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This is a research on the change of nutrients and its structure in the Pearl River Estuary by the principal component analysis (PCA) according to the data and materials on water quality observation in the last 30 years around the Pearl River Estuary. Results showed that inorganic nitrogen (DIN) presented an obvious increase trend in the last 30 years, while phosphate and silicate presented an outstanding decrease trend in this area by the influence of human activities. The average N/P ratio increased by 1.44 times, the Si/N ratio decreased by 66.8%, the Si/P ratio decreased by 18.5%, and the structure of nutrients changed significantly. According to the results of PCA, the first two principal components (PC) were extracted. PC1 was associated with GDP, population, industrial output value and wastewater discharge, which explained 80.9% of the variance. PC2 was characterized by cultivated land area, which explained 14.6% of the variance. It indicates that the change of nutrients content and structure in the Pearl River Estuary was closely related to economic development and industrial pollution discharge, and the effect of the change of land use and land cover on the change of nutrients should not be ignored.