Preservation of a healthy environment is a very important task, especially in the time of the total industrial revolution. Therefore, attempts to find new additional biomarkers of contamination are welcomed. For this aim, the functional and antioxidant properties of mussel Mytilus galloprovincialis proteins and the heavy metals Cd and Pb were explored. Mussels were collected in contaminated and noncontaminated sites in the Varna area of the Bulgarian Black Sea coast. Proteins were extracted from mussel entire soft tissue and analyzed using instrumental (Fourier transform infrared [FT-IR] spectroscopy, fluorescence, atomic absorption spectrophotometry), and biochemical (2,2'-azinobis 3-ethylbenzothiazoline-6-sulfonate) radical cation [ABTS(.+)]) methods. It was found that mussel proteins from the contaminated sites had specific qualitative changes: partial unfolding of the alpha-helix, slight shift in amide I bands, increased hydrophobicity, and fluorescent intensity in native and denatured samples. In the same mussel samples, an increased radical-scavenging capacity and increased contents of Cd and Pb in entire soft tissue were registered. Therefore, the above-mentioned indices could be used as additional biomarkers of sea water contamination.