The environmental problems generated by waste from the mining industry in the mineral extraction for business purposes are known worldwide. The aim of this work is to evaluate the microalga Muriellopsis sp. as a potential remover of metallic ions such as copper (Cu2+), zinc (Zn2+) and iron (Fe2+), pollutants of acid mine drainage (AMD) type waters. For this, the removal of these ions was verified in artificial acid waters with high concentrations of the ions under examination. Furthermore, the removal was evaluated in waters obtained from areas contaminated by mining waste. The results showed that Muriellopsis sp. removed metals in waters with high concentrations after 4–12 h and showed tolerance to pH between 3 and 5. These results allow proposing this species as a potential bioremediator for areas contaminated by mining activity. In this work, some potential alternatives for application in damaged areas are proposed as a decontamination plan and future prevention.