Based on the data of long-term (1985–1994) observations, the patterns of the seasonal variability of the spatial and vertical distribution of the concentration of suspended organic phosphorus (PSOM) in the upper layer of the deep part of the Black Sea are considered. Statistical estimations of the seasonal variations of the PSOM concentration and the relationships between the concentrations of the components of the suspended organic material (carbon, nitrogen, and phosphorus) and chlorophyll “a” in the surface layer and euphotic zone were obtained. According to the regressive equations and the data on the concentration of chlorophyll “a” calculated on the basis of the experimental and satellite observations in 1979–1986 and 1998–2010, estimates of the long-term variability of the concentrations of PSOM in these sea layers were obtained. It is demonstrated that the intra- and interannual variability of the PSOM concentrations in the open part of the Black Sea are closely related to the changes in the phytoplankton biomass and controlled by the long-term cycling of the climatic conditions and the related changes in the hydrological regime, on the one hand, and the restructuring of the plankton community in the aerobic zone of the Black Sea, on the other hand.