The integration of microalgal cultivation with industrial wastewater remediation offers a sustainable approach to mitigating environmental pollution while producing renewable biofuel feedstock. This study evaluated four green microalgae, Chlorella vulgaris, Scenedesmus abundans, Scenedesmus obliquus, and Chlorella protothecoides, for their potential to remove nutrients from fish farm wastewater (FFW) and accumulate lipids under nutrient stress. The cultures were grown for 21 days in FFW containing an initial total nitrogen (TN) concentration of 254 mg/L and phosphate-phosphorus (PO₄-P) concentration of 26.87 mg/L. Fourier-transform infrared spectroscopy (FTIR) was used to quantify the biochemical composition, revealing species-specific metabolic shifts. Scenedesmus obliquus achieved near-complete PO₄-P removal (1.28 mg/L/day), suggesting phosphorus limitation despite elevated nitrogen levels, while C. vulgaris exhibited the highest TN removal (1.09 mg/L/day), superior NO₃-N assimilation (1.76 mg/L/day), and a significantly higher specific growth rate (µ = 0.322 day⁻¹) in FFW than in standard growth medium. All cultures displayed a net accumulation of NO₂-N (up to - 0.26 mg/L/day), indicating enhanced bacterial nitrification driven by algal oxygenation. Moreover, increased chemical oxygen demand (COD) in all reactors, ranging from 35.6 to 75.6 mg/L, was attributed to the release of extracellular polymeric substances, highlighting a stress-induced response that elevated the organic carbon content of the effluent. In contrast, C. protothecoides showed growth inhibition in FFW (µ = 0.116 day⁻¹) with low TN removal (0.38 mg/L/day). Across all species, nutrient deprivation induced a redistribution of carbon from protein to storage macromolecules, reducing protein content by up to 22% while enhancing lipid accumulation. S. obliquus demonstrated the most balanced performance, maintaining growth stability, effective nutrient removal (0.97 mg/L/day), and achieving the highest lipid content (28.4%). Overall, the results identify S. obliquus as the most promising species for integrated wastewater bioremediation and sustainable biofuel production.