Wetlands have long been recognized as efficient nitrogen (N) processing systems. While widespread interest is in constructing wetlands to mitigate N pollution, there is a dearth of information about the environmental consequences following wetland dismantlement. This study elucidated the changing trajectories of water quality and N removal capacity in a headwater river that initially contained a series of constructed wetlands but later underwent wetland destruction. An estimated 17% surge in total N concentration has been reported since the wetlands’ destruction. This adverse trend is primarily attributed to a weakened in-stream N removal capacity, which was reduced to a mere 25% of the levels observed when the wetlands were operational. Further analysis confirms that the presence of wetlands actively shapes desirable environmental settings for N processing. In stark contrast, wetland destruction leads to unfavorable environmental conditions, which not only restrain in-stream anaerobic metabolisms but also trigger algal proliferation and biological N fixation. Collectively, this research provides compelling evidence of the detrimental consequences associated with wetland destruction, emphasizing the need for remedial strategies to mitigate these negative effects.