Elemental selenium (Se) is generally considered to be biologically inert due to its insolubility in water. It is a common form of Se in sediment near uranium mining and milling operations in northern Saskatchewan, Canada. Nanosized particles of many materials exhibit different properties compared with their bulk phases, in some cases posing health and ecological risks. Here we investigated the bioavailability and toxicity of Se nanoparticles (SeNPs) using 10-day waterborne and dietary exposures to larvae of Chironomus dilutus, a common benthic invertebrate. For comparison, larvae were also exposed to waterborne dissolved selenite and to dietary selenomethionine as selenized algae. Larval Se accumulation was evaluated using graphite furnace atomic absorption spectroscopy or inductively coupled plasma mass spectroscopy for total Se and X-ray absorption spectroscopy for Se chemical speciation. Exposure to nanoparticulate Se resulted in Se bioaccumulation, at high concentrations, inhibiting larval growth in both waterborne and dietary exposures; larvae predominantly accumulated selenomethionine-like species regardless of uptake route or form of Se tested. Despite the observed Se accumulation, our findings suggest there is little risk of direct SeNP toxicity to benthic invertebrates in Se-contaminated sediments in northern Saskatchewan. Nevertheless, elemental Se in sediments may be biologically available and may contribute directly or indirectly to the risk of Se toxicity to egg-laying vertebrates (fish and piscivorous birds) in Se-contaminated aquatic systems. It thus may be necessary to include elemental Se as a source of potential Se exposure in ecological risk assessments.