In order to evaluate the role of macrophytes as refuge of zooplankton on physical distribution (i.e. summer rainfall), we investigated the environmental factors, macrophytes, and zooplankton in waterside zones (macrophytes zones) and open water zones of 17 wetlands from May and August, 2011. In this study, a total of 51 zooplankton species were identified, and Polyarthra sp. and Diaphanosoma brachyurum were found to be the most dominant species. Waterside area of each wetland were occupied by a total of 10 macrophyte species, species composition and biomass (dry weight) were different in the survey sites. Zooplankton was more abundant in waterside zone than open water zones lacking macrophytes (One-way ANOVA, df=2, F=27.1, P<0.05), in particular, waterside zone of 1, 8, 9, 10, and 11 wetland were supported by high zooplankton density after summer rainfall. This wetlands were developed by various macrophyte species than other wetland, and submerged plant commonly presented. Waterside zones with various macrophyte species provides complexity to the habitat structure, should be utilized as refuge to avoid disturbance such as summer rainfall. The results indicate that macrophytes are the key components to enhance bio-diversity include zooplankton, and the inclusion of diverse plant species in wetland construction or restoration schemes will result in ecologically healthy food webs.