Two fresh water microalgae, Coelastrella sp. M-60 and Micractinium sp. M-13 were investigated in this study for their potential of biodiesel production. For increasing biomass and lipid production, these microalgae were subjected to nutrient starvation (nitrogen, phosphorous, iron), salinity stress and nutrient supplementation with sugarcane industry effluent, citric acid, glucose and vitamin B-12. The lipid productivity obtained from the isolates Coelastrella sp. M-60 (13.9 +/- 0.4 mg/L/day) and Micractinium sp. M-13 (11.1 +/- 0.2 mg/L/day) was maximum in salinity stress. The media supplemented with all the four nutrients yielded higher lipid productivity than the control. The response surface methodology (RSM) was employed to evaluate the effect of sugarcane industry effluent and citric acid on growth and lipid yield. Fatty acid profile of Coelastrella sp. M-60 and Micractinium sp. M-13 were composed of C-14, C-16:0, C-18:0, C-18:1 and C-18:2 and their fuel properties were also in accordance with international standards. (C) 2015 Elsevier Ltd. All rights reserved.