Developing effective, rapid and inexpensive methods for monitoring and conserving aquatic resources is an important issue for environmental managers. This study focuses on Mytilus edulis, a keystone species of many coastal marine communities, which is frequently used as a biomonitor for a range of pollutants. Recent advances in post-genomic technologies have provided new methods of biochemical screening, and Fourier transform-infrared spectroscopy (FT-IR) is one such method that could enable bioindicator species to be used for environmental assessment. This paper develops a methodology to apply the FT-IR approach to marine intertidal M. edulis and addresses three methodological issues: First, the optimum physical location for biofluid sampling is examined (i.e. laboratory versus field). Secondly, the effects of transportation of frozen biofluid sampling from either the field-site or laboratory to the analytical facility are considered. Finally, the effect of repeated FT-IR measurements on collected M. edulis haemolymph samples is examined. From these results we suggest sampling haemolymph from M. edulis at the top of the shore prior to immediate snap-freezing in liquid nitrogen. Sample transportation can occur on ice for up to eight hours before storage at -80 °C. FT-IR measurements should occur within three months of collection and samples should not be used or thawed more than twice. We show how this method can be used to differentiate successfully between four different estuarine environments. Ultimately, through addressing these methodological questions, we provide a protocol to allow efficient sampling and FT-IR measurement of M. edulis as collected from the intertidal areas of rocky and muddy shores. We conclude that due to current monitoring needs presented by the European Water Framework Directive such an approach could prove to be an invaluable future tool for assessing coastal water quality.