Artificial aquatic habitats including reservoirs, reclamation waters and constructed wetlands undergo dynamic ecological development, marked by continuous community turnover, trophic reorganisation and shifts in ecosystem function. Meanwhile, traditional biodiversity monitoring methods rely on morphological taxonomic surveys and microscopic identification. They are highly time-consuming, labor-intensive, and strongly dependent on taxonomic expertise. These approaches struggle to capture continuous community dynamics across multiple trophic groups and underestimate cryptic and small-sized benthic organisms. Environmental DNA detects DNA fragments released by organisms into the environment, supporting high-throughput and non-invasive surveys of biological communities. This review synthesizes representative published studies concerning eDNA applications in artificial aquatic habitats. We summarise the strengths of eDNA for biodiversity monitoring, and identify practical obstacles specific to engineered aquatic systems, including sampling bias and data correction. We further propose targeted future research prospects in artificial habitat ecological evaluation and restoration management. This review demonstrates that eDNA is a powerful tool for evaluating constructed aquatic ecosystems and highlights future opportunities via multi-technology integration to promote sustainable ecological infrastructure design.