The industrial synthesis of nitrogenous fertilizers through the Haber-Bosch process has fundamentally transformed the global nitrogen cycle, resulting in a range of environmental challenges, including increased greenhouse gas emissions and aquatic eutrophication. To address these issues and improve Nitrogen Use Efficiency (NUE), agrochemical inhibitors are increasingly utilized to regulate specific microbial and enzymatic processes. Although these compounds effectively target urease (UI), nitrification (NI), and denitrification (DI) pathways, their capacity to suppress biological functions necessitates careful consideration of ecological safety. This review systematically examines literature from 2010 to 2025, sourced from Web of Science, Scopus, and Google Scholar, with bibliometric mapping supported by VOSviewer and Harzing’s Publish or Perish. The search strategy prioritized field-scale studies and meta-analyses that provide quantitative data on soil microbial communities and aquatic toxicity, ensuring analytical rigor. The review synthesizes evidence from microbial metagenomics and high-throughput ecotoxicity testing to assess the broader impacts of inhibitors on soil health. By integrating findings from laboratory and long-term field studies, the analysis identifies latent risks such as "pollution swapping," in which the inhibition of one nitrogen-loss pathway may inadvertently accelerate another. Additionally, shifts in non-target microbial taxa and the potential for bioaccumulation are highlighted as significant ecological concerns. The synthesis of these findings demonstrates that exclusive reliance on short-term agronomic efficacy is insufficient for comprehensive environmental assessment. A multi-tiered evaluation framework is essential to reconcile immediate productivity gains with the long-term sustainability of soil ecosystem services and microbial resilience.