Wastewater with high nutrient levels continues to promote eutrophication and degrade aquatic systems, which led to the necessity of treatment systems capable of removing nitrogen (N), phosphorus (P) and organic pollutants in a single, energy-efficient step. This study presents a novel multifunctional bacterial consortium (MBC-4). Flask-scale analyses revealed excellent pollutant removal accompanied by stable growth (OD₆₀₀ patterns), which validates the ability of the MBC-4 to perform an integrated aerobic treatment. Under optimized conditions, MBC-4 demonstrated significant removal efficiencies of NH4+-N (92.17 ± 3.4%), NO₃⁻-N (90.61 ± 1.7), PO₄³ ⁻ (85.52 ± 0.25%), COD (90.05 ± 2.5%), BOD (91.48 ± 1.5%), and TSS (88.37 ± 2.0%) in 96 h from real wastewater. Slightly improved removal efficiencies were achieved in synthetic wastewater due to its more uniform composition and the full metabolic potential of the consortium. The response surface methodology revealed that optimal pH (7.4), C/N ratio (10.0), inoculant dosage (1.0% v/v), temperature (32.0 °C) and shaking speed (160–180 rpm) were key factors governing SNDPR performance. Synchronous nitrification, aerobic denitrification and phosphorus accumulation under fully aerobic conditions were confirmed by functional gene amplification (amoA, hao, napA, nirS, norB, nosZ, ppk) and enzyme assays and N and P balance. A hypothetical integrated consortium interaction model was proposed to explain coordinated nitrogen, phosphorus, and organic matter removal under aerobic conditions. Overall, MBC-4 demonstrates strong potential for single-stage aerobic remediation of wastewater/polluted water, which offers a feasible alternative to conventional multi-phase nutrient removal systems.