Mesoscale eddies strongly influence marine microbiomes, but their effects on microbiome association and stability remain unclear. We conducted 16-day shipboard microcosm experiments using surface water, DCM water, and 1:1 mixed seawater from eddy-influenced and non-eddy-influenced sites in the Kuroshio Extension. We hypothesized that eddy enhanced nutrients and light would alleviate resource competition, promoting diversity and deterministic assembly by shifting taxa from stress tolerant to growth adapted strategies. Prokaryotes and microeukaryotes responded divergently. Eddy associated conditions increased prokaryotic richness and evenness but reduced microeukaryotic richness. Microeukaryotes showed narrower niche breadth in surface and mixed treatments and stronger heterogeneous selection, especially in the DCM. Assembly was strongly depth dependent. Surface communities were restructured more than DCM communities. In surface and mixed layers, prokaryotes showed increased dispersal limitation and decreased homogeneous selection under eddy associated conditions, whereas the DCM showed the opposite. Microeukaryotes generally exhibited opposite depth dependent patterns. Co occurrence networks were more complex and robust under eddy associated conditions, mainly driven by prokaryotes. DCM networks had higher robustness and lower vulnerability. Weakened correlations between prokaryotic composition and environmental variables suggest a shift from top down environmental filtering to bottom up biotic control. These results reveal distinct adaptive strategies of prokaryotic and eukaryotic microbiomes and highlight the role of eddies in sustaining microbial resilience and ecosystem functioning in the open ocean.