Knowledge of the local parasite fauna of fish and their morphology is of vital importance. Therefore, this study was aimed to estimate the prevalence and identify the most common endoparasites genera infecting some freshwater fishes in the River Nile, southern Egypt between April 2012 and March 2013. Two hundred and sixteen freshwater fish (72 of each following species: Oreochromis niloticus, Clarias lazera and Lates niloticus), were macroscopically examined, both externally and internally, for presence of helminths and encysted metacercariae. Microscopic examination was then conducted to identify the species. The parasite fauna of this geographical area is diverse; it consisted of 4 species; one trematode (Orientocreadium batrachoides), two cestodes (Tetracampos ciliotheca and Monobothrioides chalmersius) and one acanthocephala (Rhadinorhynchus niloticus) were recorded. Moreover, five species of encysted metacercariae viz., Clinostomum complanatum, Clinostomum tilapiae, Cyanodiplostomum sp., Opisthorchis sp., and Diplostomum tilapiae were detected in this survey. Among the 216 fish examined, 70 (32.4%) were infected. The lowest rate of infestation was obtained in L. niloticus (18.1%) and highest one in C. lazera (43.1%). Furthermore, the prevalence was highest in spring season (44.4%) followed by summer (35.2%) and winter (29.6%), and was lowest in autumn (20.3%). Another interesting finding of the present investigation was the recovery of Clinostomum spp. which is considered to be one of the species could therefore represent potential health risks of eating uncooked or slightly cooked fish. This study underlined the idea that an analysis of fish-parasite fauna is very useful as pre-requisite for implementing preventative and control measures against parasitic disease.