Metagenomic sequencing of surface seawater samples collected during the spring phytoplankton bloom at Helgoland in the year 2020. Plankton samples were collected via sequential filtration on filters with three pore sizes, producing three size fractions. These correspond to the fraction greater than 10 µm in size, the fraction 3-10 µm in size, and the fraction 0.2-3 µm in size. Sequencing was done on the PacBio Sequel II (1 SMRT cell per sample) and Illumina HiSeq 2500 platform (2x 250 base pair chemistry).