Spatial heterogeneity of the thermohaline structure, biotope dynamics and organism interactions form layers of high abundance and biomass. Based on expedition data obtained during the summers of 2010–2024, this paper analyses characteristics of surface and subsurface peaks in phytoplankton biomass, chlorophyll a, total suspended matter, zooplankton (prey and gelatinous), bioluminescence intensity and sound-scattering layers (indicators of the abundance of small pelagic organisms) on the shelf off the coast of Crimea. Characteristic parameter values, layer thicknesses and depths are presented. The mechanisms of layering formation and the relationship between the structural and functional properties of the pelagic community are discussed. It was noted that at lower trophic levels, layering was regulated primarily by thermohaline stratification of the water column. At intermediate trophic levels, represented by copepods and small pelagic fishes, the dominant factor regulating stratification was the organisms' motor activity, associated with feeding behavior, reproductive behavior, defense and other behaviors. In terms of the relationship between the structure and function in a pelagic ecosystem, it was noted that the stratified distribution of organisms created vertical heterogeneity in the density of trophic interactions and consequently vertical heterogeneity in the flow of matter and energy within the community. Trophic interactions were most intense in the layers of maximum thickness due to their greater ecological capacity. These include the surface and subsurface biomass peaks of phytoplankton, zooplankton and small pelagic fishes, primarily common anchovy and sprat.