Muskrat (Ondatra zibethicus) herbivory and lodge construction create open water areas in stands of emergent vegetation. This study examined how aquatic invertebrates are affected by changes in the physical structure of plant stands created by muskrats. We compared density, species composition and functional feeding groups of benthic macroinvertebrate communities and abiotic conditions in open water areas at muskrat lodges and in adjacent cattail stands. Although total numbers of macroinvertebrates were not affected by muskrat activities, communities at muskrat lodges were less diverse than in cattail stands. Gathering collectors such as chironomid midges that feed on fine particulate organic matter were the dominant trophic group; these were significantly more abundant at muskrat lodges than in cattail stands. Scrapers, such as gammarid scuds that feed on periphyton, were also abundant; these were significantly more abundant in cattail stands than at muskrat lodges. Water temperature, dissolved oxygen, pH, conductivity and sediment organic content were different in these habitats. These results indicate that muskrats alter abiotic conditions and invertebrate communities in wetlands, which will affect food resources for wildlife and fish that feed on aquatic invertebrates in these habitats.