We analyzed the detection frequencies and concentrations for 331 organic compounds measured between 1994 and 2004 in the four largest rivers of North Germany, Elbe, Weser, Aller and Ems, and assessed the potential risk for the aquatic fauna using experimental and predicted acute toxicity data for the green algae Pseudokirchneriella subcapitata, the crustacean Daphnia magna and the fish Pimephales promelas. The detection frequency for most compounds decreased significantly from 1994 to 2004. Polycyclic aromatic hydrocarbons (PAHs) were most frequently detected, while pesticides were the most important chemical group concerning toxicity for the standard test organisms. The predicted toxicity for Daphnia magna was significantly higher than for the other organisms and reached levels envisaging acute toxic effects on the invertebrate fauna, still in 2004. Most of the compounds responsible for potential acute effects on aquatic organisms are currently not considered as priority substances in the European Union, while only 2 of 25 priority substances that have been measured occurred in levels that may be relevant in terms of toxicity for the selected test organisms. We conclude that attenuation of pesticides and other organic toxicants should play an increased role in river basin management.