Abstract. The increasing water demand due to human activities has aggravated water scarcity, and conflicts among stakeholders have increased the risk of unsustainable development. Ignoring the effects of trade-offs leads to misguided policy recommendations. This study highlights the concept of synergy among different aspects of the water allocation process. A process-based three-layer synergistic optimal-allocation (PTSOA) model is established to integrate the interests of stakeholders across sub-regions, decision levels, and time steps while simultaneously coupling reclaimed water to establish environmentally friendly solutions. A synergy degree index is constructed by applying network analysis for optimization. PTSOA is applied in Yiwu, southeast China, and is shown to be able to improve the contradictions among different dimensionalities in a complex system. Overall, 2.43×107–3.95×107 m3 of conventional water is saved, and notable improvements in management are achieved. The application demonstrates the efficiency and excellent performance of the PTSOA model.