Seasonal variations in the dissolved nutrients and organic matter (DOM) were investigated in the Yellow Sea and the East China Sea shelf waters from 2017 to 2021. The vertical profiles of dissolved inorganic nitrogen (DIN) and phosphorus (DIP) exhibited typical seasonal changes. They showed very low concentrations of DIN (0.7 ± 1.4 μM; 1.1 ± 1.5 μM; 3.1 ± 2.0 μM) and DIP (0.1 ± 0.1 μM; 0.1 ± 0.1 μM; 0.3 ± 0.2 μM) in the upper layer from spring to autumn, indicating an N-limited condition, except in areas influenced by Changjiang Diluted Water (CDW) (3.6 ± 1.5 μM for DIN) and freshwater in the southern coast of Korea (4.8 ± 3.6 μM for DIN). Dissolved organic nitrogen and phosphorus (DON and DOP) concentrations were the highest in the upper layer (<30 m) during the time of spring and autumn bloom and the lowest in summer. In spring, DON and DOP contributed up to 100% of the total dissolved nitrogen (TDN) and phosphorus (TDP). The C:N:P stoichiometry of the DOM pool in spring and autumn indicates that freshly in-situ produced DOM is N-rich compared to the DOM observed in summer and winter, resulting in a dissolved inorganic nitrogen (DIN)-limited environment in the upper layer of seawater during spring and autumn. Conversely, in summer, the highest C:N ratios (~26) of the DOM pool revealed the DOM remained after the degradation by marine bacteria and formation of the refractory pool. In winter, all nutrients were vertically uniform due to active vertical mixing. This study highlights notable seasonal variations in the cycling of DON and DOP, leading to changes in their bioavailability, subsequent ecosystem responses, and the efficiency of the carbon pump in the shelf sea.