Excessive microalgal blooms can be caused by waste disposal into natural water bodies resulting in the destruction of aquatic life. However,, microalgae are also known to efficiently remediate pollutants. After the treatment of wastewater, microalgae absorb specific nutrients and can enhance the production of bioproducts. Growing microalgae as an alternative to wastewater treatment and bioproduct production has received considerable attention due to its rapid growth rate, efficient waste removal, tolerance to stress conditions and ability to accumulate valuable products. In addition, these microorganisms have a high photosynthetic rate of CO2 fixation, oxygen production and need no arable land for their cultivation. Nevertheless, in spite of these theoretical advantages, the issues surrounding the re-use of naturally existing microalgal strains need further exploration in respect to their isolation, identification and lab growth under stress conditions. The true potential of microalgae regarding wastewater treatment and energy has yet to be fully developed. The current cultivation system does not seem to be economically feasible as most of the strains used are commercially purchased. Indigenous microalgae could be the possible answer. Ammonia, one of the major constituents of most wastewaters, contributing to odor, taste, toxicity, and eutrophication is of utmost concern. The present review focuses on the growth of microalgae under high stress of ammonia in wastewater media. It also aims to present a clear-cut methodology for the isolation of microalgae from its indigenous habitat, its growth strategy under different trophic modes of nutrition, nutrient uptake, lipid, and fatty acid production. In addition, some solutions to the problem of how to make microalgae cost-effective and more sustainable are discussed in detail.