Since the 1980 s, eutrophication in Wuliangsuhai Lake has intensified due to excessive inputs of nitrogen (N) and phosphorus (P). Identifying the main sources and their impacts is essential for effective remediation. However, hydrological processes in the region are heavily influenced by human regulation, making it difficult to clarify the mechanisms driving N and P dynamics in the densely canal-networked Hetao Irrigation District (HID). This study coupled Distributed Agro-Hydrological Model for Irrigation District (DAHMID) and Global Nutrient Model (GNM) to comprehensively simulate four decades of N and P transport from land to the river outlet. The results indicate that agricultural non-point in the HID and municipal wastewater, led to a continuous increase in riverine nutrient loads until 2012. The semi-arid climate contributes to high nutrient retention rates (exceeding 70 % for N and 80 % for P). While this reduces nutrient delivery to the outlet, it simultaneously exacerbates water quality deterioration within the basin. In addition, due to legacy nutrients in the subsurface, excessive irrigation has led to the accumulation of surplus N in the aquifer, a process that persisted until the late 2010 s and is expected to remain a major N source to water bodies in the coming decades. Despite limitations in the simulation period for validation and data reconstruction, this study provides a quantitative basis for informed nutrient management in the basin. Sustainable water quality improvement must be achieved through optimized irrigation-drainage management that reduces nutrient losses from excessive irrigation, coupled with systematically enhanced wastewater treatment efficiency.