Populations of Arctic char (Salvelinus alpinus) inhabiting Irish lakes are undergoing a rapid decline. In order to aid monitoring of this species in Irish lakes, a species/specific qPCR assay was designed and subsequently tested for the detection of Arctic char’s environmental DNA (eDNA) in an indoor mesocosm as well as in natural habitats (six lakes). Specifically, the mesocosm experiment revealed that sample volume can have significant effects on the application of eDNA approaches, whereby probability of detection depends from proximity to the source organism as well as volume of water filtered. When tested in the wild, positive amplification of Arctic char eDNA was observed in four of the six lakes sampled, proving that this approach can be successfully implemented in natural conditions. However, findings from the present study also showed that sub-optimal sampling strategies can lead to false negative results (e.g. failure to detect the species when it is present). This study corroborates findings from other research on eDNA detection of fish species, showing that despite its current limitations this approach can be a fast, non-invasive and effective tool in aid to the conservation and management of freshwater fish species.