Based on the implications of and requirements for the construction of an urban aquatic ecological civilization, an evaluation index system composed of 29 indicators, which covers five aspects, including water security, aquatic ecology, water management, water landscape, and water cultures, was established. With full consideration of the economic and social development level and regional characteristics in China and abroad, five evaluation grades, including the ideal, harmonious, basically harmonious, inharmonious, and extremely inharmonious levels, were set up. The projection pursuit evaluation model based on the real coded accelerating genetic algorithm(RAGA)was built. This model was used to evaluate the level of aquatic ecological civilization construction in Maanshan City, in Anhui Province, in 2012. The results show that aquatic ecological civilization in the city in 2012 was at a basically harmonious level, which is consistent with reality.