Microbiome analysis of seawater samples collected at stations along Svalbard Cross Shelf transects (Kongsfjorden and Rijpfjorden), at different depths, based on V4-V5 16S rRNA gene amplicon sequencing, using Illumina. Samples were collected during the Norwegian Polar Institute MOSJ-ICE 2017 plankton-monitoring program. Samples were concentrated on board through Sterivex 0.2 mm filtration and preserved at -80ºC for later DNA extraction. This dataset is part of a standardized effort for a long-term analysis of microbiome data collected at the same geographic locations and with the same methodologies, during different years. Other datasets already publicly available integrated in this long-term effort include MOSJ2016 (MGYS00003725), MOSJ2018, MOSJ2019 and MOSJ2020.