Environmental pollution is a severe and common problem in all the countries worldwide. Various physicochemical technologies and organisms (e.g., plants, microorganisms, etc.) are used to address these environmental issues, but low-cost, practical, efficient, and effective approaches have not been available yet. Microalgae offer an attractive, novel, and little-explored bioremediation alternative because these photosynthetic organisms can eliminate pathogenic microorganisms and remove heavy metals and toxic organic compounds through processes still under study. Our research team has conducted some experiments to determine the bioremediation potential of native microalgae on some pollutant sources (i.e., leachate and wastewater) and its ability to remove hazardous chemical compounds. Therefore, in this chapter, we provide the results of our research and updated information about this exciting topic. Experiments were conducted under controlled culture conditions using several native microalgae species, variable time periods, different pollutant sources, and hazardous chemicals such as ethidium bromide. The results indicated that native microalgae can remove pollutants (i.e., phosphorus, ammonia, etc.) of wastewater, leachate, and some hazardous chemical compounds such as ethidium bromide. In conclusion, native microalgae have an excellent potential for removing several pollutants and, consequently, could be used to develop bioremediation technologies based on native microalgae from the Peruvian Amazon.