Biological and environmental attributes including dispersal ability, habitat requirements, life history, geography, and hydrology have strong effects on population structure. Specifically, landscape factors and their influences on dispersal ability can determine rates of gene flow, genetic drift, and other population-level processes. Interdunal wetlands are small, highly fragmented habitats that exist patchily along the harsh and windy coastline of Lake Michigan. Additionally, they vary in hydroperiod and harbor unique insect communities. We investigated how dispersal ability determines population structure in three aquatic macroinvertebrates (Anax junius, Notonecta undulata, and Caenis amica) from Lake Michigan’s interdunal wetlands. Over 200 insects were collected from 40 wetlands ranging from Northern to Southern Lake Michigan. We hypothesized that all invertebrate populations experience strong isolation by distance with relatively low levels of gene flow among sites, but that the magnitude of isolation will vary with dispersal ability. Our preliminary CO1 sequence data from N. undulata revealed limited latitudinal structure but largely homogenous population structure; however, we expect genomic level data from RADseq techniques may uncover stronger population structure. Understanding the population structures of critical aquatic macroinvertebrates can provide valuable information to resource managers to inform best practices for conservation and preservation of interdunal wetlands.