Benthic megafauna communities in the Arctic Ocean play a vital role in deep-sea ecosystem functioning by influencing the local biogeochemistry and the global carbon cycle. Their community structure is largely driven by phytodetrital fluxes from the surface ocean, increasing their susceptibility to environmental change. This study assessed short-term variability in benthic megafauna community composition, taxonomically and functionally, across three stations (N3, HG-IV, S3) situated within the lower bathyal zone (∼2500 m) at the LTER HAUSGARTEN site, in relation to environmental parameters such as biogenic sediment components and habitat features. The analysis was based on image data and sediment samples collected in consecutive years from 2016 to 2021. Additionally, long-term changes in the density of four selected taxa were examined by comparing two periods: 2002/2004-2015 (literature-based) and 2016-2021 (this study). Over the six-year period, the community structure showed considerable temporal variability, primarily driven by changes in the density of the opportunistic sea cucumber Elpidia heckeri. Environmental parameters explained spatial variation across stations more effectively than temporal variation across years. Long-term analyses revealed a general decline in density of the selected taxa, with average density decreases ranging from 28% for a crinoid to 93% for a soft coral. These findings highlight the dynamic nature of Arctic benthic megafauna communities and their complex responses to local environmental change. The pronounced temporal fluctuations and substantial population declines underscore the urgent need to extend time-series studies both temporally and spatially to enable accurate predictions of the future state of Arctic deep-sea ecosystems.