Marine microbial eukaryotes play crucial roles in water-column ecosystems; however, there are regional gaps in the investigation of natural microbial eukaryote communities, and uncertainties concerning their distribution persevere. This study combined 18S rRNA metabarcoding, biomass measurements and statistical analyses of multiple environmental variables to examine the distribution of planktonic microbial eukaryotes at different sites and water layers in the ultra-oligotrophic Eastern Mediterranean Sea (Western Levantine Basin). Our results showed that microbial eukaryotic communities were structured by depth. In surface waters, different sites shared high percentages of molecular operational taxonomic units (MOTUs), but this was not the case for deep-sea communities (≥1000 m). Plankton biomass was significantly different among sites, implying that communities of a similar composition may not support the same activity or population size. The deep-sea communities showed high percentages of unassigned MOTUs, highlighting the sparsity of the existing information on deep-sea plankton eukaryotes. Water temperature and dissolved organic matter significantly affected community distribution. Micro-eukaryotic distribution was additionally affected by the nitrogen to phosphorus ratio and viral abundance, while nano- and pico-communities were affected by zooplankton. The present study explores microbial plankton eukaryotes in their natural oligotrophic environment and highlights that, even within restricted oceanic areas, marine plankton may follow distribution patterns that are largely controlled by environmental variables.