<p>Sluice operations significantly influence pollutant migration and transformation by altering river hydrological regimes. However, the mechanisms and ecological effects remain unclear in the high-sediment, strongly erosive environment of China’s Loess Plateau during flood seasons. This study systematically investigated the multiscale impacts of hydrological fluctuations on degradation coefficients of COD, BOD₅, NH₄⁺-N, and TP through integrated field monitoring and laboratory simulations in the Dan River, a typical sluice-controlled watercourse. Key findings include: The river’s physicochemical properties exhibited diurnal stability between 11:00 and 16:30, providing an optimal timeframe for determining pollutant degradation coefficients in the Dan River; Flow velocity exhibited the strongest positive correlations with degradation coefficients of all four pollutants (R = 0.681–0.909, <i>p</i> &lt; 0.01), showing highest sensitivity for NH₄⁺-N; Straight river reaches demonstrated greater pollutant removal efficiency than curved river reaches. Sluice-opening enhanced degradation coefficients of all four pollutants in straight river reaches but inhibited BOD₅&#xa0;and TP degradation in curved river reaches; Under controlled laboratory conditions (20&#xa0;°C), the upstream Niucun section showed higher degradation coefficients for COD, BOD₅, and NH₄⁺-N, compared to downstream sections, while TP degradation was lower. Natural conditions generally yielded higher degradation coefficients than laboratory settings, though negative coefficients occurred in curved river reaches due to pollutant accumulation. This study provides fundamental data and insights for optimizing sluice management and improving water quality in flood-prone river networks of the Loess Plateau.</p>