Introduction: Microalgal lipids have a wide range of applications, from biodiesel manufacture in the energy industry to the production of polyunsaturated fatty acids for the pharmaceutical industry. Microalgal lipid productivity and quality, however, vary greatly depending on cultivation parameters. Aims: In this study, we investigated the potential of two marine microalgae, Nannochloropsis gaditana and Dunaliella salina, to be used as feedstock for biodiesel production. Methodology: A Taguchi L4 orthogonal array design was applied to understand the effects of sodium acetate (0 or 2 g L−1), sodium bicarbonate (0 or 2 g L−1), and sodium nitrate (25 or 75 mg L−1) concentrations on biomass and lipid productivities. Fatty acid methyl ester (FAME) profiles of microalgal lipids obtained under the best conditions were determined, and FAME results were used to predict biodiesel properties. Results: Both carbon sources (sodium acetate and sodium bicarbonate) improved biomass productivity. Lipid productivity was enhanced only by sodium acetate. The highest lipid productivities obtained were 10.25 ± 1.02 and 12.12 ± 0.28 mg L−1 day−1 for N. gaditana and D. salina, respectively. Palmitic (C16:0), stearic (C18:1), oleic (C18:1), linoleic (C18:2), lauric (C12:0), and myristic (C14:0) acids were the major components of D. salina oil. The major fatty acids in N. gaditana oil were C16:0, C18:0, and C18:1. Conclusion: The great differences in FAME profiles resulted in different biodiesel properties. Biodiesel from N. gaditana oil was predicted to have a higher cetane number (73.20) than that derived from D. salina oil (59.59). D. salina oil biodiesel, however, was predicted to have better properties than N. gaditana oil biodiesel, including lower cloud point (0.46°C) and cold filter plugging point (−7.27°C).