Mercury is a priority pollutant because of its extreme toxicity, global atmospheric transport and accumulation in the food chain. Its removal from current industrial emissions as well as from previously polluted sites is therefore mandatory and should take into account the latest achievements in science and technology. A unique biotechnological process for removal of mercury from wastewater based on the enzymatic transformation reactions of live mercury resistant bacteria has been developed and operated at a Czech chloral kali electrolysis factory. This new technology is environmentally friendly and cost effective and has a much broader potential than that realized to date, which, however, needs to be assessed carefully for each new application. In the case of microbes, barriers of understanding and acceptance also must be overcome in order to promote their application. Microbiological technologies have to be integrated into a complete process remediation scheme including physical and chemical technologies, pre-treatment steps and waste disposal strategies.