Global fish consumption increased higher than that of all other animal protein foods. The image of fish as a healthy food is the main reason for increasing demand for fish meat, but there are serious safety concerns related to the presence of fish-borne zoonotic pathogen including parasites. A cross-sectional study was conducted from December 2021 to July 2022 at Lake Haramaya, Lake Tinike, and Lake Adele on Oreochromis niloticus and Clarias gariepinus fish species to determine the prevalence of Contracaecum (Nematoda) and Clinostomum (Trematoda) infection. A total of 384 individuals of C. gariepinus 241 (62.76%) and O. niloticus 143 (37.24%) were sampled from Lake Haramaya 149 (38.8%), Lake Tinike 113 (29.4%) and Lake Adele 122 (31.8%). The overall prevalence of parasite was 30.2% (116/384) and higher overall prevalence of parasite was recorded in Lake Haramaya (36.2%) followed by Lake Adele (27.9%) and Lake Tinike (24.8%). C. gariepinus was more affected than O. niloticus fish and Contracaecum parasite was more prevalent than Clinostomum parasite (37.3% and 18.2%) and (29.9% and 14.6%), respectively. The distribution of parasite was significantly affected with respect to species of fish, sex, weight, and length categories, genera of parasite, and location of parasites. The perception of respondents on fish-borne zoonotic parasite (FBZP) was affected by demographic characteristics of respondents. Human and animals were interacted with the lakes and its environment adversely which can perpetuate the life cycle of FBZP. Moreover, unsafe fish meat processing from harvesting to consumption was the main problem at the study area, which can makes surrounding people under the risk of FBZP. However, the risks associated with FBZP can be reduced through the application of good hygiene, fishing practices, inspection of fish meat, proper storage, adequate cooking of fish, and with the promotion of the community awareness.