A total number of 277 water samples were collected during distinct oceanographic cruises or at fixed stations across coastal systems of France and Senegal. The seawater samples were progressively filtered onto size-fractionated filters (representing micro, nano and pico-plankton). Metabarcoding of the V4 domain of the Eukaryotic 18S rDNA region was carried out to characterize the genetic diversity of the sampled communities. Genomic DNA was extracted following the DNA extraction kit Nucleospin Plant II (Macherey-Nagel) and the V4 markers were amplified with a taq polymerase (Phusion High-Fidelity PCR Master Mix with GC Buffer). Sequencing was performed by the Genotoul sequencing platform (get.genotoul.fr) with the Illumina MISeq method (2x250 bp). The present dataset gathers the different results issued from sequencing. This dataset was submitted to sequence cleaning, filtering, taxonomic assignment and OTU clustering, which resulted in a final dataset also presented.