Embedded in the interdisciplinary design of pelagic and benthic long-term observations at the Arctic long-term ecological research site HAUSGARTEN (78°36,46'N - 79°56,63'N 10°50,91'E - 5°22,24'W; 250 – 5500 m) in Fram Strait, environmental DNA (eDNA)-based biodiversity studies span multiple habitats and trophic levels. These studies provide valuable insights into marine ecosystem functionality and carbon fluxes, including seasonal and interannual dynamics. Since 2009, eDNA studies of pelagic eukaryotic microbial communities have regularly been conducted. Recently, these studies have been expanded to cover the biodiversity of bacteria, archaea and metazoa such as zooplankton (including gelatinous taxa) and nekton (cephalopods and fish) alongside with microbial eukaryotes. The eDNA surveys have been coupled with measurements of physical and chemical properties, such as sea-ice coverage and water masses. By applying these approaches across spatial and trophic scales in a nested approach, we characterize the dynamics in biodiversity, its role in ecological processes, with a focus on current climate change. This is achieved by considering the complexity and interconnectivity of organisms, integrating information from different disciplines across scales and habitats, and focusing on functional processes including species composition. The resulting data improve our predictive capabilities for conservation and sustainable marine management in a rapidly changing Arctic. Here, we review the design of the first interdisciplinary Arctic eDNA long-term observatory and the results of more than ten years of method development and observations.