The copper industry generates large quantities of mine tailings water. Thus, this study aims to select a microalgae species that is both tolerant and capable of the bioremoval of heavy metals from metal mine tailings water as well as the potential biorefinery of this microalgae biomass. Chlorella vulgaris and Scenedesmus spinosus were tested for tolerance to metal mine tailings water (MTW) in northern Chile and synthetic treatments of Cu and Mo (0.1 and 0.5 mg/L). Additionally, the biomass generated was characterized to evaluate its potential applications. The main results showed greater tolerance of C. vulgaris cultured in MTW treatment. In fact, high removal efficiency of Cu and Mo was detected for this microalgae in MTW: 64.7% and 99.9%, respectively. Similarly, Cu (55%) and Mo (80.3%) removal was observed at 0.5 mg/L synthetic concentration treatments after 72 h. However, cell wall fluorescence and chlorophyll parameters were mainly affected by 0.5 mg/L Cu synthetic concentration, where the mean fluorescence intensity (MFI) was 878, compared with the other treatments (≥1800). Morphological cell changes in the MTW treatment were observed using SEM images. The presence of Mo on the microalgae surface was detected by 0.47% and 0.82% in both Mo synthetic treatments exposed. Additionally, the characterization of microalgae biomass exposed to MTW showed a higher protein content and a minor difference of lipid content compared with the control treatment, which could be used in biorefinery processes. This study reveals the capability of C. vulgaris to remove heavy metals from this mine tailings water and the effect that occurs in microalgae cells.