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Zooplankton community distribution depends largely on the microhabitat characteristics of the water body. It has been reported that macrophytes provide microhabitats for zooplankton (e.g., space and food resources). To date, studies have focused on the overall influence of macrophytes on zooplankton (e.g., positive relationships with zooplankton diversity); however, the morphological characteristics of macrophytes have not been intensively studied. To fill this gap in knowledge, we investigated zooplankton abundance and diversity, macrophyte characteristics (types, dry weight, and species number), and physicochemical parameters (water temperature, dissolved oxygen, pH, conductivity, and chlorophyll a) by using the 1 × 1 m quadrat method. We surveyed 164 wetlands in South Korea during spring (May to June), prior to the summer monsoon. Patterning zooplankton distribution was accomplished using a Self-organizing map (SOM). We used 34 input variables (zooplankton genera) to train the model. The distribution of five plant habit parameters (no plant, emergent, free-floating, floating-leaved, and submerged) was investigated with a trained SOM plane, by environment data masking. Based on a U-matrix, three clusters were identified from the model. Zooplankton assemblages were positively related to macrophyte characteristics (i.e., dry weight, species number, and plant type). In particular, free-floating plants supported rotifers, such as Testudinella, and cladocerans, such as Alona, Chydorus, Diaphanosoma, and Ilyocryptus (mostly epiphytic). Submerged plants were associated with planktonic rotifers, such as Filinia, Ploesoma, Synchaeta, cladocerans, such as Daphnia, and copepods, such as Eucyclops and Macrocyclops. On the basis of these results, we suggest that the microhabitat structure, created by macrophytes, is an important factor in determining the diversity and abundance of zooplankton communities, because the different species compositions of macrophytes support diverse zooplankton genera in these habitats. The results indicate that macrophytes are the key components of lentic freshwater ecosystem heterogeneity, and the inclusion of diverse plant species in wetland construction or restoration schemes will result in ecologically healthy food webs.