The occurrence of biomarker temporal variations linked to environmental factors makes it difficult to distinguish the specific effect of pollution. The present work aims to investigate the seasonal variations of the transport activity of the multixenobiotic defence (MXD), which is used as a biological tool for the monitoring of pollution in aquatic ecosystems. The MXD transport activity was monitored monthly from August 2001 to October 2002 in zebra mussels (Dreissena polymorpha) transplanted to three sites in the Moselle River. The ‘efflux method’ was used to evaluate functional activity of MXD by assessing rhodamine B efflux with or without an inhibitor (verapamil). Environmental parameters were provided by a French regulatory agency (Water Agency) that monitors river water quality. The results of a principal components analysis describe the seasonal cycle of water characteristics and demonstrate that MXD activity is subjected to significant temporal variations. These data were described with a generalised linear model that enables it to link MXD variability to the seasonal variations of environmental parameters such as temperature or levels of organic contamination. This work proposes a modelling approach and highlights that the occurrence of seasonal variations in MXD response has to be taken into account in the interpretation of in situ monitoring studies.