In the present study, concentrations of arsenic (As), cadmium (Cd), cobalt (Co), chromium (Cr), copper (Cu), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) were measured in the muscle, gill, and gonads of the pelagic fish species Trachurus mediterraneus, Engraulis encrasicolus ponticus, and Sprattus sprattus that are important both commercially and for the ecosystems in the Black Sea. The samples were collected during 2011. The metals were determined using inductively coupled plasma mass spectrometry (ICP-MS) following an acid digestion. The highest concentrations of As, Cd, Co, Cr, Cu, Pb, and Zn were found in E. encrasicolus ponticus, whereas the greatest concentrations of Ni were found in T. mediterraneus and Mn in S. sprattus. Results showed that average metal concentrations in the tissues of T. mediterraneus, E. encrasicolus ponticus, and S. sprattus decreased in the order gill > gonad > muscle, gonad > gill > muscle, and gill > gonad > muscle, respectively, for the three species. When metal concentrations of fish tissues were compared between fish gender, there were only statistical differences in the gonads of the studied fish species (p < 0.05). The present study demonstrated that the metals have different correlations with condition factor (CF) and gonadosomatic index (GSI) of the fish species. Cr showed statistically important positive correlation to the GSI in male T. mediterraneus. Co showed statistically important positive correlation to CF in female E. encrasicolus ponticus, and also Co and Cd showed correlation to CF in male T. mediterraneus. Cd concentrations in the muscle tissues of the fish species were above the maximum acceptable concentration for human consumption.