Observing aquatic invertebrate diversity can provide ecological insights into changing environments. Research into moving waterbodies has primarily focused on rivers, with little exploration into biodiversity within ditches. Ditches often drain into larger ‘reens’, which are artificial structures designed to prevent water-logging in winter and provide livestock with water in summer There has been little investigation into ditches and reens as important habitats for invertebrates, partly due to difficulty surveying them. Often, macroinvertebrate surveys use morphological monitoring methods to understand the area’s biodiversity; however, these methods are often time-consuming, require expert knowledge, and are highly invasive. In this study, an alternative method using environmental DNA (eDNA) was applied to understand the alpha and beta diversity of ditches and reens in St. Brides SSSI, South Wales. Here, the data presented demonstrated that eDNA analysis produces far greater taxonomic information than morphological analysis and that abiotic factors, such as waterbody type and temperature, significantly impact alpha diversity, while the amount of water filtered and salinity influenced beta diversity. These results indicate the importance of utilizing consistent methods during water sample collection. In addition, ditches and reens showed differences in invertebrate diversity despite the waterbodies being connected. We anticipate that the findings from this study can aid ditch and reen management plans to ensure that invertebrate biodiversity is maintained. Furthermore, this study highlights the importance of using invertebrates as indicator species for water quality assessment and displays the benefits of using environmental DNA monitoring in combination with morphological monitoring