Microalgae have been used widely in bioremediation processes to degrade or adsorb toxic dyes. Here, we evaluated the decolorization efficiency of Chlorella vulgaris and Nostoc paludosum against two toxic dyes, crystal violet (CV) and malachite green (MG). Furthermore, the effect of CV and MG dyes on the metabolic profiling of the studied algae has been investigated. The data showed that C. vulgaris was most efficient in decolorization of CV and MG: the highest percentage of decolorization was 93.55% in case of MG, while CV decolorization percentage was 62.98%. N. paludosum decolorized MG dye by 77.6%, and the decolorization percentage of CV was 35.1%. Metabolic profiling of C. vulgaris and N. paludosum were performed using NMR spectroscopy. Based on 1D and 2D NMR data, 43 compounds were identified in the polar extract of C. vulgaris, while 34 polar metabolites were successfully determined in N. paludosum. The identified compounds included carbohydrates, amino acids, organic acids, dipeptides, steroids and phenols. Statistical analysis was carried out to recognize the pattern of metabolite variation between control and dye treated samples. Principal component analysis (PCA) and hierarchical cluster analysis showed that samples treated with MG are clearly separated from the control in both types of algae. Based on heat map data, the level of carbohydrates and amino acids concentrations are strongly affected by bioremediation of MG dye compared with CV dye. In conclusion, the present study proved that CV and MG dyes are considered as stress factors and the studied algae species exert their bioremediation activity without the dyes being absorbed into the cells.