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Floodplain wetlands in semi-arid regions have intricate channel-floodplain networks with highly variable and unpredictable wet and dry phases related to changes in hydrology and geomorphology. We tested the hypothesis that the presence of different hydro-geomorphic habitats in those systems drives structural and functional differences in aquatic communities. To test this hypothesis, we examined the densities and species composition (structural variables), and primary productivity and respiration (functional variables) of plankton communities, and water chemistry in three spatially explicit channel, floodout and lagoon habitat types inundated by environmental water releases in the Macquarie Marshes, semi-arid Australia. Significant differences were recorded among the community-level structural and functional variables among the three habitats. Greater densities of phytoplankton, zooplankton and planktonic bacteria were observed in a hydrologically isolated floodplain lagoon. The lagoon habitat also had greater primary productivity of phytoplankton and planktonic respiration compared with the channel and floodout. Our results suggest that water release to meet environmental flow requirements can be an important driver of planktonic diversity and functional responses in semi-arid wetland systems by inundating diverse, hydro-geomorphically distinct habitats.