The aim of this work was to assess the influence of physical, chemical, and hydrochemical factors on the characteristics of bottom sediments in various areas of the shelf of the Crimean Peninsula. The data obtained during the cruises of the RV “Professor Vodianitsky” in the fall of 2018 and summer of 2019 were analyzed. Hydrochemical analyses of the bottom waters were carried out using standard hydrochemical methods. Profiles of dissolved oxygen, hydrogen sulfide, and oxidized and reduced forms of iron in pore waters were obtained, and the geochemical characteristics of bottom sediments were determined. The features of their spatial and vertical distributions were considered. Pelite-aleuritic sediments with inclusions of sandy material and shell detritus prevailed in the coastal zone of the Crimean shelf. The organic carbon content varied from 0.5–0.6% in the gravel–sand sediments of the Kerch pre-strait area to 2.5–2.7% in the northwestern part. The prevalence of suboxic conditions was noted, and the main processes in the sediment upper layer were controlled mainly by reactions involving iron. In some areas of the southern coast of Crimea and the Kerch pre-strait area from the Sea of Azov, the development of anoxic conditions in the surface layer of bottom sediments was recorded.