Determination of appropriate effluent quality limits (EQL) for wastewater treatment plants in China is a complicated process involving multiple factors that need joint consideration. Based on advantages of compiling the energy and material flows as well as the emissions into air, water and soil, life cycle assessment (LCA) presents a standardized approach for evaluation of EQL alternatives. However, challenges arise when incorporating more factors is indispensable, especially for the elements concerning downstream receiving water body, official watershed planning and stakeholder's participation. To this end, an integrated LCA-based decision-support platform named HIT.WATER scheme is proposed, linking the currently available LCA system with Water Quality Model (WQM), Plackett–Burman (PB) design and Conjoint Analysis (CA). A demonstrative case study was conducted to illustrate the processing procedures. Results obtained in the current study show that the officially defined river functions and the downstream cross-section distances resulted in more significant effects on the assessment outcome than other factors such as self-purification coefficients and weighting factors. Nevertheless, the comparisons among EQL alternatives were carried out and the differences were observed, which were dynamic, varying with the changed conditions of either natural factors (e.g. downstream distances) or human factors (e.g. officially defined river functions). Quantitatively presenting the dynamic comparisons to indicate the differences among the alternatives was a principal function of the HIT.WATER scheme. In particular, the approach allows the environmental impacts of EQL examined from various perspectives, which is conducive to the preclusion of “one-size-fits-all” determination with sustainability consideration. Stakeholder's participation was achieved through a transparent decision-making process, and their selection and judgment criterion could be explicitly presented using quantitative metrics. We conclude that the HIT.WATER scheme can be applied to broader scales where the evaluation of paradigm shifts (technological advancement or effluent standard changes) in sewage systems is necessary.