Summary The Aral Sea, which has been affected by lake level lowering of approximately 25 m and a salinity increase from 10 to >100 g/l since 1963, represents, along with the Amu Dary Delta a dynamic hydrological system under an arid climate regime. The system receives river water inflow at high seasonal and inter-annual variability from remote alpine source areas. In the Amu Darya Delta, there is a distinct salinity contrast between the low-salinity river water (∼1 g/l) and the salinity of the unconfined GW (GW unconf : 10–95 g/l). The GW unconf levels are predominantly controlled by the seepage of the river water inflow and GW discharge into the shrinking Aral Sea. In June 2009 and August 2009, we sampled water from various sources including surface waters, GW unconf , lake water and soil leachates for chemical analyses. Evaporative enrichment, precipitation/dissolution of gypsum and precipitation of calcite drive the GW unconf to an NaCl(SO 4 ) water type presenting a positive correlation between Na and SO 4 . We model the hydrochemical evolution of the GW unconf in a box model which considers the capillary rise of near-surface GW, the precipitation of minerals in the unsaturated horizon and the seasonal re-flushing of adhesive residual brines and soluble salts. The model documents a rapid increase in salinity over a few annual cycles. Furthermore, the model simulations demonstrate the importance of the aeolian redistribution of soluble salts on the hydrochemical GW evolution. In a lab experiment, halite, hexahydrite and starkeyite are precipitated during the late stages of evaporative enrichment from a representative local brine. Processes specific to different water compartments plausibly explain the variations of selected element ratios. For example, the precipitation of low-Sr calcite in irrigation canals and natural river branches of the delta lowers Ca/Sr. The dissolution of gypsum in soils (Ca/Sr mole ratio ∼ 150) and the possible precipitation of SrSO 4 associated with Sr-depletion in adhesive residual brines increases Ca/Sr in seepage and re-increases Ca/Sr in the unconfined GW. Aral Sea water, which receives high-Ca/Sr surface and groundwater inflow, developed due to continued precipitation of high-Ca/Sr calcite the almost lowest Ca/Sr ratio (∼25) over time. We observed spatial variations in the GW unconf composition: (i) ammonium levels increase strongly due to interaction with lake sediments rich in organic matter and (ii) distinct increases in levels of nitrate, U, Mo and Se locally reflect oxygenation when GW levels decrease. The Amu Darya Delta acts as a sink for boron (uptake via terrestrial vegetation) and a source for bromide (release by degradation of organically-bound Br). Our results concerning the hydrochemical evolution of the GW unconf and additional data from the Aral Sea constrain the parameter ‘GW discharge’ in water budget models of the lake and improve the basis for palaeoclimatic interpretations of sediment records from the Aral Sea.