Water is one of the possible transmission routes for water- and foodborne parasites to humans. Echinococcus multilocularis is a parasite, which causes alveolar echinococcosis (AE). Nevertheless, no environmental studies have been performed as yet to confirm the occurrence of E. multilocularis in water supplies. Accordingly, 105 water samples of 50 L volume were collected from surface waters (lakes, rivers, canals) and wells in the Warmia-Masuria Province (Echinococcus endemic area) and Pomerania Province (Echinococcus non-endemic area), Poland. The water was filtered and subsequently analysed with nested PCR and real-time PCR. E. multilocularis DNA was found in two (1.9%) samples, which originated from two lakes localised in the Warmia-Masuria Province. Sequencing of the positive samples confirmed that the PCR products were fragments of the E. multilocularis mitochondrial 12S rRNA gene. This is the first investigation describing E. multilocularis detection in environmental water samples, using molecular diagnostic tools. The results indicate that water could be considered as a potential source of E. multilocularis infections in humans and animals, in endemic areas.