This study assessed the evolution of wastewater systems during the rapid urbanization of Beijing, with special focuses on the carbon footprints and growing underground WWTPs (u-WWTPs). Specifically, the Bishui plant (in situ constructed u-WWTP) was assessed in detail regarding eco-environmental benefits. Our results showed that, the direct emission intensity of 65 WWTPs decreased from 0.47 to 0.24 kg CO2eq/m3, when the electricity intensity increased from 0.22 to 0.39 kWh/m3 from 2010 to 2020. Bishui u-WWTP emitted 36.6 kt CO2eq/year (0.09 kg CO2eq/m3), with electricity intensity of 0.43 kg CO2eq/m3. Additionally, compare to the hypothetical relocating scenario, it saved 6.67 × 104 m2 land and 33.0 kt CO2eq/year, and the created urban river carries 6.5 × 1013 J/year heat outside town. The evaluation and balance of choice for conventional or underground WWTP should be made case by case. However, this study demonstrated that u-WWTP is not only a construction manner, but a sustainable management model with positive eco-environment effects, algin with future city expansion, and circular economy visions.