This study comprises Illumina and PacBio HiFi read metagenomes and 16S rRNA gene amplicons generated from surface seawater samples of the 0.2 - 3 µm fraction that were collected around Herschel Island, Canada, in July-August 2019 and July 2022. Surface seawater samples were collected and sequentially filtered through a 10, 3 and 0.2 µm pore-size polycarbonate membrane filter. In 2019, 500 ml of seawater was filtered through the 0.2 - 3 µm fraction, and in 2022, 200 ml was filtered. DNA was extracted using Qiagen PowerSoil Pro Kit (2019) and ZymoBIOMICS DNA/RNA Miniprep kit (2022). 16S rRNA gene amplicons: DNA extracts were PCR amplified using the primers 341-F (CCTACGGGNGGCWGCAG) and 805-R (GACTACHVGGGTATCTAATCC) that target the V3-V4 region of the 16S rRNA gene. Following purification, PCR products from each sampling year were pooled (one library per year) and sequenced on an Illumina HiSeq2500 (2019 pool) and Illumina HiSeq3000 (2022 pool). Illumina metagenomes: Library preparation was performed according to Ultra Low Input Library Protocol. Four samples from 2019 were sequenced on an Illumina HiSeq3000 (2019) and four samples from 2022 were sequenced on an Illumina NextSeq2000 - both in 2 x 150 bp paired-end mode. PacBio metagenomes: One sample from each sample year was selected for PacBio Sequel II sequencing. Libraries were prepared according to the Ultra Low Input Library Protocol of PacBio, and the two samples were multiplexed and sequenced on a single SMRT 8M cell.