The current study was aimed to investigate the performance of three native microalgae in primary-treated municipal wastewater with regard to their nutrient removal, water quality improvement for reuse, and in vivo Chl-a -based biomass production. The microalgae species belonged to three different taxonomic classes, namely blue–green blue-green algae Nostoc muscorum , diatom Navicula veneta , and green microalgae Chlorella vulgaris . The comparative phytoremediation potentials of the microalgae species and the consortium were evaluated for 7 days-exponential growth phase employed in the batch systems. The results showed that the interaction between in vivo Chl-a concentration and residual concentration of TN, TP, and COD was notable. COD, TN, and TP treatment efficiencies were in the ranges of (85.7–95.7%), (72–96.9%), and (86.07–99.8%), respectively. The final concentrations of TN, TP, and COD in effluent provided by N. veneta treatment complied with EU Directive 91/271, EU Directive COM (2018)337, and national legislation, whereas the results of C. vulgaris partially complied with these legislations. Concerning the phycoremediation efficiency and the growth characteristic of the monoculture and mixed culture of the native microalgae, it was concluded that the monocultures in most cases were superior to the consortium culture. Diatom N. veneta had the highest growth rate (0.88 ± 0.04 day −1 ), Chl-a-biomass yield (50.45 ± 1.5 mg L −1 ), and removal efficiency (96.9 % TN, 99.8 % TP, 95.7 % COD). The results also reveal that the native species effectively reduce TN, TP, and COD concentrations of wastewater, and the diatom N. veneta may be a strong novel candidate for phytoremediation systems. • Three native microalgae were tested for their removal performances of pollutants in pre-treated municipal wastewater. • In vivo Chl-a fluorescence was significantly associated with the residual concentration of TN, TP, and COD. • Diatom Navicula veneta is a novel candidate in the sustainable bioremediation of municipal wastewater. • Phycoremediated municipal wastewater by diatom fulfilled the limit values of EU Directive 91/271 and EU COM(2018) 337.