Lipid productivity of microalgae depends considerably on the method of its cultivation. In the present study, a two-stage culture strategy was conducted to cultivate Chlorella vulgaris to enhance lipid productivity. In the first stage, C. vulgaris was grown in the synthetic medium to obtain maximum biomass concentration. Wastewater is used as a medium for growing microalgae to have commercial and environmental aptitudes for biomass production. The nutrient removal efficiencies were 80.5% (COD), 70% (TN), and 78% (TP). In the second stage, the synergistic effects of nitrogen and NaCl concentration on the lipid productivity was investigated by response surface methodology (RSM) for 2 days. The optimum conditions for relatively high lipid productivity (up to 80 mg L−1 day−1) were 2.6 mg L−1 of nitrogen, 6.3 g L−1 of NaCl, and 4.9 g L−1 of biomass concentration. The value which was predicted by model was in good agreement with the experimental value, as it was determined by the validation experiments. Saturated fatty acid composition was increased by 27.3% under optimized medium compared with synthetic medium, which is very suitable for biodiesel production. According to the above results, it is concluded that the combination of multiple stress conditions can lead to a cost-effective technology of microalgae lipid production.