Eutrophication poses a profound threat to the provisioning of ecosystem services in lakes worldwide. Understanding how eutrophication, alongside other biotic and abiotic factors, drives sediment nitrogen removal is essential for maintaining the intrinsic purification capacity of ecosystems and safeguarding water security. To address this, we conducted a systematic investigation of 17 representative lakes across the Eastern China Plain using <sup>15</sup>N stable isotope tracing, 16S rRNA amplicon sequencing, and metagenomics profiling. This study aims to quantify the contribution of the anammox to nitrogen removal, elucidate the impacts of eutrophication on overall nitrogen removal, and identify the critical biotic and abiotic factors driving these processes. Results revealed that while denitrification was the dominant process across all lakes, anammox made substantial contributions of up to 34.3 %, exhibiting a distinct environmental dependency. Eutrophication significantly amplified both the overall nitrogen removal capacity and the relative contribution of anammox, with local physicochemical properties and microbial communities demonstrating a pronounced joint driving effect on these processes. Notably, the observed decoupling among microbial community structure, functional gene abundance, and nitrogen removal rates highlights a significant discrepancy between genetic potential and active expression. This discrepancy is further manifested by the superior environmental adaptability of functionally redundant denitrifying bacteria compared to narrow ecological niche anammox bacteria. Furthermore, we demonstrate that macro scale factors, including spatial, climatic, and anthropogenic, indirectly drive nitrogen removal by reshaping local water-sediment physicochemical properties, rather than acting as direct determinants of process rates. Collectively, this study enriches our fundamental understanding of nitrogen removal, particularly the anammox process, and its multidimensional drivers in the Eastern China Plain lakes. We advocate that future lake management strategies must rigorously account for the overarching constraints jointly imposed by trophic status, alongside spatial and climatic gradients, to ensure the sustainability of nitrogen purification ecosystem services.