Wastewater Treatment Plant (WWTP) effluents are important sources of antibiotics, antibiotic resistance genes (ARGs) and resistant bacteria that threaten aquatic biota. Antibiotic effects on host-associated microbiomes, spread of ARGs and the consequences for host health are still poorly described. This study investigated changes of the Daphnia magna associated microbiome exposed to the recalcitrant antibiotic doxycycline under artificial reconstituted lab water media (lab water) and treated wastewater media. D. magna individual juveniles were exposed for 10 days to treated wastewater with and without doxycycline, and similarly in lab water. We analysed 16S rRNA gene to assess changes in community structure, and quantified ARGs abundances by qPCR from both Daphnia and water (before and after the exposure) and monitored Daphnia offspring production. Daphnia-associated microbiome in WWTP was significantly different from that in lab water, mostly by differences in the relative abundance of the predominant taxa. Results showed that in lab water, doxycycline impaired Daphnia reproduction and reduced the presence of Limnohabitans sp., which are dominant bacteria of the D. magna-associated microbiome. Contrarily, treated wastewater promoted fecundity and increased diversity and richness of Daphnia-associated microbiome. The detected ARG genes in both lab water and treated wastewater medium included the qnrS1, sul1, and blaTEM,, and the integron-related intI1 gene. The treated wastewater contained about 10 times more ARGs than lab water alone. There was an increase of sul1 in Daphnia cultured in treated wastewater compared to lab water, along with a higher relative abundance of Ideonella, Flavobacterium and Acidovorax, likely candidates of carrying ARGs. In addition, there were signs of a higher biodegradation of doxycycline by microbiomes of treated wastewater in comparison to lab water. Thus, results suggest that Daphnia-associated microbiomes are influenced by their environment, and that bacterial communities present in treated wastewater are better suited to cope with the effects of antibiotics.