<p>Hydrodynamic disturbance is a pervasive but poorly understood regulator of nitrogen (N) removal in urban secondary wetlands. Herein, this study quantified the response of sediment nitrification and denitrification to a gradient of flow disturbances across a growing season, linking functional changes to microbial community dynamics in both planted and unplanted zones. Both potential nitrification and denitrification rates (PNR and PDR) consistently increased with both seasonal progression and disturbance intensity. High-intensity disturbance enhanced PNR by up to 6.04% and PDR by up to 3.6% compared to undisturbed controls, with a more pronounced effect in unplanted sediments. These functional enhancements were directly driven by a restructuring of the microbial community. High disturbance enriched key nitrifying bacteria (<i>Methylotetracoccus</i>, <i>Nitrospira</i>) and increased their contribution to the <i>amoA</i> genes. Concurrently, it stimulated denitrifying bacteria (Candidatus_Competibacter, <i>Rubrivivax</i>) and elevated the abundance of <i>narG</i>, <i>nirK</i>, and <i>nirS</i> genes. Correlation analysis revealed that disturbance-induced changes in sediment NH₄⁺-N and dissolved oxygen were the primary drivers of these microbial shifts. This study demonstrates that hydrodynamic disturbance is a critical lever for controlling N-transformation potential in urban wetlands.</p>