Monitoring biodiversity patterns and their changes in Arctic coastal ecosystems is critical under ongoing climate changes. However, common current approaches require high effort and expertise which in turn limit the spatial and temporal scale of monitoring. Here, we investigated both the fish and marine invertebrate communities across Svalbard using a multi-marker environmental DNA metabarcoding approach. We analysed marine water, sediment and zooplankton filtered from marine water collected from sites influenced by the warm West Spitsbergen Current and the cold East Spitsbergen Current. Following metabarcoding amplification using mitochondrial COI, 12S, 16S and nuclear 18S markers and high-throughput sequencing, we retrieved an extensive overview of Svalbard marine biodiversity. While water and sediment samples collected across Svalbard showed a homogenous biodiversity signal across regions, zooplankton samples revealed clear spatial differences in community composition, with significantly distinct assemblages in the northwest and southeast of Svalbard. We identified potential bioindicator species for use in rapid assessment of impacts of marine temperature increase, and confirmed observed patterns of ongoing shifts in community structure as a response to climate changes. Overall, our findings show that species composition depending on fine-scale climate variation of Arctic waters can be effectively studied and monitored using environmental DNA. These insights can help us understand current and evolving climate-driven changes.