A three-species system using algae (Chlorella pyrenoidosa), bacteria (Bacillus cereus), and fungi (Rhizopus oryzae) removed up to 92% of organic waste, 90% of nitrogen, 88% of phosphorus, and 88–96% of residual antibiotics from swine wastewater in just 14 days. Adding the plant hormone 5-deoxystrigol at 10⁻⁶ M boosted removal efficiency by another ~4–5% by supercharging microbial growth and enzyme activity. The multi-species consortium outperformed single-organism treatments by 12–18%, showing fungi–algae–bacteria teams can strip both pollution and antibiotic residues from factory-farm water far more effectively than conventional methods.