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Oxbow lakes are important components of the floodplain systems of lowland rivers. During flood events, oxbows are connected with the main river channel, and behave as lotic systems, while during inter-flood periods, these lakes can be considered as lentic ecosystems. Rivers are generally poor in planktonic organisms and their sediments contain scarce biological remains in comparison to lentic water ecosystems. However, due to their alternating running and standing water regime, sedimentary biological remains of oxbow lakes can be used as proxies for tracking changes of past hydrological regimes. In this study we investigated how cladoceran communities respond to flood events, and whether flood events can be recognized by community analysis of cladoceran remains. A sediment core from Marótzugi-Holt-Tisza oxbow lake was analyzed for identification of past flood events based on changes in the subfossil Cladocera community. Floods were defined based on the proportion of fine sand (50 µm grain size) in the oxbow sediments. If the fine sand portion was <3%, the water regime of the oxbow was considered as lentic, otherwise it was lotic. Both organic and pigment contents were significantly higher in the core sections deposited during lentic stages. Thirty-four Cladocera species were determined in this core, all common to littoral habitats of eutrophic shallow lakes in Hungary. One planktonic (Bosmina longirostris) and four chydorid species (Alona rectangula, Acroperus harpae, Alonella nana and Chydorus sphaericus) were dominant throughout the core and contributed >90% of total remains. Discriminant analysis on cladoceran data confirmed that lotic and lentic hydrological stages were characterized by different Cladocera species associations. Bosmina longirostris, Chydorus sphaericus, Alona rectangula, Acroperus harpae, Leydigia leydigi, A. quadrangularis and A. nana were mainly responsible for the differences between lotic and lentic species assemblages. Our results revealed that Cladocera remains can be used to track changes in the hydrological regime of oxbow lakes.