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As a part of Korean-Russian joint expeditions in the East/Japan Sea during 2012 and 2015, a set of total and small (<2 μm) phytoplankton NO₃⁻ and NH₄⁺ uptake rate estimations were carried out. The study aimed to assess the spatio-temporal variations in dissolved inorganic nitrogen (DIN) assimilation by the total and small phytoplankton. The results show that the total NO₃⁻ uptake rates during 2012 varied between 0.001 and 0.150 μmol NL⁻¹h⁻¹ (mean ± SD = 0.034 ± 0.033) and that the total NH₄⁺ uptake rates ranged between 0.002 and 0.707 μmol NL⁻¹h⁻¹ (mean ± SD = 0.200 ± 0.158). The total uptake rates during 2015 were ranged from 0.003 to 0.530 (mean ± S.D. = 0.117 ± 0.120 μmol NL⁻¹h⁻¹) for NO₃⁻ and from 0.008 to 1.17 (mean ± S.D. = 0.199 ± 0.266 NL⁻¹h⁻¹) for NH₄⁺. The small phytoplankton NO₃⁻ and NH₄⁺ uptake rates during 2015 ranged between 0.001 and 0.164 (mean ± S.D. = 0.033 ± 0.036) μmol NL⁻¹h⁻¹ and 0.010–0.304 (mean ± S.D. = 0.101 ± 0.073) μmol NL⁻¹h⁻¹, respectively. Small phytoplankton’s contribution to the total depth-integrated NO₃⁻ and NH₄⁺ uptake rates ranged from 10.24 to 59.36% and from 30.21 to 68.55%, respectively. The significant negative relationship observed between the depth-integrated total NO₃⁻ and NH₄⁺ uptake rates and small phytoplankton contributions indicates a possible decline in the DIN assimilation rates under small phytoplankton dominance. The results from the present study highlight the possibility of a reduction in the total DIN assimilation process in the East/Japan Sea when small phytoplankton dominate under strong thermal stratification due to sea surface warming. The present study’s findings agree with the model projections, which suggested a decline in primary production in the global warming scenario.