The increasing global demand for biodiversity conservation has made the accurate acquisition of biodiversity data a pressing challenge worldwide. Essential Biodiversity Variables (EBVs), as core indicators for biodiversity monitoring, provide a scientific foundation for both global and regional conservation policies. While traditional monitoring methods have contributed valuable data, they remain limited by high costs, low efficiency, and sampling difficulties. Remote sensing technology offers an effective global solution for the derivation of EBVs, but its application to aquatic biodiversity monitoring remains constrained, particularly with respect to genetic diversity. Environmental DNA (eDNA), as an emerging tool, enables efficient and precise detection of diverse species within environmental samples, thereby supplying richer datasets for the development of EBVs. This paper highlights the potential of eDNA technology in advancing EBV construction and examines its prospects in biodiversity conservation in China, with the goal of fostering stronger integration between scientific research and policy-making. Using the six classes of EBVs as an analytical framework, this study reviewed 23 national and regional guidelines for aquatic biodiversity monitoring in China. The results revealed a strong dominance of community-level indicators, with approximately 95% of guidelines focusing on community composition, while genetic diversity, quantitative population dynamics, and ecosystem structure and function remain poorly represented. Considerable inconsistencies also existed among guidelines issued by different administrative sectors, limiting long-term comparability. Environmental DNA, with its high sensitivity, non-invasive sampling, and broad taxonomic coverage, offers a promising approach to address these structural gaps and support the development of EBV-aligned aquatic biodiversity monitoring systems.