The paper analyzes the data obtained during field studies in water areas with intensive water exchange: Kalamita Bay (2011, 2012), Feodosiya Bay (2006), and the Kerch Strait (2007, 2008). The content of heavy metals (Zn, Ni, Cr) in the bottom sediments of the studied water areas was determined using X-ray fluorescent spectroscan MAKS-G. Spatial heterogeneities in the distribution of Zn, Ni, Cr in the bottom sediments of Kalamita Bay, Feodosiya Bay, and the Kerch Strait were assessed, with the organic matter content taken into account. A comparative analysis was carried out of the organic matter content in the bottom sediments of the studied water areas. The organic matter not only forms the type of sediments, but also determines their ability to accumulate various substances, including macro- and micronutrients. It is shown that the bottom sediments of Feodosiya Bay and the Kerch Strait contain increased levels of organic carbon. Correlation relations between the contents of heavy metals and organic carbon as one of the main sediment-forming components of the bottom sediments were calculated using the method of constructing matrices of pair correlations. A high level of correlations between Zn, Ni, Cr and organic carbon contents (0.7–0.8) was determined in the bottom sediments of Kalamita Bay and the Kerch Strait. In the bottom sediments of Feodosiya Bay, high correlation coefficient with Corg content (0.9) was observed only for Zn. The hydrodynamic regime of water areas with intensive water exchange (especially in the Kerch Strait) determines the spatial heterogeneity of the particle size distribution of bottom sediments, especially the fine fraction and the organic matter associated with it, which also affects the behaviour of the studied metals.