Our study has been conducted along the coastline of the eastern Gulf of Finland for three years. It had been shown that accumulation of algal biomass caused by the “green tide” events significantly influenced the metal distribution in the surface sediments. Metal concentrations differed significantly under algal mats and at the sites, which were free of algae. Our study showed significant changes in metal concentrations (Zn, Cd and Pb) along the coast in study years, which, in our opinion, reflect influence of the ports Vysotsk and a new one - Bronka. Principal component and classification analysis extracted two main factors, which can be interpreted as a factors related to the distance from a river mouth and to the input from the new anthropogenic sources. Taking into account a global climate change and the results of our study, we may conclude that in the future extended macroalgal blooms may provoke intense sediment contamination by organic matter and associated metals.