The paper presents the results of studies of the Kalamitsky Bay bottom sediments pollution level with microelements and heavy metals (Pb, Zn, Cu, Ni, Co, Cr, V, As, Sr, Ti, Fe, Mn) in comparison with the content of these microelements and heavy metals in the Balaklava Bay sediments. The paper analyzes data obtained during expeditions on the R/V Professor Vodyanitsky in the Kalamitsky Gulf in August 2011 (seaward part) and on the R/V Rioni in September 2012 (coastal area) as well as in the Balaklava Bay in October 2018. Content of microelements and heavy metals in bottom sediments of the studied water areas was determined by the X-ray fluorescence method using Spectroscan MAX-G device. For the water area of the Kalamitsky Gulf, the features of the studied trace element spatial distribution are considered, groups of trace elements with different spatial distribution patterns are identified. The correlation analysis determined influence of physicochemical characteristics of the sediments on distribution and accumulation of trace elements. In the water area of the Kalamitsky Gulf, a statistically significant correlation was observed of nickel, iron and zinc content with the clay fraction; dependance of increased concentrations of zinc, nickel and chrome on the content of organic carbon and predominance of lead in highcarbonate sediments. For the Balaklava Bay, the maximum positive values of correlations with the pelitic-silty fraction were noted for iron, manganese, vanadium and chrome; organic carbon correlates with chrome, iron, nickel and copper, whereas carbonates correlate with strontium. Similar patterns were observed earlier in the Sevastopol region bays, Feodosiya Gulf and Kerch Strait.