In ecosystem, the generation of catastrophic events arises from the cooperative impact of the external stressing factors and the internal unsteady factors existing in an ecological structure, which should be fully taken into account for regional ecological risk assessment. At present, research on external stressing factors is much focused on the natural disasters (such as storm flood disasters) and research on external contaminants is in large part concentrated on discharged heavy metals. But in fact, other contaminants such as nitrogen and phosphorus can also lead to harmfulness to ecosystem. Due to the high level of the concentration of these contaminants in excess of standard and their great effect on receptors, it is necessary to regard them as important factors and to introduce them into ecological risk assessment system. Such a choice is to ensure the assessment results being more systematic and comprehensive.Daphnia, as a receptor in this paper, is employed for analysis of the ecological risk of the east, south and west parts of Dongting Lake. Based on the historical information, flood disaster, industrial pollution, agricultural pollution and anti-schistsome infection pollution are selected as risk sources, and exposure assessment as well as hazard assessment has also been conducted. In the process of ecological risk assessment, toxicity pollution indexes (aims at N, P, heavy metals and so on), which characterize effect of toxic contamination on normal life of receptor, are defined by the ratios of normal concentration to Lethal Concentration 50～48 hours (LC_(50)-48). For heavy metals, owing to a lot of research on them, we can get toxicity pollution index values easily. However, it is hard for TN (total Nitrogen), TP (total phosphorus) to get their values due to the lack of research on LC_(50)-48 of TN and TP abroad and at home. As a result we propose an extrapolation method to calculate the toxicity coefficient and acquire their values of 1.4 and 27, and thus estimate toxicity pollution index of TN and TP according to the comparison between toxicity coefficient and LC50-48 of heavy metals. In view of the uncertainty of risk, the uncertainty coefficient is chosen in the process of our regional ecological risk assessment. Specifically, we consider the natural and sample uncertainty when determining flood disaster index, ecology indexes (including biological index, diversity index, importance index, and so on) and fragility index, and the model uncertainty when determining toxicity pollution index (including TN, TP and heavy metal toxicity pollution index). After the normalized and weighted disposal, the final results of ecological risk assessment in Dongting Lake are obtained.The results show that biological index and importance index, whose values are 40 and 40.9, respectively, of the west part of Dongting Lake is the highest. These mean that the ecological structure is presently reasonable and the attention to its ecosystem is yet necessary for avoidance of its deterioration. Diversity index of the south part of Dongting Lake is the highest, which means that the species are rich and the protection of them is therefore an urgent affair. Fragility and disaster index of the east part of Dongting Lake, with the values of 3.7 and 12.4, respectively, are comparatively high. So preventing the change of peripheral condition and increasing plant coverage rate are necessary. Toxicity pollution index of the south part of Dongting Lake is higher than that of others, so decreasing the wastewater discharge is necessary. Analyzed from risk resources, the flood disaster is the biggest restrictive factor, and the pollution is the next. It is also concluded from the research that the ecological risk of the west part of Dongting Lake is the highest, that is, facing the same risk, the damage of the west part of Dongting Lake is the most serious. Certainly, the ecological risk of the east and south parts of Dongting Lake is also high. Therefore the effect of the outside change on the ecological system in the two parts should not b