Seawater samples were collected and amended with a variety of nutrient treatments. Incubations were then stored on deck at in situ light and temperature conditions with samples collected at 0 hours and 96 hours to examine the effects of nutrient amendment on open-ocean protist communities. This BioProject contains RNA-seq data from whole community libraries depleted for rRNA, in which prokaryotic sequences dominate. Libraries selected for polyadenylated mRNA (enriched for eukaryotic transcripts) were sequenced for the same samples and can be found under BioProject PRJNA690575.