The features of the distribution of the concentrations of hydrogen sulfide, methane and the number of sulfite-reducing clostridia in the mud of the Bugazsky, Kiziltashsky and Vityazevsky limans and Chembursky lake were studied, and their physiological and chemical conditions and levels of anthropogenic loading were assessed. The tendency of reduction of the content of the studied reduced gases from the surface to the lower layers of mud was established, with relatively low concentrations of methane in the limans and abnormally high concentrations in the Chembursky lake, subject to strong anthropogenic influence. It is shown that high concentrations of methane and hydrogen sulphide in mud of water bodies that are planned for use for human treatment, indicate good therapeutic properties of peloids. At the same time, for those same reservoirs (limans) that are simultaneously used for extraction and reproduction of hydrobionts, the presence of high concentrations of reduced gases in the upper layers of bottom sediments and near-bottom water layers, as a rule, will promote the development of pestilence phenomena, which will adversely affect the development of the fishing industry. For reservoirs for both fishery and medical purposes, the high content of reduced gases and the abundance of pathogenic microflora may indicate contamination. The established rectilinear relationships between the number of sulfite-reducing clostridia and the concentrations of methane and hydrogen sulfide indicate the participation of sulfite-reducing clostridia in the processes of methane and hydrogen sulfide formation in the mud of the reservoirs of the Taman Peninsula. Sanitary-microbiological assessment of mud of the studied reservoirs shows that the muds studied cannot be recommended for using with medicinal purposes.