With consideration of three principles, ecological functional perfection, ecological environmental protection, and ecological energy saving, an assessment index system including ten indices was established to evaluate the effects of ecological construction of the Nanjing Waterfront. Based on the projection pursuit evaluation model(PPE), which uses the genetic algorithm(GA)to optimize the projection direction, the values of the optimal projection function were adopted for grade assessment. The results show that, during the first construction period of the Nanjing Waterfront, the Hexi area falls into grade Ⅰ, with a perfect ecological effect, and the Xiaguan District, Jiangpu District, and Pukou New District fall into grade Ⅱ, and the following indices should be improved: the wetland coverage ratio, the percentage of discharged wastewater reaching the standard, the green coverage ratio, the percentage of water reaching the water quality standard, and the renewable energy utilization rate.