16S V4 rDNA amplicon and 18S V4 rDNA amplicon sequencing data from summer 2016, 2017 oceanographic expeditions in the Western North Atlantic, capturing prokaryotic and eukaryotic microplankton community structure. The associated study sought to identify relationships between shifts in community structure and microplankton abundances and changing patterns of net community production, nitrogen fixation, and macronutrient and trace micronutrient concentrations.