In recent years, microalgae biodiesel has attracted expressive attention and investment, once it was considered a potential resource for energy. Although the wide use of microalgae biodiesel is restricted by its high production cost. For cost-efficient and sustainable production of biodiesel from microalgae, a proper understanding of the variables and their impacts on physiology of the strains is required. In this study, a simple factorial design 2 3 was used to find optimal conditions for the cultivation of Ankistrodesmus sp. and Chlamydomonas sp. in batch culture. The three components considered were nitrate, phosphate and sodium chloride, used to assess the metabolic versatility of the strains in brackish conditions. The results showed that culture medium with 0.04 g•L −1 nitrate, 0.01 g•L −1 phosphate and 5.0 g•L −1 sodium chloride resulted to be the most effective condition to growth and fatty acids accumulation. Using this optimal condition, Ankistrodesmus sp. and Chlamydomonas sp. increased in 2.1 and 2.4 folds their fatty acids yield, respectively. Importantly, this protocol reduced 75% of the nitrate and phosphate concentrations of the original medium (ASM-1). Additionally, fatty acids analysis found that these strains were mainly constituted of C16-C18, in accordance with the requirements for biodiesel production. The simple factorial design applied here proved to be an important tool towards a better understanding of synergistic effects of tested factors on microalgae metabolism, and the resulting information could be used effectively to improve microalgae cultivation.