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The mobility and toxicity of selenium (Se) is a strong function of oxidation state, which in turn is affected by Eh and pH. Elevated levels of Se in fish from Lake Macquarie, NSW are potentially linked to reported high levels of Se in the sediment. Therefore, an understanding of the biogeochemical cycling of Se between the various environmental compartments in the Lake is important in predicting the formation and release of mobile and potentially toxic Se oxyanions to the water column. A computer-based dynamic model, developed in SPEEDUP, is described. The model simulates the biogeochemical cycling of Se in an estuarine ecosystem between the sediment and the water column. Model parameters were obtained from the literature and from data specific to Lake Macquarie. Transport of Se between and accumulation of Se within the various compartments is predicted. Selenium is expected to accumulate in volatile, organic and selenate forms in the water column, and to predominate as selenide in the sediment. The model is designed to allow future expansion into different environmental compartments, including air, biota and plants.