The aim of this study was to find a reliable biomarker of seawater pollution. For this purpose the contents of Zn and Cu, proteins and antioxidant activity in mussels Mytilus galloprovincialis collected from polluted and non-polluted sites of the Bulgarian Black Sea coast were compared. To determine the above-mentioned indices atomic spectroscopy, Fourier Transform Infrared (FT-IR) spectroscopy, fluorescence, differential scanning calorimetry (DSC), and two antioxidant tests were used. It was found that the amounts of Zn and Cu were significantly higher in the mussel proteins from the polluted than from the non-polluted sites (P<0.05). FT-IR spectroscopy and fluorescence revealed specific qualitative changes in secondary and tertiary structures in mussel proteins in the samples from polluted sites. The thermodynamic properties of proteins and the changes upon denaturation were correlated with the secondary structure of proteins and disappearance of alpha-helix. Purified protein scavenging activity against 2, 2'-azinobis (3-ethylbenzothiazoline-6-sulfonate) radical cation (ABTS(*+)) was significantly higher in mussel samples from polluted than from non-polluted sites. Therefore, the changes in Zn and Cu concentration, in protein's secondary and tertiary structures and antioxidant activity in mussels M. galloprovincialis from polluted sites can be a reliable biomarker of the level of the seawater pollution.