A characteristic feature of the Arctic landscape is the presence of a large number of shallow lakes and ponds, which contain flourishing benthic microbial mats. Microbial mats predominate the biomass, nutrient cycling and productivity of freshwater polar ecosystems. This is the first description of the prokaryotic and unicellular eukaryotic community diversity from benthic under-ice microbial mats from a perennially ice-covered High-Arctic lake, Ward Hunt Island, Canada. Given the different environmental conditions in the benthic under-ice and the littoral zones, we wanted to verify how different the microbial communities would be in those two regions of the lake. Microbial mats were sampled from two depths in the benthic zone and from one littoral site to also assess any depth diffference in the microbial community. The under-ice sites have lower light availability and are more stable environments than the littoral sites. Consequently, we hypothesized that the microbial communities from the two zones would be taxonomically distinct and to test this hypothesis, we sequenced the 16S and 18S ribosomal rRNA and rRNA genes from triplicate microbial mat samples from these sites. Sequencing was performed via MiSeq Illumina technology. High Arctic aquatic ecosystems are facing unprecedented changes as a result of ongoing global warming. Projected scenarios include changes in snow cover that is a central feature of northern landscapes, but with unknown implications in terms of ecosystem connectivity and functioning. In this study, we characterized the diversity and composition of microbial communities (Bacteria, Archaea and Eukaryota) in distinct interconnected habitats that are part of the same watershed. The different habitats (snow, watertrack, lake, stream, inshore ocean) were sampled along a hydrologic continuum at Ward Hunt Island (latitude 83° North) in the Canadian High Arctic. We investigated the microbial connectivity along a longitudinal gradient within Ward Hunt lake watershed on two distinct levels : on the community and population levels. To achieve this, we explored the diversity and composition of potentially active microbial communities using Illumina sequencing of the 16S (Bacteria and Archaea) and 18S (Eukarya) rRNA along the water continuum from snowbanks to inshore ocean. Specifically, we tested the following hypotheses: First, snow hosts a diverse microbiota and secondly, snow is a source of microbial diversity for downstream communities, connected via water flow.