The Yangtze River Estuary has become increasingly challenged by various destructive threats to its ecosystem such as the frequent occurrence of harmful algal blooms. Four cruises were carried out in the Yangtze River Estuary and its adjacent area in 2006. Ten variables including CODMn, PO43--P, SiO3-Si, NO3--N, NO2--N, NH4+-N, TN, TP, TOC and chl-a were analyzed by exploratory data analysis. Nitrate was the dominant form of TN throughout the year. Principal component analysis (PCA) was applied to estimate the sources of nutrients contamination in 2006. Two principal components (PCs) were extracted, namely, CODMn, PO43--P, NO3--N and TN for PC1, NO2--N and chl-a for PC2. Influenced by anthropogenic sewage, PC1 near Shidongkou, Bailonggang, Xinhe and Zhuyuan outlets was higher than other stations. The primary influencing factor of PC1 were the contaminants carried by runoff from the Yangtze River. And the dominating factors of eutrophication in 2006 were CODMn, PO43--P, NO3--N, TN and chl-a in the Yangtze River Estuary and its adjacent area.