One of the biggest global challenges in the mining industry is managing the risks associated with contamination by potentially toxic elements (PTEs) resulting from their activity. The oxidation of sulfides is the main cause of polluted mine drainage through the leaching of PTEs from mine waste and mine galleries to the water systems. Mine drainage can be highly acidic and often has a high concentration of PTEs, particularly arsenic, one of the environment’s most toxic elements. PTEs endanger the ecosystem’s equilibrium and raise worries about human and animal health. Some species of algae which can be naturally present in mine drainage waters, such as Spirogyra sp. And Chlorella sp., have a high capacity for absorbing PTEs from wastewater and may thrive in harsh environments. As a result, algal-based systems in bioremediation were studied and carefully analyzed, since their capacity to remove heavy metals and hazardous contaminants from polluted mine water have already been shown in previous studies. Biofuels derived from microalgal biomasses are a viable alternative to fossil fuels that can lead to a circular bioeconomy. This study reviews and analyses Chlorophyta-based bioremediation systems with application to mine waters focusing on Spirogyra sp. and Chlorella sp., since they are naturally present in mine drainage and can serve as a study model to better understand their application in bioremediation.