Abstract: Signs of accelerated eutrophication have appeared in the Three Gorges Reservoir (TGR), and algal blooms have occurred in some areas especially the tributaries. However, little is known about the spatial and temporal distribution of the nutrients, such as phosphorus and nitrogen, and how it affects the growth of algae. To answer this question, we collected water samples from five different sections of the TGR in August and November of 2012 and in January and April of 2013. We analyzed the concentrations of chlorophyll-a (Chl.a) and nitrogen/phosphorus in different forms in the samples. We also applied the enzyme labeled fluoresce (ELF) method to detect the extracellular alkaline phosphatase excreted from algal cells. The concentrations of total phosphorus (TP) and Chl.a showed the same seasonal trend but unrelated spatial patterns. The concentrations of both were higher in spring and summer. The level of TP was higher in the main stream than that in the tributaries, whereas the level of Chl.a was higher in the tributaries (P0.05). Among the five sections, the concentration of TP was the lowest in Wushan in both the main stream and the tributaries (P0.05), but the concentration of Chl.a did not significantly vary between different sections. The level of TP decreased along the direction of the water flow until it reached Zigui where the TP level was significantly elevated. There was significantly negative correlation between the concentration of Chl.a and those of TP, dissolved total phosphorus (DTP), soluble reactive phosphorus (SRP), and nitrate nitrogen (NO3--N)(P0.01). In the contrast, the level of Chl.a was positively correlated to the levels of total nitrogen (TN), TN/TP and NO3-/SRP (P0.01). These suggested that nitrogen might moderately promote the growth of algae. Furthermore, sorption and deposition of phosphorus by suspended solids may decrease its bioavailability, and this was supported by the fact that the concentrations of TP and Particulate Phosphorus were significantly higher at the bottom of the Wushan section. Various algal species in different sections and seasons produced extracellular phosphatase, indicating that phosphorus was the key limiting factor of the growth of algae. Therefore, the current status of phosphorus and nitrogen and their effects on the hydrological condition should be taken into consideration in the eutrophication control and the management of the TGR.