Long term monitoring of atmospheric wet and dry depositions and associated nutrients fluxes was conducted on the coast of Japan facing the East China Sea continuously for 1 year and 2 months, with the origin of air mass investigated based on isotope analyses (Sr, Nd, and NO₃). During the same period, intensive observations of ocean conditions and the chemical composition of sinking particles collected using sediment traps were conducted to investigate the effects of atmospheric deposition-derived nutrients on phytoplankton blooms. Dry-deposition-derived nutrient inputs to the surface ocean were larger during autumn to spring than in summer due to the effect of continental air mass occasionally carrying Asian dust (yellow sand). However, these nutrients fluxes were limited (1.1–1.5 mg-N m⁻² day⁻¹ on average) and didn't appear to cause phytoplankton blooms through the year. Although average dissolved inorganic nitrogen (DIN) concentrations in rainwater were lower in oceanic air masses compared to continental air masses, wet-deposition-derived nutrient inputs to the surface ocean on rainy days during the summer (26.0 mg-N m⁻² day⁻¹ on average) were large due to higher precipitation from oceanic air masses. Wet-deposition-derived nutrients significantly increased nutrient concentrations in the surface ocean and seemed to cause phytoplankton blooms in the warm rainy season when nutrients in the surface were depleted due to increased stratification. The increase in phytoplankton biomass was reflected in increased particle sinking into the bottom layer, as well as changing chemical characteristics. The supply of flesh phytoplankton-derived labile organic matter into the bottom layer could be expected to promote rapid bacterial decomposition and contribute to the formation of hypoxic water masses in early summer when the ocean was strongly stratified. Atmospheric deposition-derived nutrients in East Asia will have important impacts on not only the oligotrophic outer ocean but also surrounding coastal areas in the warm rainy season.