A total number of 200 Clarias gariepinus were collected a live from two different ecosystem (100 Clarias gariepinus from each locality),where locality1 (Drainage Canal {Al-Gharbiya Drainage Canal}) and locality2 (River Nile Branch {Bahr Teara}) and examined for presence of endoparasitic helminths, Clarias gariepinus infected with cestodes (infestation rate was 19% and 4% in Drainage Canal and River Nile Branch, respectively) as: Polyonchobothorium clarias and Monobothrium spp. with an infestation rate 32.9% and 67.1%, respectively in Drainage Canal and 25% and 75%, respectively in River Nile Branch and nematodes (infestation rate was 41% and 23% in Drainage Canal and River Nile Branch, respectively) as: Procamallanus laeviconchus and Paracamallanus cyathopharynx with an infestation rate 56.3% and 43.7%, respectively in Drainage Canal and 55.2% and 44.8%, respectively in River Nile Branch hence, infestation rate of endoparasitic helminths in Drainage Canal was higher than River Nile Branch. The water of Drainage Canal was more polluted with heavy metals as (Fe, Cu, Hg, Pb, Ni, Mn and Cd) than the water of River Nile Branch while, Zn within Permissible limits. Heavy metal residues in the organs of Clarias gariepinus in River Nile Branch were higher than Drainage Canal. Heavy metals were bioaccumulated in Clarias gariepinus in order: liver> kidney> muscle in the two localities (River Nile Branch and Drainage Canal).