This study investigated the effects of different metal ions (Mg2+, Al3+ and Fe3+) on the growth, lipid accumulation and sedimentation of Scenedesmus sp. in the fatty acids medium. Results showed that appropriate concentrations of Mg2+ and Fe3+ can promote the microalgal lipid production and sedimentation in batch culture. Compared with Mg2+, Fe3+ was found to be more effective and the biomass concentration of 1.02 +/- 0.6 g L-1, lipid content of 31.7 +/- 1.7% and sedimentation efficiency of 91.2 +/- 2.5% were obtained at 45 mu M Fe3+. Al3+ addition can enhance the sedimentation efficiency, while it had inhibitory effect on the biomass and lipid production. Meanwhile, anaerobic fermentation effluent was a suitable feedstock for algal cultivation. The semi-continuous microalgal reactor was steady and efficient, and more than 96% of volatile fatty acids in effluent can be removed. The average lipid concentration and sedimentation efficiency in semi-continuous mode reached 0.39 g L-1 and 92.7%, respectively. This study provides a promising process for enhancing lipid production and waste reduction.