In the framework of the SpongePOP project, sediment and water samples were collected during two sampling campaigns, namely SpongePop 1.0 (SP1 17 May-1 June 2014) and SpongePop 2.0 (SP2 15-31 July 2014), from eleven stations covering different sites along the Pasvik River and the adjacent fjords. Microbial communities promptly respond to environmental perturbations, and their response can be researched in alterations in their diversity. In this was used 16S rRNA gene amplicon sequencing to describe the bacterial community composition in water and sediment through the sub-Arctic Pasvik River and part of the Varangerfjord.