Based on detailed hydrological and hydrochemical surveys carried out in each of the four seasons of 2008, Amursky Bay in the north west quadrant of the Japan Sea was found to experience seasonal hypoxia. The primary process of hypoxia formation is a microbiological degradation of the "excess" amount of diatoms under rather low photosynthetic active radiation in bottom layer and weak water dynamics. The microbiological decay of dead diatoms under light deficient conditions intensively consumes dissolved oxygen and produces phosphates, ammonium, silicates, and dissolved inorganic carbon. Existence of a phytoplankton "excess" is caused by phytoplankton bloom resulting from nutrient pulses into Amursky Bay. There are two main sources of these nutrients: the waste waters of Vladivostok city and discharge from Razdolnaya River. The river delivers more than two times the amount of nutrients than the waste waters of Vladivostok. It is suggested that the phytoplankton "excess" might be caused by an enhanced supply of nutrients delivered into the surface layer resulting from the increased discharge of the river on a short time scale. Our data suggest that hypoxia is seasonal, with a peak at the end of summer. The upwelling of the Japan Sea water in the beginning of the fall season and its advection across the shelf is the primary process by which the hypoxia is destroyed. During the winter, strong vertical mixing due to termohaline convection makes the water column uniform and brings more oxygen into the water along with high primary production under the ice. Thus, during the winter season, the ecosystem of Amursky Bay recovers completely.