The project, called LevandeVikar, is a joint initiative of the CostClim group, comprised of Stockholm University and the University of Helsinki. Its aim is to investigate microbial communities in shallow bays in the Stockholm area, specifically methane-producing communities, including both archaea involved in methane production and methane-oxidizing bacteria. Coastal sediments contribute significantly to methane emissions in the Baltic Sea; however, the dynamics and role of these shallow bays and their microbial communities in this context are poorly understood. The main objective is to determine the types of microbial communities inhabiting six different bays and their methane, carbon, and nitrogen metabolic pathways. To this end, sediment samples were taken from the six bays at two different depths: 0–1 cm and 20–22 cm. Subsequently, 39 DNA samples were extracted and sequenced in triplicate to obtain metagenomic data.