From these samples, 202 genera distributed across more than 15 phyla were detected using eDNA metabarcoding, of which only 9%–15% were also identified through species collection at the same sites. Despite limited sample volumes (only 30 L water in total) and sequencing depth, eDNA metabarcoding identified 202 marine genera, covering 15 phyla and complementing biodiversity information obtained from species collection using traditional benthic trawls, cores, grabs, and net tows, representing a combined total of 634 genera, covering 23 phyla for eDNA and species collection. Overall differences between sampling approaches varied between ports, with eDNA‐based alpha richness being higher than species collection sample‐based richness in Churchill (PERMANOVA, p < .001; Table S5), similar in Deception Bay (PERMANOVA, p = .4; Table S5), and lower in Iqaluit (PERMANOVA, p < .001; Table S5). In addition, this approach provides numerous advantages due to its time‐efficient and nonintrusive nature (Deiner et al., 2017). Doc. Environmental DNA (eDNA) is organismal DNA that can be found in the environment. Blue squares represent Churchill, yellow circles Deception Bay, and magenta triangles Iqaluit. NL, AL‐R, MS, PA, and LB interpreted the data. Thus, eDNA community structure represented greater community dissimilarity than what was observed for plankton communities but less dissimilarity than what was observed for benthic communities (trawl, grabs, and cores). Indeed, we observed an increasing fraction of unknown OTUs from Churchill north to Iqaluit. This project was funded by ArcticNet, POLAR Knowledge, Fisheries and Oceans Canada Aquatic Invasive Species Monitoring Program, Nunavut Wildlife Management Board, and Nunavik Marine Region Wildlife Board. eDNA along with eSolve DNA Indexing System provides the forensic biology laboratory a robust and turnkey Laboratory Information Management System designed to facilitate every aspect of processing evidence from accessioning to final disposition. However, gaining a better understanding of Arctic invertebrate community structure and how it may vary over time is challenging due to the heterogeneous distribution of species, uncertain taxonomy, and limitations due to sampling under ice cover (Jarosław, Mioduchowska, & Petković, 2016; Ministry of Environment, 2006). Sea‐surface temperature in Hudson Bay and Hudson Strait in relation to air temperature and ice cover breakup, 1985–2009, Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all‐taxa biotic surveys, Benthic non‐indigenous species in Ports of the Canadian Arctic: Identification, biodiversity and relationships with global warming and shipping activity, Projecting present and future habitat suitability of ship‐ mediated aquatic invasive species in the Canadian Arctic, Establishing a baseline for early detection of non‐indigenous species in ports of the Canadian Arctic, Ecological risk assessment of predicted marine invasions in the Canadian Arctic, Life in the World’s oceans: Diversity, distribution, and abundance, Marine biodiversity: Patterns, threats and conservation needs, Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys, Local observations of climate change and impacts on traditional food security in two northern Aboriginal communities, Characterization of the 18S rRNA gene for designing universal eukaryote specific primers, The sceptical optimist: Challenges and perspectives for the application of environmental DNA in marine fisheries, Biodiversity and phylogeography of Arctic marine fauna: Insights from molecular tools, Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types, Seasonal dynamics of meroplankton assemblages at station L4, Spawning synchrony and aggregative behaviour of cold‐water echinoderms during multi‐species mass spawnings, Intergovernmental Panel on Climate Change (IPCC), Global warming of 1.5°C. vi + 93 p, The use of sandstone blocks to test hypotheses about colonization of intertidal boulders, Changes in communities: An approach to statistical analysis and interpretation, The ecologist’s field guide to sequence‐based identification of biodiversity, Biodiversity of benthic assemblages on the Arctic continental shelf : Historical data from Canada, Current state and trends in Canadian Arctic marine ecosystems: II. This approach involves the collection and detection of DNA that has been released by organisms into the surrounding environment through metabolic waste products, gametes, or decomposition (Hansen, Bekkevold, Clausen, & Nielsen, 2018; Taberlet, Bonin, Zinger, & Coissac, 2018). Heterotrophic food web, pelagic‐benthic coupling, and biodiversity, Transport distance of invertebrate environmental DNA in a natural river, Environmental DNA metabarcoding: Transforming how we survey animal and plant communities, Environmental DNA reveals that rivers are conveyer belts of biodiversity information, Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding : the effects of filter material , pore size and extraction method, Persistence of environmental DNA in freshwater ecosystems, Étude de référence sur la biodiversité du mésozooplancton dans quatre ports de l’Arctique canadien en vue d’une augmentation de l’activité maritime, de l’exploitation des ressources et du réchauffement climatique, Evaluation of marine zooplankton community structure through environmental DNA metabarcoding, The ade4 package: Implementing the duality diagram for ecologists, Evaluating a multigene environmental DNA approach for biodiversity assessment, Can DNA‐based ecosystem assessments quantify species abundance?

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