Marine microeukaryotes can be characterized metabolically and taxonomically through transcripts and proteins, but it is unclear to what extent these biochemical pools are concordant in natural communities. Using an autonomous underwater vehicle, the microbial communities were vertically sampled along the western North Atlantic Ocean. Taxonomy and function were examined using a paired metatranscriptomic and metaproteomic approach. Only protein pools demonstrated strong shifts in vertical structure at the supergroup level, with foraminifera, radiolaria, picozoa, and discoba enriched below 200m, and fungi enriched in seawater collected from below 3,000m. Relatively few haptophyte transcripts were observed in surface waters, yet they were a substantial fraction of the eukaryotic protein pool. We furthermore observed a difference in taxonomic annotations, with on average 38% of eukaryotic proteins unable to be confidently annotated below the supergroup level compared to 21% of transcripts. These proteins were functionally enriched in cytoskeletal components and may represent abundant, evolutionarily conserved proteins. Possible explanations for discrepancies between biochemical pools include lineage-specific loss of protein or RNA during lab processing, differences in RNA/protein composition and ratios among taxonomic groups, growth rate effects, and/or cell lysis during in situ filtration. These findings underscore the utility of paired omics for comprehensively reconstructing microbial community dynamics.