<p>The Water–Sediment Regulation Scheme (WSRS) artificially controls water and sediment processes in the lower Yellow River (LYR), while altering the longitudinal distribution of nutrients along the river. Affected by the confluence of tributaries and other complex factors, the spatial and temporal distribution patterns of nutrients during the water and sediment regulation (WSR) period are extremely complex. From June to August 2023, twelve sampling stations were established along the Yellow River, spanning from Xiaolangdi (XLD) to the Yellow River Estuary (YRE). Nitrogen (N) and phosphorus (P) were measured at these sites during three stages: the water regulation stage, the sediment regulation stage and the after-WSRS stage. This river segment is high nitrogen and low phosphorus, with nitrate nitrogen (NO₃⁻-N) and dissolved inorganic phosphorus (DIP) being the dominant forms. The Yiluo, Qin and Dawen rivers, as crucial tributaries, play a major role in regulating nutrient levels in the LYR as both sources and sinks. The result of PCA identified that PC1 (34.5%) correlated positively with flow, SSC, N, and P, and negatively with temperature and pH. PC2 (15.5%) linked to D₅₀, SSA, and EC. During the WSR stage, dissolved nitrogen and phosphorus fluxes of the Yellow River Estuary accounted for 15.21% and 17.33% of their respective annual totals in 2023. The DIN/DIP ratio indicated that the lower Yellow River exhibited a phosphorus-limited potential eutrophic state, and the concentrations of ammonia nitrogen (NH₄⁺-N) and total phosphorus (TP) have not consistently met the Class II standard of <i>Environmental Quality Standards for Surface Water of China</i> (GB3838-2002). Therefore, monitoring phosphorus pollutant inputs during the water–sediment regulation stage is of particular importance to river basin management agencies. This study enhances our understanding of nutrient transport during WSRS and offers a fresh perspective on nutrient delivery regulation in the LYR.</p>