Burullus lagoon is the second largest lake in Egypt. However, there has never been a comprehensive survey which studied nineteen potentially toxic elements in sediments and plants and evaluated the associated potential risk. Thus, we aimed to study the total and potentially available content of As, Al, Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Sb, Se, Sn, Tl, V, and Zn in the sediments and common reed (Phragmites australis) at thirty two sites along the entire lagoon and connected drains. Contamination Factor (CF), Pollution Load Index (PLI), Geo-accumulation Index (I_geo), and Enrichment Factor (EF) were calculated to assess the grade of contamination. Element accumulation factor (AF) and bio-concentration ratio (BCR) were also calculated. Aluminum showed the highest median (mg kg⁻¹) total content (41,200), followed by Fe (30,300), Mn (704.7), V (82.0), Zn (75.5), Cr (51.2), Cu (47.8), Ni (44.3), As (31.9), Tl (24.6), Co (21.4), Se (20.3), Sb (17.6), Sn (15.6), Mo (11.3), and Hg (16.6 μg kg⁻¹). Values of the EF, CF, and I_geo showed that the sediments were heavily contaminated with As, Sb, Se, Tl, Mo, Sn, Co, Ni, and Cu. The drained sediment had significantly higher values of total and potentially available element content than the lagoon sediments. Sediments of the middle and western area showed significantly higher contents of total and available elements than the eastern section. The BCR and AF values indicate that the studied plant is efficient in taking up high amounts of Zn, Fe, As, Sn, Tl, Ni, Mo, Mn; then Co, Cu, and V. The results exhibit a dramatic contamination at certain sites of the lagoon, and the studied PTEs have a predominant role in contamination-related ecological risk. Further investigations concerning redox-induced mobilization of PTEs in sediments, the risk of fish contamination and the potential health hazards are highly recommended.