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The acquisition of Antibiotic-Resistance Genes (ARGs) by natural bacteria caused by antibiotic abuse is causing serious problems for human and animal welfare. Here, we evaluated the influence of three cladoceran species on Antibiotic-Resistant Bacteria (ARB) and tetracycline-resistance gene (<i>tet</i>(A)) copies, and discussed the effect of these biological interactions on the distribution and diffusion of ARGs in freshwater ecosystems. Bacterial community and <i>tet</i>(A) abundances in water samples collected from wetlands were strongly influenced by cladoceran presence. The presence of <i>Daphnia obtusa</i> dramatically decreased ARB and <i>tet</i>(A) abundance compared to that with other cladoceran species (<i>Chydorus sphaericus</i> and <i>Simocephalus vetulus</i>). Interestingly, we found a high abundance of Flavobacteriales in the microbiomes of cladoceran species. Considering that Flavobacteriales species are potential carriers of the <i>tet</i>(A) gene, their adsorption and assimilation with cladocerans could significantly impact the reduction of <i>tet</i>(A) in water. Field surveys also showed that <i>tet</i>(A) abundance could be low if the dominance of <i>D. obtusa</i> in each wetland was high. This study highlighted the need for ecological interactions and a broad range of niches in the food web when discussing the fate of ARGs in freshwater ecosystems.