Gelatinous zooplankton (GZ), here understood as pelagic cnidarians and ctenophores, are an important component of marine ecosystems. Their diversity and distribution reflect local hydrological settings especially well, thus allowing the development of biotic indices for studying climate-mediated changes in the world’s oceans. The effects of global warming are most pronounced in the Arctic Ocean and have been further accelerated by the strengthening inflow of relatively warm Atlantic waters (AtW) via the Fram Strait, referred to as Atlantification. Here, we use the GZ distribution to describe the current state of Atlantic water inflow into the Arctic Ocean and to discuss the future of this fragile ecosystem. For this purpose, we characterized the abundance, diversity, and demography of the GZ identified from vertically stratified samples (down to 1000 m) collected in the Fram Strait along two latitudinally parallel transects of varying influence of AtW. Overall, we identified 17 taxa, with Aglantha digitale, Dimophyes arctica and Mertensia ovum being the most abundant. We then contrasted our jellyfish and ctenophore data with both biotic and environmental ecosystem characteristics and analysed the associations between the GZ community and water mass distribution. We showed that the more abundant GZ community was found along the southern transect; that the sampling depth and bathymetric zone played the most important roles in structuring the GZ diversity; that water mass distribution affected GZ demography; and that AtW was dominated by A. digitale, that constituted 66% of the total GZ abundance. Our results, although temporarily limited, suggest that the Atlantification will promote the expansion of boreal species into the Arctic, and could lead to a less diverse, but more abundant GZ community in the future. In addition, we compare in detail the GZ community found in different water masses, at different depths, and in different bathymetric zones, and supported with literature data, discuss the future of the European Arctic under the scenario of increasing inflow of Atlantic water.