A histopathological study was organized addressing the impact of endo-parasitic infection and water quality on 296 Bagrus bajad collected from Ismailia Canal waters from March 2021 to September 2021. Endoparasites were shown to infect 68.92% of fish. Based on the type of parasite, the highest parasitic infection was associated with trematodes, followed by nematodes and cestodes. Some physicochemical parameters such as water temperature, pH, ammonia, nitrite, nitrate, total alkalinity, dissolved oxygen, hardness, and total dissolved solids have been simultaneously investigated. The prevalence of parasites recorded an increase during summer. Histopathological changes in the infected fish's intestine, liver and muscles were also recorded. Pathological alterations in the intestine of the infected fishes showed necrotic enteritis, manifested by desquamated and necrotic villus epithelium and inflammatory cell infiltration within lamina propria and submucosa. Whereas, the liver of the infected fishes showed devastating focal areas of congested necrosis, represented by losses of cellular details. Moreover, the muscles of the infected fishes showed chronic inflammatory reactions around the remnant of parasites and degeneration of myofibers with focal areas. In conclusion, the parasitic infection might have negative impacts on fish wealth and human health.