Mainly due to the underlying geology, the Danube and its tributaries show a spatially distinct pattern in their elemental and isotopic composition. Fish store the local chemical information in their hard parts, allowing the determination of their origin and bearing the potential to answer important ecological questions such as migration habits. Focusing on freshwater fish, this study is the first conducted on the European chub (Squalius cephalus (L.)) and the barbel (Barbus barbus (L.)). Water and fish samples were taken from different rivers along the course of the River Danube in Austria and characterized for their microchemical composition. Water samples were clustered to identify isozones which represent areas with similar chemical signatures. Then, the microchemical information in the fish otoliths was analysed in order to find out whether they could be matched with the chemical information of their origin, or with the corresponding isozones. The incorporation of the chemical information was studied in more detail, revealing the effects and influences of the time fish were exposed to specific conditions in a river, the season, temperature and geological background. For this purpose, chub and barbel were transferred from a river with calcareous background to a river with siliceous background and vice versa. The fish were held in cages under semi-natural conditions. Water chemistry was sampled before and after the exposure, while temperature was monitored during the whole experiment. After 11 to 13 weeks of exposure, the hard parts of ten fish were analysed. The analysis was conducted using solution-based and laser ablation inductively coupled plasma mass spectrometry, respectively, whereby a quadrupole instrument (ICP-QMS) was used for trace element analysis and a multiple collector instrument for strontium isotope ratio analysis (MC-ICPMS).