The factors that control the seasonal variability of the concentration of suspended matter, nutrients, dissolved forms of metals and phytoplankton biomass in coastal waters of the eastern part of the Amurskii Bay were determined. It was shown that the runoff of the Razdolnaya River determined the seasonal variability in suspended matter content, values of the chemical oxygen demand (COD), silicates, Fe, Mn, Cu, and Ni significantly affected the concentration of nitrates. The advection of sea water is the main source of phosphates and dissolved forms of Zn and Cd. In the autumn and winter seasons, the gradual decrease in the concentration of silicates and phosphates was related to phytoplankton activity. In the spring and summer seasons, the growth of phytoplankton determined the variability of the phosphate and nitrate contents and compensated for the effect of the Razdolnaya River runoff. It is concluded that the phytoplankton biomass, rather than variations in riverine flow, caused the long-term variability of the nitrate and phosphate concentrations in the coastal waters of the Amurskii Bay.