AbstractLocalized hypoxia can reduce available habitat, restrict movement and limit the abundance of aquatic invertebrates. Although cultural eutrophication, coupled with the effects of climate change, is likely to increase the frequency and extent of hypoxia in aquatic ecosystems, little is known about how oxygen gradients in small reservoirs influence spatial distribution and abundance of aquatic invertebrates. The present study evaluated the effects of environmental and biological attributes on seasonal and spatial variation of macroinvertebrates and explored how hypoxic conditions influenced littoral, benthic and pelagic macroinvertebrate communities in Lake Alvin, South Dakota. Data on reservoir conditions, in conjunction with macroinvertebrate sampling from May to October 2009–2011, were applied in an information theoretic approach to evaluate factors affecting invertebrate abundance. Hypoxic conditions were present from May to September in the lacustrine zone impacting 10%–39% of the water column. Benthic invertebrates were typically absent from the lacustrine zone during periods of severe hypoxia and were most abundant in the shallow, well‐oxygenated riverine zone. Littoral invertebrates were negatively related to the per cent of the hypoxic water column, suggesting fish, confined to shallow waters by hypoxia, may be consuming a larger portion of littoral invertebrates in their diets. Cladocera and Copepoda densities were influenced primarily by water depth and monthly precipitation. The larger size of Daphnia found in the hypoxic‐prone transitional and lacustrine zones suggested low oxygen concentrations may provide a refuge from fish predation. The results of the present study demonstrated spatial variations in near‐bottom oxygen concentrations were important predictors of macroinvertebrate and zooplankton abundance and size structure in Lake Alvin and that macroinvertebrates, particularly benthic and littoral invertebrates, could benefit from measures taken to reduce summer hypoxia.