We describe a methodology to investigate the potential of given microalgae species for biodiesel production by characterizing their productivity in terms of both biomass and lipids. A multi-step approach was used: determination of biological needs for macronutrients (nitrate, phosphate and sulphate), determination of maximum biomass productivity (the “light-limited” regime), scaling-up of biomass production in photobioreactors, including a theoretical framework to predict corresponding productivities, and investigation of how nitrate starvation protocol affects cell biochemical composition and triggers triacylglycerol (TAG) accumulation. The methodology was applied to two freshwater strains, Chlorella vulgaris and Neochloris oleoabundans, and one seawater diatom strain, Cylindrotheca closterium. The highest total lipid content was achieved with N. oleoabundans (25–37% of DW), while the highest TAG content was found in C. vulgaris (11–14% of DW). These two species showed similar TAG productivities.