The present investigation was carried out on two species of freshwater fishes Oreochromis niloticus niloticus and Clarias gariepinus collected from EL-Ibrahimia and EL-Malah canals at Assuit province. Water samples were also collected for determination of some water quality parameters and the concentration of certain heavy metals including Cu, Cd and Pb. The results of water quality analysis indicated significant differences between the two selected sites. The examination of the intestinal parasites in both investigated fish species indicated that O. niloticus niloticus harbors one species of acanthocephalans, Acanthosentis tilapiae at the two investigated sites while, Clarias gariepinus was found harboring one species of nematodes, Paracamallanus cyathopharynx at site(1) and one species of trematodes, Orientocreadium lazeri at the two sites.  The results also indicated that the mean concentration of the three heavy metals in water at site (1) are ranked as Cu > Cd > Pb, while at site (2) they are ranked as Cu > Pb > Cd with a highly significant difference (P<0.01) between the two investigated sites. The data also showed a differences between the fishes and their parasites from heavy metal ranking point of view, where it is ranked as Cu > Pb > Cd  in  both infected and uninfectedfishes. In case of parasites heavy metals concentration at site (1) the investigated heavy metals are ranked as   Pb > Cu > Cd in both Acanthosentis tilapiae and Orientocreadium lazeri, while they are ranked as Pb > Cd > Cu at site (2) in Acanthosentis tilapiae and Pb > Cu > Cd in Orientocreadium lazeri. Also, a significantly higher concentration of heavy metals was recorded in the parasites compared to their host fishes.