Fipronil is an insecticide which, based on its mode of action, is intended to be predominantly toxic towards insects. Fipronil bioaccumulates and some of its transformation products were reported to be similar or even more stable in the environment and to show an enhanced toxicity against non-target organisms compared to the parent compound. The current study investigated the occurrence of Fipronil and two of its transformation products, Fipronil-desulfinyl and Fipronil-sulfone, in water as well as muscle and liver samples of eels from the river Elbe (Germany). In water samples total concentrations of FIP, FIP-d and FIP-s ranged between 0.5–1.6ngL−1 with FIP being the main component in all water samples followed by FIP-s and FIP-d. In contrast, FIP-s was the main component in muscle and liver tissues of eels with concentrations of 4.05±3.73ngg−1 ww and 19.91±9.96ngg−1 ww, respectively. Using a physiologically based toxicokinetic (PBTK) model for moderately hydrophobic organic chemicals, the different distributions of FIP, FIP-d and FIP-s in water and related tissue samples could be attributed to metabolic processes of eels. The measured concentrations in water of all analytes and their fractional distribution did not reflect the assumed seasonal application of FIP and it seems that the water was constantly contaminated with FIP, FIP-d and FIP-s.