The processes governing the biogeochemical structure of the upper layer water column in the central Black Sea are studied using a one-dimensional coupled physical-biogeochemical model. It is an extention of the previous models (Oguz, et al., 1996; 1997) including the oxygen dynamics and its coupling with the plankton production, particulate matter decomposition and nitrogen transformation, a simplified representation of the microbial loop involving dissolved organic matter generation and bacterial production, as well as the denitrification and hydrogen sulphide oxidation processes. The model thus considers dynamically a fully coupled system of the processes taking place at the euphotic zone, the oxycline, suboxic and anoxic layers. The pelagic food web is represented by two groups of phytoplankton (diatoms and flagellates), three size groups of zooplankton (microzooplankton, mesozooplankton and macrozooplankton). The macrozooplankton group represents essentially a particular gelatinous species group called the medusae "Aurelia aurita" The model simulations reproduce reasonably well the observed annual plankton structure involving a series of successive phytoplankton and zooplankton peaks over the year. In the presence of medusae, the yearly phytoplankton distribution possesses more pronounced summer bloom structures due to stronger "top-down" control of these gelatinous carnivores. The position of the nitrate maximum is shown to be intimately related with the location of the onset of trace level oxygen concentrations as they control the lower limit of the nitrification and the onset of the denitrification in the water column. The model successfully simulates the observed seasonal and vertical variations of the dissolved oxygen in response to its atmospheric and photosythetic productions, and losses during the particulate matter decomposition and nitrogen transformations. The simulations support the presence of an oxygen deficient zone (the so-called the Suboxic Layer) below the 15.6 sigma-t level within the interior Black Sea. The upper boundary of the suboxic layer varies depending on the two opposing mechanisms; the oxygen consumption in the remineralization and. nitrification and the ventilation associated with the vertical diffusive transport from the oxycline. Its lower boundary always coincides with the vanishing H2S concentrations near the 16.2 sigma-t level. In the case of complete oxygenation of this zone, the SOL disappers all together as the positions of vanishing oxygen and H2S concentrations converge to a common point, implying that their overlapping is not possible under the realistic oxidation rates.