This paper present in situ experiments in Pengxi River of the Three Gorges Reservoir by selecting Anabaena flos-aquae, Microcystis aeruginosa, Eudorina sp. and Cyclotella hubeiana as dominate algae species, monitoring nitrogen (Cell-N) and phosphorus (Cell-P) concentrations of these algae cells in three operating periods, and measuring total nitrogen (TN) together with total phosphorus (TP) concentrations in ambient water body. Combined with our previous findings, the state of nutrient limitation is evaluated via critical (supply) N/P ratio, cellular N/P ratio and Guildford's TN/TP ratio evaluating standard, providing research foundation of limitation evaluation for revealing the eutrophication processes as well as algae physiological characteristics of tributary waters in the Three Gorges Reservoir. The results of in situ research showed that these three evaluation standards presented the same state of nutrient (nitrogen or phosphorus) limitation. Specifically, in low water period, phosphorus was deficient, and no obvious nutrient limitation were presented at initial cultivation stage while phosphorus limitation was appeared at last cultivation stage. In high water period, both initial and last cultivation phase observed no obvious nutrient limitations. In discharge period the initial stage showed nitrogen limitation while the final stage appeared phosphorus limitation because of the frequent change of nutrient. Though each algae in different water periods presented various nutrient limitations, on the whole, the threshold range of critical N/P ratio and cellular N/P ratio have significantly and promisingly indicative effect, the nutrient state of water body can be preliminarily evaluated from the perspective of physiology of algae cells.