Mercury (Hg) is one of the most hazardous contaminants that may be present in the aquatic environment. Inorganic Hg discharged to lakes and watercourses by industrial enterprises may be converted to organic methylmercury (MeHg), a highly toxic compound that is readily accumulated by aquatic biota. Despite a vast body of literature on the subject, many of the Hg transformation and distribution processes operating in the natural aquatic environment are still poorly understood. The current work includes a detailed investigation of the mutually interacting factors that influence the conversion of inorganic Hg to MeHg, and identifies areas where further research is needed. Two case studies of industrial Hg pollution were carried out to investigate the impacts of these industries on the surrounding environment, and in particular on aquatic ecosystems. The first study at a derelict chlor-alkali plant in northern Kazakhstan found that a nearly lake was severely impacted by Hg from past wastewater inputs, resulting in a serious build-up of Hg in the aquatic food chain. Potential risks to the local population were evaluated and remediation options for the lake were considered in the light of experiences made at other sites. The second case study investigated the transport, fate and bioavailability of Hg in the Nura, an industrially contaminated river in central Kazakhstan. In this study, a significant inverse relationship was found between total Hg concentrations and the percentage of MeHg formed in sediments. This appears to indicate that at high Hg levels in severely contaminated sediments, the accumulation of MeHg may be limited by increasingly efficient demethylation processes, which may be the underlying reason why MeHg levels in surface water are often found to be higher at less contaminated downstream sites compared to upstream sites. It could also be one reason why Hg concentrations in fish on this river did not decrease significantly for a considerable distance downstream from the source of the pollution.