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Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an emerging survey technique that has the potential to transform biodiversity monitoring in freshwater ecosystems. We provide a brief overview of the primary methodological aspects of eDNA sampling that ecologists should consider before taking environmental samples in the field. We outline five key methodological considerations: (i) targeting single species vs multiple species; (ii) where and when to sample; (iii) how much water to collect; (iv) how many samples to take; and (v) recognising potential sources of false positives. The need to account for false negatives and false positives in eDNA surveys, and the power of species occupancy detection models in accounting for imperfect detection, is also discussed.