In the current work, we investigated the concentration of Ni and Pb in different organs of Phragmites australis to evaluate its potential application as a phytoremediator to remove these two metals from contaminated water and sediment in Lake Burullus (a Ramsar site in Egypt). Above- and below-ground biomass of P. australis, water and sediment were sampled monthly for 1 year at six sites of Lake Burullus (three sites represent each of the northern and southern parts of the lake) using six randomly distributed quadrats (each of 0.5 × 0.5 m) at each sampling site. Significant variation was detected for Ni and Pb concentrations in the sediments and waters between the northern and southern sites of the lake. The biomass of P. australis in the southern sites was greater than that in the northern sites; in addition, the above-ground biomass was higher than the below-ground biomass. The above-ground organs accumulated higher concentrations of Ni and Pb than the below-ground organs. The Ni and Pb standing stocks data indicated that the organs of P. australis extracted higher amounts of Ni and Pb per its area from the southern rather than the northern sites. In the current study, the Ni and Pb above-ground standing stocks increased from the early growing season (February) and reached its peak during August and then decreased. The highest monthly Ni and Pb standing stock (18.2 and 18.4 g m− 2, respectively) was recorded in the above-ground organs of plants in the southern sites in August. The bioaccumulation factor of Ni was 157.6 and 153.4 in the northern and southern sites, respectively, whereas that of Pb was 175.3 and 158.3. The translocation factor of Ni and Pb from the below- to above-ground organs was generally > 1. Thus, this reed species is a potential candidate for Ni and Pb phytoextraction. Based on our results, P. australis could be used for the extraction of Ni and Pb to reduce the pollution in Lake Burullus, if the above-ground biomass is harvested at its maximum value in August, as was the case regarding the maximum standing stock of Ni and Pb.