The features of the vertical distribution of chlorophyll a, particulate organic carbon and its isotopic composition, total suspended particulate matter (SPM), and the structure of the phytoplankton community in the Middle and South Caspian Sea in May–June 2012 are discussed. The subsurface chlorophyll a maximum (SCM) was found everywhere at depths of ~20 to 40–60 m. The position of this layer is confined to the depth of the seasonal thermocline, which is determined by the development of a cold-water (dark) phytocenosis. The genesis of this layer was studied. The increase in chlorophyll a concentration in this layer is caused by an abundance of phytoplankton or an increased concentration of this phytopigments per algal cell. The highest values of the studied organic compounds and phytoplankton biomass are revealed as close to the seasonal thermocline extending from the southern periphery of the Derbent Depression to the Apsheron Sill, which is determined by the bottom topography. The presence of chlorophyll a at depths exceeding 300 m (up to ≥1 mg/m3) was revealed. This was supported by findings of individual algal cells containing chlorophyll a and even their accumulations in the deep water layer. The most probable mechanisms responsible for the presence of these cells at the deep water level are discussed in the paper. The vertical distribution of the values of the organic carbon isotopic composition is primarily controlled by the vertical structure of phytoplankton and chlorophyll a in the water column up to ~500 m and by biogeochemical processes at the redox barrier (~600 m layer). The relative stability of chlorophyll a and the stability of pheophytin a in anaerobic environments were verified. A significant amount of weakly transformed chlorophyll a was found close the sea bottom.