This study conducts a comprehensive investigation of the sediment dynamics of West Lake. The research finds intricate relationships between sediment nutrient release and various environmental factors. Sedimentological tests suggest that the concentrations of TN, TP, and NH 4 + -N in sediment are mainly influenced by the physicochemical properties of sediment and overlying water. Laboratory experiments uncover that a temperature increase of 2−3 °C can elevate phosphorus efflux from sediment by approximately 15%. The presence of submerged plants, mainly in areas with direct water diversion, is linked to a decrease in nutrient efflux from sediment at a rate of about 25%. Analysis of microbial communities in sediment samples indicates the dominance of Proteobacteria and Bacteroidetes, which are proposed to play a key role in degrading organic matter and nutrient recycling in sediment. The activity of these microorganisms is estimated to reduce the level of nutrient efflux from sediment by 18%. Principal component analysis further verifies the spatial heterogeneity among sampling sites, with the primary principal components explaining 68% of variations. These findings not only provide insights into biogeochemical processes in freshwater ecosystems but also underscore the importance of integrated management to ensure long-term sustainability of aquatic environments.