In this study, we aimed to explore the commercial potential of various microalgae variants found in Al-Asfar Lake, Saudi Arabia, which have not been extensively investigated previously. We conducted a comprehensive analysis of the metabolic profiles of algae isolated from Al-Asfar Lake. The isolated algae were subjected to molecular analysis using specific primers for the Chlorophyceae class to confirm their identity. Subsequently, we compared the concentration of metabolites in the locally isolated Chlorella vulgaris from Al-Asfar Lake with five commercially available algae (Tetraselmis, Nannochloropsis, Chlorella vulgaris, Spirulina, and Isochrysis). To perform the metabolomics analysis, we employed untargeted ultra-performance liquid chromatography (UPLC) coupled with mass spectrometry (MS) analysis, which yielded a total of 168 metabolites from the microalgae samples. The data were further analyzed using MetaboAnalyst. The results revealed two distinct clusters of microalgae: the first cluster comprised Chlorella vulgaris and the microalgae isolated from the lake, while the second cluster consisted of two sub-clusters, with Isochrysis grouped with Tetraselmis, and Nannochloropsis clustered with Spirulina. Notably, the metabolites of Al-Asfar Lake algae showed a remarkable similarity to Chlorella vulgaris. These findings have significant implications for the environmental aspect of Al-Asfar Lake, shedding light on critical insights into the metabolites and commercial potential of the lake’s microalgae. The valuable insights gained from this research can be utilized to investigate the impact of nutrient abundance on the lake’s biodiversity, enhance microalgal biomass production for biofuel applications, and explore the reuse of lake water in agriculture and environmental restoration projects. Overall, our study provides important groundwork for understanding the potential of Al-Asfar Lake microalgae and their application in various industries, contributing to the sustainable development and environmental health of the region.