Water shortages and water pollution are a global problem. Increases in population can have further acute effects on water cycles and on the availability of water resources. Thus, wastewater management plays an important role in mitigating negative impacts on natural ecosystems and human environments and is an important area of research. In this study, we modelled catchment-scale hydrology, including water balances, rainfall, contamination, and urban wastewater treatment. The entire water resource system of a basin, including a forest catchment and an urban city area, was evaluated synthetically from a spatial distribution perspective with respect to water quantity and quality; the Life Cycle Assessment (LCA) technique was applied to optimize wastewater treatment management with the aim of improving water quality and reducing CO₂ emissions. A numerical model was developed to predict the water cycle and contamination in the catchment and city; the effect of a wastewater treatment system on the urban region was evaluated; pollution loads were evaluated quantitatively; and the effects of excluding rainwater from the treatment system during flooding and of urban rainwater control on water quality were examined. Analysis indicated that controlling the amount of rainwater inflow to a wastewater treatment plant (WWTP) in an urban area with a combined sewer system has a large impact on reducing CO₂ emissions because of the load reduction on the urban sewage system.