The northern part of the Elbe river in Germany is one of the most highly polluted rivers in Europe, in particular with toxic organotin compounds. Two major anthropogenic sources are the Hamburg harbour area with intensive docking activities and a chemical plant in Bitterfeld close to the Mulde river in eastern Germany. Tributyltin is leached from the antifouling paints and enters the water phase. Thus, the Hamburg harbour area is highly contaminated with tributyltin and its degradation products, di- and mono-butyltin. Untreated run-off waters of an organotin plant in Bitterfeld contaminate the Mulde, a tributary of the Elbe, extensively. The Mulde sediments contain butyltin compounds of the order of mg of Sn per kilogram of dry mass. In Raguhun sediments, concentrations of tetrabutyltin and tributyltin were 1.8 ± 0.4 mg of Sn per kilogram of dry mass and 1.1 ± 0.2 mg of Sn per kilogram of dry mass, respectively. Remobilization of the sediments during high water periods transports the contaminants along the Mulde river into the Elbe river. Tetrabutyltin can be detected in the Elbe river as far as Cuxhaven and its estuary. To evaluate the ecological impact, fish tissues were analysed for their butyltin content and the data were correlated with the butyltin content in the surrounding water. The analysis of different fish tissues: liver, kidney, gills and the edible tissue, shows a clear enrichment of the tributyltin species. In the liver, tributyltin concentrations of up to 200 ng of Sn per gram of wet tissue were found. Bioconcentration factors were calculated to be of the order of 4500–9000. Tetrabutyltin could not be found in all the tissues, whereas it is present in water. The low bioavailability of tetrabutyltin is presumably caused by the low amount of tetrabutyltin in the dissolved constituents of water. Up to 99% of the tetrabutyltin content in water is bonded to particulate matter. The butyl groups influence the toxic behaviour of the butyltins. Although the toxic effects of butyltins on different organisms are well investigated, the genotoxic potential of the butyltins has received much less attention. The SOS-Chromotest was used to evaluate their genotoxicity. All the butyltins were found to be genotoxic; dibutyltin was the most genotoxic (10–40 µg of Sn per litre) followed by tri-, tetra- and mono-butyltin. An enhancement of the genotoxicity of all butyltins was observed using spiked lake water instead of distilled water. For the analysis of the butyltin compounds sodium tetraethylborate was used as in situ ethylating agent in the buffered samples. No pre-extraction steps with complexing agents are necessary. The extraction yields of all butyltin compounds are in the range of 82–94% for water; 76–88% for suspended particulate matter, sediment and soil; 80–94% for organisms; and 76–97% for air samples. The limit of detection of GC–AAS is 25 ± 5 pg of Sn per microlitre injected volume (3σ of the baseline noise).