Wastewater treatment, along with the simultaneous production of valuable chemical compounds, including lipids by microalgae is a challenging but attractive study. Towards this goal, the candidate microalgae were selected from culture collections or isolated from wastewater in this study. The initial screening test using microalgae revealed that various eukaryotic as well as prokaryotic microalgae showed steady growth in municipal wastewater samples. Among them, Tetraselmis sp. NKG400013 and Parachlorella kessleri NKG021201 from culture collections, and Chloroidium saccharophilum NKH13 from the wastewater sample exhibited high biomass productivity. Furthermore, P. kessleri NKG021201 and C. saccharophilum NKH13 showed high lipid productivity (56 ± 1 mg/L/day for NKG021201, 35 ± 10 mg/L/day for NKH13). During this cultivation, 99% of nitrogen and 82% of phosphorous compounds were removed from the wastewater sample by the strain NKG021201. Analysis of fatty acid compositions of P. kessleri NKG021201 and C. saccharophilum NKH13 revealed that lipids derived from these microalgae were suitable for the application of biodiesel fuels, indicating that these microalgae were promising for wastewater treatment and lipid production.