As a consequence of coal-fired power station operations, elevated selenium concentrations have been reported in the sediments and biota of Lake Macquarie (NSW, Australia). In the present study, we applied an ecosystem-scale model to determine how selenium in a seagrass food web is processed from sediments and water through diet to predators, using stable isotopes (δ13C and δ 15N) to establish the trophic position of organisms. Trophic position, habitat and feeding zone were examined as possible factors influencing selenium bioaccumulation. Selenium concentrations ranged from 0.2 µg/g dry weight in macroalgae species to 12.9 µg/g in the carnivorous fish Gerres subfasciatus. A mean magnification factor of 1.39 per trophic level showed that selenium is biomagnifying in the seagrass food web. Habitat and feeding zone influenced selenium concentrations in invertebrates, while only feeding zone was the significant factor influencing selenium concentrations in fish. The sediment: water partitioning coefficient (Kd) of 4180 showed that partitioning of selenium entering the lake to particulate organic material (POM) is occurring and consequently availability to food webs from POM is high. Trophic transfer factors (invertebrate = 1.9, fish = 1.2) were similar to those reported for other water bodies, showing that input source is not the main determinant of the magnitude of selenium bioaccumulation in a food web, but rather the initial partitioning of selenium into bioavailable POM. This article is protected by copyright. All rights reserved