In August 2002, new hydrochemical and hydrophysical data were collected in the Aral Sea. The survey includes cross-sections in three locations: within the Small Aral close to Tastubek Bay, in the Large Aral at the northern tip that is Tschebas Bay and within the western basin at Chernishov Bay. All three locations represent different stages in the hydrochemical evolution of the Aral Sea. Depth profiles of pressure, temperature, conductivity, pH and dissolved oxygen were measured with a YSI 6600 profiler. Water samples were taken with a Niskin bottle and analyzed for dissolved oxygen and nutrients by standard photometric methods. Major anions and cations were analyzed by ion chromatography and ICP-OES, respectively. Benthic flux experiments were carried out with sediment cores in a batch mode assay on-site. In the Small Aral, the changes in the hydrochemical properties are not as dramatic as in the Large Aral. The Small Aral represents a brackish inland water body with salinities of 17–18 g kg−1. The wind-mixed layer reached 8 m during the survey. The salinity is vertically and horizontally almost uniform. Below 8 m, a temporally hypoxic layer forms during summer. Salt redissolution was found to be an important source of salt in the water. About 33.5 g SO42− m−2 day−1 and about 30.7 g Cl− m−2 day−1 are released from the sediment in summer. In the Large Aral, the salinity distribution is uniform in shallow waters (less than 5 m) but varies strongly in deeper water. Tschebas Bay at the northern tip of the large Aral represents a shallow lagoon with a maximum depth of about 6 m. The water column was well mixed down to the bottom (~6 m) having salt concentrations of 82 g kg−1 on average. Almost no gradients in dissolved substances were observed. It is suspected that salinity is balanced by fresher water inflow originating from the Syr Darya flowing south and by groundwater exfiltration. Chernishov Bay in the north of the western basin is meromictic. Below a wind-mixed layer, a very strong pycnocline of 20 g kg−1 per m at 5 m depth isolates the water below from exchanges with the water above and led to the formation of huge anoxic water body down to the bottom at about 25 m depth. Below 10 m, the water contains hydrogen sulphide. The salt concentration increases from 82 g kg−1 in the surface water to 110 g kg−1 at depth. The salt release from the sediment is as high as 1143 g SO42− m−2 day−1 and 1626 g Cl− m−2 day−1. Benthic release of salt is considered as an important source for salt in the bottom water of the western basin and in sustaining the stable density stratification.