<p>Liangzi Lake bears important ecological functions in the metropolitan area of the middle reaches of the Yangtze River, yet these functions face worsening endogenous pollution from sediments due to historical aquaculture and agricultural runoff. Given this, this study investigated the vertical distribution of nitrogen and phosphorus indicators in sediments of the lake, quantified nutrient diffusion fluxes to the overlying water, and analyzed their correlation. The results showed a significant concentration gradient, with the average concentration of ammonia nitrogen (NH₄⁺-N) in the interstitial water being four times that of the overlying water, indicating significant release potential. The NH₄⁺-N diffusion flux ranges from 4.01 to 7.16&#xa0;mg·(m²·d)⁻¹ (mean 5.61&#xa0;mg·(m²·d)⁻¹), and its high diffusion flux areas are concentrated in Liangzi Island, Niushan Lake in the north and Ezhou area; Orthophosphate (PO₄³⁻-P) flux is −0.08–0.14&#xa0;mg·(m²·d)⁻¹ (mean 0.014&#xa0;mg·(m²·d)⁻¹), and the diffusion area of high PO₄³⁻-P is concentrated in Xiliangzi Lake. Correlation analysis shows that the diffusion flux of NH₄⁺-N is significantly positively correlated with organic matter (OM) and is also affected to varying degrees by sediment nitrogen content and water content (WC); The diffusion flux of PO₄³⁻-P is significantly negatively correlated with the overlying water PO₄³⁻-P. Overall, this study provides a key theoretical basis for the “zoning policy” strategy needed for endogenous control.</p>