This research, conducted as part of our wastewater treatment project utilizing algal technology, analyzed how varying doses of carbon dioxide (CO₂) influence the structural dynamics of microalgae species. The study employed a factorial design experiment and batch culture systems, using Principal Coordinate Analysis (PCoA) and distance-based Redundancy Analysis (dbRDA) to assess changes in algal species composition in response to different CO₂ concentrations and physico-chemical variables. Primary-treated municipal wastewater was used as the growth medium. The results demonstrated that CO₂ plays a crucial role in shaping the composition and diversity of algal species during wastewater treatment. Moreover, we found that the performance of specific microalgal strains clearly depends on CO₂ concentration, highlighting the importance of tailored inoculation strategies. This research provides a foundation for developing algae-based predictive models, improving wastewater treatment methods and advancing more efficient and environmentally sustainable treatment systems. Incorporating eco-friendly algal technologies can significantly enhance and modernize wastewater management.