Purpose Although the water quality of the Rhine River in Europe has improved, contaminated sediments may still threaten fish populations. This is particularly likely in Upper Rhine oxbow lakes, which are connected to the main river channel only at one end, except for extreme flood events. The impact of such extreme flood events on the sediment toxicity has, however, not yet been investigated, although numerous oxbow lakes exist with varying degrees of connection to their main river channels. Materials and methods We evaluated contaminants in sediments taken at ten sites along a 600-m transect in an oxbow lake in a nature reserve that receives sediment contamination only from the main river. Sediment was analysed for polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs) as well as dioxins (PCDDs) and furans. The dioxin-like activity was measured using in vitro bioassays (7-ethoxyresorufin-O-deethylase (EROD) assay) on RTL-W1 cells. The distribution of sediment contaminants and effects in bioassay were compared within the oxbow lake and with other European water systems. Results and discussion Chemical analysis of the 16 priority PA Hs (1.12-2.16 mg kg − 1 ), ∑PCDD/Fs (1.62-4.17 μg kg −1 ) and ∑PCB congeners 77, 81, 105, 118, 126, 156 and 169 (2.3-3.1 μg kg −1 ) showed low to moderate sediment contamination. However, all sediment samples showed dioxin-like activities with bio-TEQ values between 3.62 and 7.92 ng g −1 in an EROD induction assay using RTL-W1 cells. These values were higher than those reported for other, larger river systems. Both contaminant levels and toxicity data clearly suggest a spatially homogenous exposure profile throughout the oxbow lake. This homogenous profile was caused most likely by extreme floods, which lead to a large input of river sediments and a mixture with remobilised lake sediments. Conclusions This study illustrates the relevance of flood event-related contaminant input from the main river channel for connected oxbow lakes. This may impair their function as reproductive and developmental fish habitats. As the probability and temporal pattern of flood events in river systems may change due to climate change, this may also have direct consequences for the sediment contamination in connected oxbow lakes, and thus affect their ecological function for fish.