The present investigation was carried out to assess the spatial and seasonal variations in heavy metals concentrations in water, sediments as well as belowground and aboveground parts of the dominant macrophyte Phragmites australis along contaminated El-Qabouty junction Canal. Analyses of 12 heavy metals content (Br, As, Co, Ni, Fe, Cr, Hg, Zn, Cd, Pb, Se, Mn) in water, hydrosoil and plant samples were collected from two sites along El-Qabouty Canal and seasonally analyzed using XRF. The results recorded the highest concentrations of Co, Mn, As, Cr and Fe in water with 9.73, 9.79, 24.89, 26.38 and 47.57 mg/l, respectively in spring season at the southern site nearby industrial drain output. Seasonally, the pollutant content was lower in winter. Higher concentrations of Co, Cr, Hg, Ni, Pb, Se and Zn were recorded in belowground parts for P. australis at the norther site of the canal in summer. The bioaccumulation factors (BF) of heavy metals were more than one and in the order Hg>Se>Br>Pb>Zn>Mn with values 174.38, 106.26, 52.30, 18.49, 7.21, 2.98, respectively. The translocation factors (TF) of As and Cd were 15.97 and 12.58, respectively. The obtained results and indices indicated that P. australis can grow and tolerate in highly contaminated waste water and is a good candidate to serve as hyper-accumulator, phyto-stabilizer and bio-monitors of heavy metals.