The paper presents the results of modeling the possible changes in the structure of the population of Calanus euxinus Hulsemann, 1991 copepods in the Black Sea under the influence of deoxygenation that began in the late 1980s. Over the past 50 years, the depth of oxygen penetration in the deep sea has decreased by almost 50 m. The lower “life limit” of zooplankton in the Black Sea corresponds to the upper boundary of the suboxic layer, where intense copepod aggregation occurs at an oxygen concentration of 10 μM /L. In 1955–1976, this boundary was 130–140 m across the sea, but due to eutrophication and climate change since late 1980s, it has risen in deep water areas to 70–80 m. As a result, the dense copepod layers near the redoxcline and especially their reserve population stock, consisting of non-migrating individuals in diapause, may have been subjected to intensive eating by the Black Sea sprat, which lives to a depth of 100 m and can tolerate hypoxia. To explore this process, we created a new population dynamics model for C. euxinus, which makes it possible to assess changes in the abundance and structure of the population under conditions of a quasi-stationary state and during intensive predation of individuals in diapause. The model describes the dynamics of the Сalanus population based on a statistical description of the relationship between the growth of individuals, their fecundity, the duration of diapause, mortality, and environmental conditions: the concentration of food suspension and temperature in the layer of vertical migration. We put forward the hypothesis that the access of small pelagic fish to the concentration layers of copepods in diapause has a key effect on significant changes in the Black Sea ecosystem, associated with a decrease in the supply of forage plankton and fluctuations in the abundance of pelagic fish.