Mangroves play a crucial role in filtering pollutants from water and sediments. However, excessive accumulation of potentially toxic elements (PTEs) has harmful effects on marine organisms. This article investigates the concentration and distribution of PTEs in water, sediment, and the roots of endangered mangrove species in Chabahar Bay, a subtropical coastal wetland. The relationship between PTE absorption and accumulation rates with flow rate, mangrove extent, and sedimentation was also explored. Water, sediments, and aerial roots samples were taken at four stations along the wetland from upstream fresh water toward outfall. According to the results, Cd had more distribution in sediment and water samples and plants did not play as adsorbent in the study area. The lowest and highest PTEs concentrations were detected in water and sediment media, respectively. The average concentrations of PTEs in the sediments in the Chabahar Bay were Fe > Cr > Zn > Ni > Cu > Pb > Co > As > Cd while in aerial roots of the mangroves were Fe > Zn > Ni > Cr > Cu > Co > As > Pb > Cd. Except Zn, As, and Cd, there was a good correlation between increasing PTEs content in the sediments with decreasing flow velocity and increasing vegetation density along stations 3 to 4. In addition, the amount of PTEs uptake by the mangroves was less than that of global wetlands. The results also demonstrated a greater uptake in aerial roots in saline water for Cr, Ni and Co. Since the absorption rate of PTEs by the aerial roots of pneumatophores is slower than that in sediments, elevated concentrations of PTEs in the sediment can disrupt the entire ecosystem, leading to a potential decline in biodiversity. These toxins can enter the food chain, affecting not only organisms directly interacting with the sediment but also higher trophic levels, such as fish and birds.