In order to explore the temporal and spatial variation of nutrients and chlorophyll a and their relationship in the Three Gorges Reservoir, nutrients and chlorophyll a were monitored chronically and frequently in Gaoyang Lake in Pengxi River in the Three Gorges Reservoir from May 2013 to May 2014. The study showed that the thermal stratification affected the vertical distribution of chlorophyll a and nutrients. The water thermal stratification in Gaoyang Lake occurred in early March and disappeared in the middle of September, and there was no stratification in winter ( November to February of the second year). Chlorophyll a in the surface water increased from 14.92 microg x L(-1) to 183.73 microg x L(-1) and then the chlorophyll a concentration decreased with the increasing depth of the mixing layer ( epilimnion) in the spring of 2014. Furthermore, phosphorus concentration was significantly different among layers when the water stratified and the concentration gradient of TP between the surface and the bottom was (0.18 +/- 0.04) mg x L(-1). When water was not stratified in Gaoyang Lake, the surface, middle and bottom layers had similar concentrations of chlorophyll a and nutrients, respectively. Nitrate N and dissolved phosphorus were the major components of TN and TP, respectively, during the high water level period in Gaoyang Lake with nitrate N accounting for 71.4%-95.4% of TN and dissolved phosphorus 42.7%-94.% of TP, showing that the backwater from the mainstream of Yangtze was the main source of nitrate N and dissolved phosphorus in Gaoyang Lake.