Microalgae have become an important means of wastewater treatment. As a sustainable and economical method of wastewater treatment, microalgae not only purify wastewater from different sources, but also use wastewater as growth matrix to produce valuable biological products, biomaterials and bioenergy. However, given the complexity of compounds in wastewater and the challenge of increasing removal efficiency at a lower cost through treatment technology optimization, more research is required. In this paper, the application of indigenous microalgae in wastewater treatment was analyzed, and the wastewater was divided into four parts: nutrients such as nitrogen and phosphorus, chemical oxygen demand (COD) and biological oxygen demand (BOD), contaminants of emerging concern and heavy metals. In addition, the joint treatment of wastewater by microalgae and other methods such as microalgae-yeast system, microalgae-bacteria system, microalgae constructed wetland system and microalgae-sludge system were also discussed. Finally, the immobilization technology of microalgae and the future development trend and challenges of microalgae in the treatment of water pollution are analyzed. This will provide useful information for wastewater treatment.