A field survey was conducted in a freshwater lake system in the Athabasca Basin, northern Saskatchewan, Canada that receives treated metal mining and milling process effluent containing elevated levels of selenium. Whole sediment, pore water, surface water, and chironomid larvae were analyzed in an attempt to link whole sediment selenium speciation to various environmental factors, including selenium availability to benthic macro-invertebrates, a trophic level through which selenium can enter the diet of higher trophic level organisms. Speciation was measured using synchrotron-based selenium K-edge X-ray absorption spectroscopy (XAS). All lake averages of sediment samples (reference or exposure sites) contained a significant proportion (approximately 50%) of elemental selenium which is relatively insoluble in water, immobile, and not considered to be bioavailable. The presence of elemental selenium was confirmed by extended X-ray absorption fine structure (EXAFS) analysis of select samples. Inorganic metal selenides were also found in whole sediment samples and confirmed using micro X-ray fluorescence imaging. Dissolved selenium concentrations in pore water were correlated to the amount of selenite in whole sediments provided that the sites were classified according to whole sediment sand content. Sand content itself is likely inversely correlated to sediment organic matter content, adsorption sites, and redox potential.