Freshwater crayfish are bioindicators of environmental pollution, often used for the assessment of heavy metal (HM) presence in the tissues, a time-consuming and expensive task. In this study, we propose the use of the vibrational spectroscopy to detect in a fast, non-destructive and sensitive way the presence of HM in the cephalothorax exoskeleton of the freshwater crayfish. Incorporation of HM into the cephalothorax exoskeleton was investigated under controlled laboratory conditions. In particular, the cephalothorax exoskeleton of five crayfish species (Astacus leptodactylus, Procambarus clarkii, Austropotamobius pallipes, Faxonius limosus, and Pacifastacus leniusculus) was analyzed by attenuated total reflection–Fourier transformed infrared (ATR–FTIR) spectroscopy in the presence or absence of cadmium (Cd), chromium (Cr), lead (Pb), nickel (Ni), and zinc (Zn) up to 4 weeks at various concentrations (0.01, 0.1, 1, 10, ppm). The ATR–FTIR profile of the crayfish cephalothorax exoskeleton was compatible with the presence of amorphous calcium carbonate, chitin, and proteins. The incubation with the HM revealed two main modifications: the shift of the peak from 859 to 872 cm⁻¹ and the appearance of a peak at 712 cm⁻¹. Both are ascribable to the HM interaction with calcium carbonate. The absorbance of both peaks increased along with the time of incubation, and the HM concentration. We conclude that ATR–FTIR analysis can be a useful, quick, and cost-sensitive tool to detect HM presence in the crayfish cephalothorax exoskeleton. However, it has to be regarded as a non-specific analytical technique for assessing HM contamination, since it is unable to discriminate between different HM.