Abstract Wetlands research and restoration has become one of the critical concern due to their importance in providing ecosystem services. This study proposes a holistic methodology to assess the wetland ecosystem based on cosmic exergy as a thermodynamic orientor. This new approach is applied to two typical wastewater treatment facilities (an activated sludge system and a cyclic activated sludge system) and to a constructed wetland ecosystem in Beijing for comparison. Results show that the Beijing wetland ecosystem gains positive net present ecological value of 3.08E+14 J c regarding its total life cycle. Comparison with the activated sludge system and cyclic activated sludge system, shows that the wetland ecosystem has greater dependencies on local resources (22% vs. 0% vs. 0%) and renewable resources (67% vs. 38% vs. 31%) as well as a larger ecological sustainability index (0.64157 vs. 0.00005 vs. 0.00008). This implies that the wetland ecosystem is more environmentally friendly and sustainable method for water treatment.