The fate of selenium (Se) inputs from coal-fired power station operations in a marine dominated estuary, Lake Macquarie NSW, is explored, as well as Se toxicity, including sublethal and population effects. Selenium is rapidly adsorbed to sediments, and food webs are based on benthic food sources. Selenium is remobilised from sediments by volatilisation and diffusional processes following bioturbation. It is then transferred into food chains via benthic microalgae, deposit feeders and filter-feeding organisms processing suspended sediments. Historically, Se has been found to accumulate in fish to levels above those considered safe for human consumption. After the remediation of a major ash dam in 1995, Se inputs to Lake Macquarie have declined, and the Se concentrations of sediments have also reduced partially due to the deposition of cleaner sediment but also due to the formation of volatile dimethyl selenide. Bioturbation of oxidised surface sediments also results in the release of inorganic Se. In response to decreases in sediment Se concentrations, molluscs and fish Se concentrations have also reduced below deleterious levels, with most fish now being safe for human consumption. Selenium cycling involves the transformation of inorganic species (Se0, SeII, SeIV, SeVI) in sediments and the water column to dimethylselenide and dimethyl diselenide by bacteria with the accumulation of organic Se species in plant detritus (selenomethionine) and animals (selenomethionine and selenocysteine). Dissolved Se concentrations in Lake Macquarie, except near ash dam inputs, have always been well below those that cause toxicity. There is evidence based on Se sediment-spiking studies, however, that Se is probably causing sublethal effects. When undertaking risk assessments of Se, careful consideration should be given to understanding the fate of Se inputs and remobilisation into food webs as not all systems act in accordance with published studies that generally have high Se concentrations in the water column and phytoplankton-based food webs.