Biological early warning systems represent a set of tools that may be able to respond to certain chemical monitoring requirements of recent European legislation, the Water Framework Directive (WFD2000/60/EC), that aims to improve and protect water quality across Europe. In situ biomonitoring was performed along the rivers Meuse (NL), Aller (GER) and Rhine (F) within the frame of the European Union-funded Project SWIFT-WFD. Gammarus pulex was used as a test organism during the evaluation of the Multispecies Freshwater Biomonitor® (MFB), an online biomonitor to quantitatively record different behaviour patterns of animals. At the river Meuse G. pulex reacted to pulse exposure of either a mixture of trace metals or of several organic xenobiotics, by showing up to 20% decreased locomotory activity (already at the 1st pulse) and increased mortality (at 2nd or 3rd pulse only). G. pulex deployed within the MFB system were observed to survive well at the monitoring station on the Aller (100%) and monitoring did not result in the measurement of chemical irregularities. In contrast, deployment at the monitoring station on the Rhine river demonstrated that the test organism was able to detect chemical irregularities by up to 20% decreased locomotory activity in the animals. The MFB proved to be an alert system for water quality monitoring at sensitive sites and sites with accidental pollution.