Selenium (Se) is a contaminant of concern in Canada mainly due to its teratogenic effects on fish and birds. However, few studies have assessed the effects of Se on invertebrates in a field setting. The objective of this experiment was to assess potential community‐level impacts of Se additions on zooplankton and benthic macroinvertebrates in a boreal lake ecosystem. From June to August 2018, Se (as selenite) was added to six limnocorrals in Lake 239 at the International Institute for Sustainable Development–Experimental Lakes Area, Northwestern Ontario, Canada, to achieve mean measured aqueous concentrations of 0.4, 0.8, 1.6, 3.4, 5.6 and 7.9 µg Se/L, with three untreated limnocorrals serving as controls (background Se = 0.08–0.09 µg/L). Periphyton, phytoplankton, and invertebrates (zooplankton and benthos) were monitored for 63 days. Zooplankton community composition shifted as a function of Se exposure, with Cladocera biomass and density decreasing with increasing Se concentrations. Similarly, cumulative abundance and biomass of Heptageniidae decreased with increasing Se treatment throughout the experimental period. The present study demonstrated that Se can have impacts on aquatic invertebrates at environmentally relevant exposure levels, and that future ecological risk assessments should consider the impacts of Se on both vertebrates and invertebrates. Environ Toxicol Chem 2022;41:95–107. © 2021 SETAC