The pattern of association between water canals lining, water quality and aquatic vegetation in Beheira and Giza governorates was studied. Samples of water and Aquatic plants were collected from the examining sites during four seasons in two successive years. Results showed that water conductivity and total dissolved salts in lined sites were significantly lower than those of unlined ones (P<0.01& P<0.05) in both governorates. In Beheira, Zn, Fe and Cd in lined and unlined sites were significantly increased(p < /em><0.001, p < /em><0.01& p < /em><0.05) during summer comparing with the other seasons. In contrast, in Giza, the highest values of Zn, Pb, Cu, Fe and Cd were recorded in autumn in both lined and unlined sites. The percentage of occurrence and density of the plants were highly significant (p < /em><0.01, p < /em>< 0.001) higher in unlined sites compared to the lined ones during all seasons in both governorates. In Beheira, Eichhornia crassipes plant was completely absent during all seasons in lined sites compared to the unlined ones. In Giza, E. crassipes (83.3%) and C. demersum (50%) were highly significant (p < /em>< 0.001) higher in unlined sites compared to the lined ones (50% and 0.0, respectively) during summer. The correlation coefficients depicted very good associations between plants and heavy metals in lined sites during spring for more than 50% and more than75% in summer (r=0.58; p < 0.05). A strong positive correlation for all metals studied, Cd (0.658), Cu (0.758), Fe (0.589), and Pb (0.781) was observed. It can be concluded that watercourses lining may reduce the distribution of aquatic vegetation which rendered the current of water and preserving water with good quality. There was a strong inverse correlation between the plants and heavy metals in lined canals.