There is a growing literature on the detection of species-specific DNA fragments in water to reveal animals' presence in aquatic environments. Analysis of Rees etal. (Journal of Applied Ecology, 2014, 51, 1450) and additional publications highlight the downside of the method and suggest that some conclusions have to be toned down. Non-detection of species-specific DNA fragments in a water sample does not automatically imply the absence of the target species. A positive signal does not necessarily mean the species is present because the environmental DNA (eDNA) could have been transported or preserved after an animal's death. Detection of aquatic invertebrates is weakly documented. The effect of species abundance on detection efficiency is not always established.Synthesis and applications. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration.