In order to assessment the nutritional status of the water ecosystem accurately and make integrated decision， a Fuzzy Assessment based on Maximum Entropy（FAME）is developed through the maximum entropy principle coupled with the randomness and fuzzy. Using TOPSIS (Technique for Order Preference by Similarity to Ideal Solution)，set the decision-making water bodies measure number as ideal solution, the max-difference number between the evaluation result and the measure result as the negative ideal solution, then Multiple Criteria Decision Making (MCDM) is established. According to the measured data validation of 12 lakes, the results of FAME basically consistent to the other results of the three methods(stochastic assessment method，fuzzy assessment method and grey evaluation method) is separately 83.3%、91.7%、917%. It is concluded that all these four methods are comparable computation precision, but FAME improves the resolution of evaluation nutritional status of water body at all levels. MCDM can solve the incompatibility of evaluation indexes of water nutritional status，making the results more close to the actual situation. FAME and MCDM can be applied to the comprehensive evaluation of water quality and decision-making.