Three wetland‐shallow lakes were studied with the aim of analysing the processes and factors that control hydrochemistry and evaporite deposits in them in basins of the Pampean Plain, Argentina. In this sense, water balances and analysis of the water content of the lakes with normalized water difference index were made, and geologic‐geomorphological characteristics and groundwater flows were defined. Groundwater, surface water and evaporite samples were taken, along with sediment samples from wetland‐shallow lakes and surroundings. In situ pH, electrical conductivity and temperature, and laboratory chemical determinations of major ions of the water were measured. x‐ray diffraction (XRD) and scanning electron microscope (SEM)‐energy dispersive spectroscopy (EDS) analyses of evaporite and sediment samples were carried out. The results obtained allow the identification of two different systems. One of them is represented by Leubucó wetland‐lake basin, which is topographically higher and smaller than the other system, with Na‐HCO3 and Na‐Cl/SO4 groundwater inflows, with high concentrations of Ca2+ and Mg2+. In periods of high evaporation, the regional water table drops, and due to its topographic position, the lake dries. These determine the formation of thick layers of halite associated with magnesium salts on surface, and gypsum layers interbedded with clastic sediments. The other system involves de la Sal and Chasilauquen wetland‐lake basins, which have larger extensions. They receive Na‐HCO3 and Na‐Cl/SO4 groundwater inflow, but with low Mg2+ and Ca2+. Their lower topographic position determines that even during deficit periods, the water table intercepts the lakes surface and therefore, lakes have a shallow surface water level almost all the year, which is hypersaline, Na‐Cl type. These systems only have thin evaporite crusts, composed of halite and thenardite at the edges of the lakes, and the formation of Ca‐Mg sulfates is not observed. It is concluded that topographic position, basins size, geology, groundwater inflow and evaporation are the main processes and factors controlling hydrochemistry and evaporitic deposits.