New strains of green microalgae were isolated and screened for growth and the production of lipids from municipal wastewater. It was shown that the strain Micractinium sp. IC-76 has a biomass productivity of 37.18 ± 4.12 mg L−1 d−1 and a lipid content of 36.29 ± 0.11%, with a total content of saturated and monounsaturated fatty acids of 71.9%. The efficiency of nitrogen (N-NH4) and phosphorus (P-PO4) removal was 96.4 ± 0.7 and 77.8 ± 5.6%, respectively. The metabolic differences at the exponential and stationary phases of growth between the closely related strains with different patterns of lipid accumulation were revealed via gas chromatography mass spectrometry metabolic profiling. The strain Micractinium sp. IC-76 in the stationary phase of growth shows a significant difference in carbohydrate metabolism, especially sucrose concentration. High lipid induction during cultivation in wastewater was also driven by changes in the biosynthesis of amino acids, fatty acids and the tricarboxylic acid cycle.