To improve nutrients removal from wastewater and enhance lipid production, cultivation of Chlorella vulgaris in wastewater with waste glycerol generated from biodiesel production using scum derived oil as feedstock was studied. The results showed that nutrients removal was improved and lipid production of C. vulgaris was enhanced with the addition of waste glycerol into wastewater to balance its C/N ratio. The optimal concentration of the pretreated glycerol for C. vulgaris was 10gL−1 with biomass concentration of 2.92gL−1, lipid productivity of 163mgL−1d−1, and the removal of 100% ammonia and 95% of total nitrogen. Alkaline conditions prompted cell growth and lipid accumulation of C. vulgaris while stimulating nutrients removal. The application of the integration process can lower both wastewater treatment and biofuel feedstock costs.