This is the first study presenting temporal changes of the macrofauna biodiversity along the bathymetric gradient from the shelf to abyssal depths in the eastern Fram Striat. In this region, between 2004 and 2008, a significant increase in surface water temperature was observed due to the transport of Atlantic water from lower latitudes and was defined as a Warm Water Anomaly (WWA). Effects of the WWA in the eastern Fram Strait were observed across the entire food web, from the pelagic to the deep seafloor. The material for our study was collected before (in 2000) and after the WWA (in 2010 and 2017) at station depths ranging from 203 m to 5561 m. Samples of macrofauna and surface sediments were collected with use of a box corer to analyze species composition and functional traits, and environmental characteristics in sediments. We explore the influence of environmental changes on the structure (species composition and diversity) and functioning (functional trait composition and diversity) of macrofauna communities. An increase of primary production in surface waters during and after the WWA was reflected in a higher food availability at the seafloor from shelf to abyssal depths. Warming induced environmental changes led to an increase of macrofauna density and taxonomic diversity at all water depths. Macrofauna species composition significantly changed after the WWA. At all study sites, macrofauna functional diversity increased after the warm period. Functional trait composition changed significantly along the bathymetric transect. Despite changes in the taxonomic composition, macrofauna communities at the shallowest stations showed high functional redundancy, i.e., trait composition remained unchanged after the WWA. At water depths below 1500 m, where functional redundancy was significantly lower, functional trait composition changed significantly after the WWA. Our results suggest that macrofauna communities on the shelves are more resistant to environmental changes compared to deep-sea assemblages in the eastern Fram Strait.