The growth performance, nutrient removal, lipid accumulation and morphological changes of Cyanobacterium aponinum OUC1 and Scenedesmus obliquus which were cultured in secondary effluents from two wastewater treatment plants: Tuandao Wastewater Treatment Plant (ETD) and Licun River Wastewater Treatment Plant (ELR) were investigated. The results showed that both C. aponinum OUC1 and S. obliquus have superior growth performances in both undiluted effluents, while the better of them was that in ETD effluent, with cell densities of C. aponinum OUC1 and S. obliquus increased by 159% and 66% over that of BG11 (control), respectively. Regarding nutrient removal, S. obliquus could completely remove inorganic phosphorus, and decrease ammonia nitrogen in ETD effluent by 81%. In addition, both C. aponinum OUC1 and S. obliquus cultivated in ETD exhibited extraordinary potential for biofuel production, increasing lipid productivities by 133% and 89% of that cultivated in ELR, respectively. As to ultrastructural changes, the differences in the lipoidal globules and glycogen granules of S. obliquus and C. aponinum OUC1 among the ETD and ELR treatments were mostly related to phosphorus limitations. The findings from this research reveal the probability using the secondary effluents as cultivation media to enhance algal biomass, nutrient removal and lipid productivity.