Water level is a major feature and indicator of hydrological regimes of lakes, as affecting water volume, water quality and habitat of lakes. It is considered as a key factor affecting ecosystem health of lakes. How to estimate an ecological water level for lakes has long been an important scientific issue in lake science research. Based on multiple-year water level data of the Lake Poyang, water level indicators were identified from natural water level regimes to build up a new water level for the lake. Water level indices based on natural regimes are grouped as duration, timing, and rate of change for high and low water levels to represent lake ecological water level. The proposed method based on this study can improve lake ecological water level estimation by supplying a more detailed description of water level process which is not available from the traditional methods. Based on this new method and daily water level data of Duchang Station in the Lake Poyang from 1952 to 2000, interval of ecological water level of the Lake Poyang was estimated to underpin the decision-making for ecological and water conservancy management of the Lake Poyang.