Aquatic snails serve an important role in the ecosystem. They also play an essential role in the life cycle of many parasites as hosts and may pose risks to animal and human health. In Australia, the role of snails in the transmission of parasites of livestock is well studied. However, despite the country’s unique biodiversity and wildlife, little is known about the role of snails in the transmission and survival of parasites in other ecosystems, including aquatic and aquaculture systems. This study aimed to determine the occurrence of parasites in freshwater snails in the eastern Murray Darling Basin. A total of 275 snails were collected from various localities, including aquaculture fishery ponds and natural creeks during the summer and autumn months in the southern hemisphere. Three different species of freshwater snails, all common to the area, were found, including Bullastra lessoni (n = 11), Isidorella hainesii (n = 157), and Haitia acuta (n = 107), of which 9.1%, 1.3%, and 4.7%, respectively, were found to be harboring various developmental stages of Trematoda. No other parasite was found in the examined snails. Parasites were identified as Choanocotyle hobbsi, Plagiorchis sp. and Petasiger sp. based on the sequences of their ITS2, 18S, and 28S ribosomal DNA region. Herein, we report a native parasite Choanocotyle hobbsi in an introduced snail, Haitia acuta, from both natural and aquaculture ponds. As there are no genetic sequences for adult specimens of Petasiger spp. and Plagiorchis spp. collected in Australia for comparison, whether the specimens collected in this study are the larval stage of one of the previously described species or are a new, undescribed species cannot yet be determined. Our results also suggest snails collected from aquaculture ponds may be infected with considerably more parasites.