Lakeshore areas provide important habitat for aquatic invertebrates in shallow lakes. However, these zones are prone to anthropogenic disturbances that include shoreline development, urbanization, nutrient inputs, agricultural and(or) recreational use. Among recreational uses, public access sites are often developed to accommodate boaters and facilitate lake access via boat ramps. Although the ‘foot print’ associated with boat ramp structures can be relatively small compared to total shoreline coverage, little is known about the relative effects of boating activity on littoral zones and macroinvertebrate communities. In this study, we assess the relative impact of boating-related activities on aquatic macroinvertebrate communities at high-use (primary) and low-use (secondary) boat ramps on five glacial lakes of eastern South Dakota. Macroinvertebrate assemblages were dominated by few taxa that included Chironomidae, Corixidae, Caenidae, and Amphipoda. Moreover, boat ramp use did not influence abundance or diversity of aquatic macroinvertebrates. Habitat, specifically substrate composition, was also similar between primary and secondary boat ramps despite more intense use associated with primary boat ramps. Our results support related findings that aquatic invertebrate assemblages in the Prairie Pothole Region are structured by regional environmental variability (climate, habitat, and water quality) resulting in communities with characteristically low diversity and tolerant taxa. This may explain why small-scale disturbance associated with boating activity has no discernable effect on macroinvertebrate assemblages in glacial lakes of the Prairie Pothole Region.