The analysis of DNA fragments and their assignment to individual species – an increasingly well‑established approach – is transforming biodiversity assessment. Samples collected from waterbodies permit rapid biomonitoring of aquatic ecosystems. However, environmental DNA (eDNA) analysis is not without pitfalls. For this reason, guidelines for practitioners have now been developed by a group of experts – including Eawag scientists – coordinated by the Federal Office for the Environment. These guidelines, covering the whole process from sampling to data interpretation, should help to ensure that eDNA applications produce reliable results.