saline one emphasizes the dynamic nature of this environment.