Lake Michigan drowned river-mouth wetlands have a unique geomorphology and hydrology. Macroinvertebrate communities in these systems respond to multiple biotic and abiotic factors that are not well understood. In June and August 2003, we sampled macroinvertebrate communities at 22 sites in four Lake Michigan drowned river-mouth wetlands. Sites were distributed along gradients of anthropogenic disturbance, vegetation, and sediment types. The relative influences of anthropogenic disturbance, vegetation, and sediment type on macroinvertebrate community composition were determined using non-metric multidimensional scaling (NMDS) and multi-response permutation procedures (MRPP). The depth of organic deposits best explained the gradients revealed with NMDS and MRPP for both sampling dates. The MRPP did not detect differences in community composition among vegetation types and wetlands with different levels of anthropogenic disturbance. These results suggest that 1) macroinvertebrate community structure in Great Lakes drowned river-mouth habitats is influenced substantially by sediment characteristics, and 2) anthropogenic practices that affect the deposition of organic sediment in coastal wetlands (e.g., eutrophication and hydrologic manipulation) will likely affect macroinvertebrate community structure.