This work is a continuation of research on the quantitative assessment of the level of heavy metal pollution (Fe, Mn, Zn, Cu, Cd, Pb, Ni) of the ecosystem components of the estuary region of the Northern Dvina River. In this article, to assess the levels of contamination with the studied metals of the ecosystem of the estuary region of the Northern Dvina River in the area of the greatest anthropogenic impact (the area of the urban agglomeration Novodvinsk-Arkhangelsk-Severodvinsk), we use the method of comparative analysis with the conditional background area of the object of study, taking for it – the section of the river located above the urban development. Using spatial mapping of the values of the enrichment coefficients for the components of the aquatic ecosystem, areas with an abnormal excess of the metal content in the mollusk tissues, bottom sediments and the bottom water layer were identified. It is established that the area adjacent to the central part of the city and to the industrial zone on the left bank is subject to the greatest anthropogenic load in the water area of the top of the river delta. The most likely sources of contamination with the considered heavy metals (HM) are the ingress of surface wastewater (meltwater and rain storm runoff), untreated municipal wastewater and direct near-atmospheric transport. The analysis of mollusk tissues proved to be a more informative and indicative approach to the assessment of HM pollution in water areas with complex hydrological and hydrochemical gradients of the environment, compared to the bottom layer of water and bottom sediments.