Biomagnification of trace elements is increasingly evident in aquatic ecosystems. In this review we investigate the drivers of biomagnification of mercury (Hg), arsenic (As) and selenium (Se) in aquatic food webs. Despite Hg, As and Se biomagnify in food webs, the biomagnification potential of Hg is much higher than that of As and Se. The slope of trophic increase of Hg is consistent between temperate (0.20), tropical (0.22) and Arctic (0.22) ecosystems. Se exerts a mitigating role against Hg toxicity but desired maximum and minimum concentrations are unknown. Environmental (e.g. latitude, temperature and physicochemical characteristics) and ecological factors (e.g. trophic structure composition and food zone) can substantially influence the biomagnification process these metal (oids). Besides the level of bioaccumulated concentration, biomagnification depends on the biology, ecology and physiology of the organisms that play a key role in this process. However, it may be necessary to determine strictly biological, physiological and environmental factors that could modulate the concentrations of As and Se in particular. The information presented here should provide clues for research that include under-researched variables. Finally, we suggest that biomagnification be incorporated into environmental management policies, mainly in risk assessment, monitoring and environmental protection methods.