This study aims to investigate the use of metallothionein as a biomarker and its environmental impact on aquatic systems. According to the species’ characteristics, the interactions of toxic elements with living organisms in marine water can lead to biomagnifications in the trophic chain or bioconcentration of what is in the water. In many aquatic organisms, the presence of metallothionein proteins was studied. The chemical analysis of these bioindicators establishes, therefore, a sensitive method for the measurement of bioavailability which, over the years, allows for the quantification of the current pollution agents in the environment. Two study areas were selected along the Latium coasts. They are differentiated by their economic activities and their kind and level of environmental impact (mainly on marine pollution). These areas were selected in order to differentiate the maximum degree of both economic development and environmental quality. In particular, the presence of pollutants in the sea due to land activities was evaluated to compare the quality of the fishing products obtained from locations subject to various environmental impacts. The heavy metal concentrations were evaluated in water samples taken from different 30 sections of the fishes in order to understand the metabolism and origin of these contaminants. The primary metals studied were: mercury (Hg), zinc (Zn), nickel (Ni), lead (Pb), cadmium (Cd), and copper (Cu). All data produced were analyzed via multivariate analyses in order to provide a final and reliable indicator.