Among potential toxic elements (PTEs), arsenic (As) and mercury (Hg) are well known for the toxicity of their different chemical species and diffusion in the environment via several anthropic sources (i.e., industrial settlements, mining activity). Bottom sediments often become a repository for As and Hg, although they may be considered a potential secondary source of these elements into the water column depending on their speciation and mobility. Focusing on the most recent studies (since 2019) on the occurrence of As and Hg in contaminated aquatic sediments, the aim of this review is to give an overview of the current understandings on the complex biogeochemical cycle of these elements in this environmental media. The main biogeochemical factors governing the transformations of As and Hg among their different chemical species were synthesized, highlighting those driving the formation of more mobile and/or bioavailable forms. Additionally, the most advanced analytical techniques for the determination of the different chemical species of As and Hg in sediments are briefly presented. Display omitted •Sediments are sink or secondary source of arsenic (As) and mercury (Hg).•Mobility of As and Hg is strongly related to their speciation in sediments.•Various techniques are available for As and Hg speciation assessment.•Redox conditions, sulphur, and iron strongly affect As and Hg cycles.•Resuspension is a critical redistribution pathway for As and Hg in the water column.