<p>The Yellow Sea and the northern East China Sea are dynamic marginal seas influenced by nitrogen inputs from various sources. This study investigates the seasonal and spatial variations in nitrate cycling using nitrogen and oxygen isotope analyses (<i>δ</i>¹⁵N and <i>δ</i>¹⁸O) in the southern Yellow Sea and the northern East China Sea during summer and fall. In summer, isotope data indicate that the upper layer water influenced by Changjiang Diluted Water (CDW) is shaped by phytoplankton nitrate assimilation and mixing, while offshore waters beyond CDW influence are nitrate-depleted. In fall, as nitrate was replenished, offshore nitrate isotopic compositions reflected continued assimilation. However, the paired <i>δ</i>¹⁵N–<i>δ</i>¹⁸O values diverged from the expected assimilation line, suggesting the influence of atmospheric nitrate deposition—characterized by high <i>δ</i>¹⁸O and low <i>δ</i>¹⁵N—as an additional source, with only a minor contribution from nitrogen fixation. Nearshore waters exhibited weaker isotopic gradients between the upper and lower layers and lower <i>δ</i>¹⁸O values than offshore regions. This was attributed to vertical mixing of low-<i>δ</i>¹⁸O nitrate from the lower layer, not riverine input. During the transition from summer to fall, nitrate concentrations increased by ~ 5&#xa0;μM and <i>δ</i>¹⁵N decreased by ~ 1‰ in the lower layer of the southern Yellow Sea (SYS). This suggests that remineralization is the dominant process controlling nitrate isotopes in the study area. The predominance of remineralization distinguishes the eastern SYS from the western SYS and the northern Yellow Sea, where sedimentary processes modify nitrate concentrations and isotopic ratios. These findings highlight the complex interplay among physical transport, biological uptake, and internal nitrogen regeneration across regions of the Yellow Sea.</p>