The accumulation of potentially toxic elements (PTEs) in aquatic ecosystems has become a global concern, as PTEs may exert a wide range of toxicological impacts on aquatic organisms. Submerged plants and the microorganisms attached to their surfaces, however, have displayed great potential as a means of coping with such pollution. Therefore, it is crucial to understand the transport pathways of PTEs across sediment and organisms as well as their accumulation mechanisms in the presence of submerged plants and their biofilms. The majority of previous studies have demonstrated that submerged plants and their biofilms are indicators of PTE pollution in the aquatic environment, yet relatively little is known about PTE accumulation in epiphytic biofilms. In this review, we describe the transport pathways of PTEs in the aquatic environment in order to offer remarkable insights into bioaccumulation mechanisms in submerged plants and their biofilms. Based on the literature cited in this review, the roles of epiphytic biofilms in bioaccumulation and as an indicator of ecosystem health are discussed. •PTEs transport through different media in aquatic environments.•Bioaccumulation mechanisms of PTEs were studied for submerged plants and biofilms.•Submerged plants and biofilms served as indicators of PTE pollution.•Potential bioaccumulating and bioindicating roles of epiphytic biofilm is addressed.