Marine mussels are useful, robust model organisms that have been widely used as biomonitors. In the natural environment they can be subjected simultaneously to a mixture of environmental stresses (hypoxia, starvation) and to pollutants. In this study Mytilus edulis was used to investigate the effects of two pesticides, atrazine and lindane, which have different modes of action but produce similar changes in behaviour (depression of ventilation and feeding) in the mussels, and can cause starvation and mild hypoxia. Acetonitrile/(H2O)-H-2 (60/40% v/v) extracts of foot muscle from animals subjected to hypoxia, or starvation, or low or high doses of pesticide were analysed using H-1 NMR spectroscopy to produce metabolic fingerprints associated with these treatments. Discriminant analysis based on metabolites that showed significant differences between treated and control animals gave a clear separation between all treatment groups. The fingerprints of atrazine treated animals were clearly separated from those of animals that were starved or subjected to hypoxia. The high and low doses of atrazine were also well separated. Lindane treatment was separated from control animals in a dose dependent way, and was associated with an increase in the concentration of alanine, and a decrease in all of the other identified metabolites (including osmolytes). This is consistent with a general depression of activity. This limited study demonstrates the potential of the metabolomic approach to provide a separation of the effects of poisoning from those of environmental stress.