Microplastic pollution in aquatic environments is a growing global concern. Microplastics, defined as plastic fragments smaller than 5 mm, accumulate in freshwater reservoirs, especially in urban areas, impacting resident biota. This study examined the effects of microplastics (MP) on the performance and microbiome of Daphnia, a keystone organism in freshwater ecosystems, through both in situ sampling of freshwater ponds and a controlled 23-day in vitro exposure experiment. Using bacterial 16S ribosomal RNA gene amplicon sequencing and whole-genome shotgun sequencing, we analyzed the microbiome's composition and functional capacity in relation to microplastic pollution levels. Urban ponds contained higher microplastic concentrations in water and sediment than natural ponds, with distinct differences in plastic composition. Bacterioplankton communities, defined as bacterial assemblages in the water column, were more diverse and richer than Daphnia-associated microbiomes. Overall, the in situ study showed that the composition of the Daphnia-associated community was influenced by many factors including microplastic levels but also temperature and redox potential. Functional analysis showed increased relative abundances of polyethylene terephthalate degradation enzymes and antibiotic resistance genes in microbiomes from high-microplastic ponds. In the in vitro experiment, the bacterioplankton inoculum source significantly influenced Daphnia survival and microbiome composition. Network analysis identified specific taxa associated with MP within the Daphnia microbiome. Our findings highlight that urbanization leads to higher microplastic and antibiotic resistance gene burdens, influencing host-associated microbiomes through taxonomic shifts, functional enrichment, and survival outcomes, with potential implications for the resilience of aquatic ecosystems.