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This data article aimed to evaluate the influencing mechanisms of the nutrients and the level of eutrophication in the Yangtze River estuary. The seasonal characteristics of nutrients (dissolved inorganic nitrogen (DIN), SiO3-2–Si, and PO43-P) in the seawater of the Yangtze River estuary were analyzed by conducting surveys in spring and summer of 2019. The findings revealed that the concentrations of all nutrient at the surface and bottom layers were lower in spring compared to summer. NO3–N was typically the major form of DIN. Runoff was identified as the primary source of DIN and SiO32−–Si, while PO43−–P originated from a various sources. The SiO32−–Si, while PO43−–P values in the surface and bottom layers during the spring and summer were higher than the Redfield values, indicating an imbalanced nutrient distribution. Furthermore, discrepancies were observed in the distributions of DIN/PO43−–P, SiO32−–Si/DIN, and SiO32−–Si/PO43−–P in the Yangtze River estuary. Through an examination of the ratio of DIN/PO43−–P absorbed by phytoplankton, PO43−–P was identified as a potential limiting factor for nutrition in the sea area of the Yangtze River estuary during spring and summer. The Eutrophication Index (E) values for both spring and summer were found to be higher than the eutrophication threshold, indicating severe eutrophication in the studied sea area.
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