The study evaluated the use of Chlorella vulgaris for bioremediating hydroponic wastewater and producing biomass under different cultivation modes and to explore the economic implications of microalgal biofuels. Total nitrogen (TN) removal efficiency was 98.5% in mixotrophic conditions and 96% in heterotrophic conditions, and total phosphorus (TP) was completely removed (>99%) in both cultivation conditions. TN removal was higher for that which was cultivated under the mixotrophic mode of cultivation. The maximum biomass production (1.26 g/L) and biomass productivity (0.1108 g/L/day) were also reported for mixotrophic conditions. Lipid content was slightly higher for that which was cultivated under heterotrophic conditions: 33 wt% on an ash-free dry weight (AFDW) basis. The highest lipid production was obtained under mixotrophic growth (0.341 g/L). Higher net profit was obtained for both mixotrophic and heterotrophic cultivations: 30.6 million $/year for a plant capacity of 3.29 × 104 tone/year and 30.12 million $/year for a plant capacity of 3.17 × 104 tone/year respectively. Sensitivity analysis showed that biodiesel and nutritious supplements from soluble protein have the greatest impact on the process economics regarding mixotrophic cultivation, while biodiesel and feeds from insoluble protein have the largest effect on the process economics regarding heterotrophic and autotrophic cultivations.