The active layer of permafrost in Ny Ålesund, Svalbard (79°N), is increasing in thickness at a rate of ~one vertical centimeter per year in most locations around the Bayelva River in the Leirhaugen glacier moraine. Microbes in the active layers may drive organic carbon degradation and greenhouse gas production, creating a positive feedback on climate change. However, the microbial metabolisms relating to the environmental geochemistry and population dynamics have not been well characterized. We tested if organismal abundance was related to site or stratigraphy by analyzing metagenome assembled genomes (MAGs) from 56 highly resolved intervals of five active layer permafrost sites. Two sites were collected in the winter time (April 2018) and three were collected in the summer (September 2019). The MAGs’ read recruitment to metagenome libraries showed an Actinobacteria population that was dominant when the soils were thawed (September 2019) and when the surface soil were covered in snow (April 2018). Inversely, another group of Actinobacteria dominated the deeper depths while the soils were frozen and were nearly absent during the thawed/summer season. We show that microbial populations in the Svalbard active layer shift by depth and season, maintaining populations of continuously metabolically active microbes at all depths, year-round.