We investigated seasonal variations in the dissolved nutrients and organic matter (DOM) in the Yellow Sea and the East China Sea shelf waters from 2017 to 2021. 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 were the lowest in summer. In spring, DON and DOP contributed up to approximately 90% and 80% of the total dissolved nitrogen (TDN) and phosphorus (TDP), respectively. 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 (∼27) of the DOM pool revealed the DOM remained after the degradation and formation of the refractory pool by marine bacteria. 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 and subsequent ecosystem responses in the shelf sea.