Abstract: Comparative in-situ experiments were conducted to systematically investigate the effects of hydrodynamic conditions on hydrochemical parameters and nutrient dynamics, with a focus on nitrogen transformation, in a shallow lake. The denitrification efficiency of the system was quantitatively assessed. The results indicated that, compared to the static control area, the introduction of hydrodynamic circulation disrupted the typical aerobic–facultative anaerobic–anaerobic stratification commonly observed in shallow lakes, establishing a dynamic alternating oxic (AO) system. This alteration led to stabilization of conductivity and dissolved oxygen (DO) levels, a reduction in chemical oxygen demand (COD), and an 11.59% decrease in total nitrogen concentration. By promoting the exchange of water and nutrients between surface and bottom layers, the AO mode enhanced the microbially driven nitrification-denitrification coupled process, preventing excessive nitrogen accumulation and improving the lake’s ecological environment. Furthermore, a method to determine the optimal circulation flow rate required to achieve the desired nitrogen removal efficiency was provided based on pollutant degradation rates. These findings highlight the critical role of hydrodynamic management in aquatic ecosystem restoration and provide valuable theoretical and empirical support for water ecological rehabilitation.