The paper analyzes content and spatial distribution peculiarities of macro- and microelements in the bottom sediments of Sevastopol bays, Feodosiya Gulf and Kerch Strait. Bottom sediment sampling was performed from 2005 to 2008 as well as in 2015, 2016, and 2018. Concentrations of macro- (Ti, Fe, Mn) and microelements (As, Pb, Zn, Cu, Ni, Co, Cr, V, Sr) were studied by X-ray fluorescence analysis using Spectroscan MAKS-G spectrometer. The maximal content of Cr, Co, Ni, Zn, Pb, Sr exceeding the geochemical background was found in the water areas with difficult water exchange, which include bays of the Sevastopol region under intense anthropogenic influence: the Yuzhnaya Bay, Gollandiya Bay and Kilen-Bay. In the Kazachya Bay, the least polluted in the Sevastopol bay system, the content of Cr, Co, Ni, Zn, Pb, As, Sr also exceeded their geochemical background. As illustrated by the Balaklava Bay, the paper shows the influence of local pollution sources (the Balaklavka River runoff and municipal waste water) on the microelement distribution. Sevastopol bays are characterized by high concentrations of the studied elements in the bottom sediments. In the water areas with active water exchange, i. e. Feodosiya Gulf and Kerch Strait, concentration of the studied elements, except for Ni, Zn and Cr, did not exceed on the average the geochemical background of the open Black Sea shelf areas.