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The sediment-water transition zone in an aquatic system is key role to the distribution of contaminants between the surface water and sediment pore water. Maharlu Lake is a seasonal hypersaline lake in the central part of the Maharlu Basin in Southern Iran. Wastewater of various types produced within the basin is released into the seasonal freshwater rivers that ultimately drain into the lake. Samples were collected through one complete period of the lake water-level fluctuation. Lake surface water and shallow sediment pore water samples were collected three times at three piezometric stations at different distances from the river inflow points. Lake sediment samples were collected twice, and water samples from the inflowing rivers were collected five times. Changes in surface runoff and agricultural wastewater inflows were responsible for seasonal hydrochemical changes and changes in the As concentrations in the inflowing rivers. Data from the stations close to the river inflows indicated that the dissolved As concentrations across the sediment-water interface in Maharlu Lake are mostly controlled by evaporation and interactions between the surface water and shallow pore water. However, data from the station far from the freshwater inflows indicated that the brine and precipitated evaporites were at equilibrium and redox processes (e.g., iron (hydr)oxide dissolution and secondary sulphide precipitation) control the dissolved As concentration in pore water. The results confirmed the role of lake water evaporation in As enrichment and As sequestration by secondary sulphide minerals in sediment below the sediment-water interface. Climate change may alter the lake chemistry and As behavior in near future.