Aquatic macrophytes determine the physical structure of many microhabitats in water and strongly influence the distribution of various aquatic animals. In this study, we analyzed the main microhabitat characteristics that affected the spatial distribution of invertebrates in shallow wetlands of South Korea (Jangcheok Reservoir). Environmental variables, macrophyte biomass, and invertebrate groups were used to analyze invertebrate distribution using a self-organizing map (SOM). Thirteen invertebrate groups were mapped onto the SOM, and each group was compared with the distribution of environmental variables and macrophyte biomass. Based on a U-matrix, five clusters were categorized according to Euclidean distance on the SOM. Invertebrate groups were closely related to macrophyte biomass. In particular, Lymnaeidae, Physidae, Viviparidae, Ecnomidae, and Hydrophilidae were abundant in quadrats with a high cover of Paspalum distichum and Nelumbo nucifera. Bithyniidae and Coenagrionidae were strongly associated with Trapa japonica and Hydrocharis dubia, whereas Planorbidae, Corduliidae, and Hydrophilidae were abundant with a high cover of Typha orientalis. Similar habitat preferences were found in a survey of gastropod distribution on the surface of each macrophyte species. The results clearly indicated that invertebrate distribution clusters were related to the spatial distribution of aquatic macrophytes in a shallow wetland.