A major challenge in ecology is understanding whether observed changes are the result of short-term cycles or long-term environmental changes. This study leverages data collected over a 20 yr period from the Long-Term Ecological Research observatory HAUSGARTEN (Stn HG-I; 79°N, 6°E, 1300 m deep) to disentangle dynamics in epibenthic megafauna. We compared community composition to environmental factors using linear models and redundancy analyses. In all cases, combinations of factors associated with cycles and long-term changes were included in best-fit models. Faunal density and species richness increased and then decreased over the study period. Community structure made a partial return to the 2002 state in 2022, suggesting cyclicality. There was turnover in species composition over the study period, likely reflecting long-term environmental change. The North Atlantic seastar Pontaster tenuispinus was first observed in 2018, and the Arctic eelpout fish Lycodonus flagellicauda was not observed after 2012. Our study demonstrates that complex interactions of environmental factors influence community structure in the Arctic deep sea. The 20 yr study period was not sufficient to capture a full cycle in epibenthic megafauna community composition, which may have a period of >20 yr. Overlaid on this pattern are the long-term impacts of rising ocean temperatures and a changing food supply regime. Continued monitoring will likely show further non-linear responses to environmental change.