Ecosystems deeper than 2,000 m cover ~60% of the Earth's surface and represent the world's most vast biome. Although megafaunal organisms play an important role in deep benthic ecosystems and contribute significantly to benthic biomass little is known about their temporal dynamics. Established in the Fram Strait in 1999, the LTER (Long-Term Ecological Research) observatory HAUSGARTEN enables us to study the composition of Arctic epibenthic megafaunal communities through the analysis of seafloor photographs from repeated camera transects. This, in combination with annual sampling campaigns, which have yielded data on faunal, bacterial, and biogeochemical properties at the seafloor, as well as on the local hydrography and the vertical export of organic matter, allows us to identify drivers of temporal variations in megafaunal abundances, diversity and community structure. Here, we present the first time-series results from a northern and the southernmost stations of the observatory (N3 and S3, ~2500 m depth) from 2004 to 2015, obtained via the analysis of images acquired by a towed camera system (Ocean Floor Observation System). We assess variability in megafaunal densities, species composition and diversity as well as biotic and abiotic factors, which may cause the trends observed. There were significant differences in megafaunal abundance, diversity and abiotic factors between years at both stations with N3 in particular seeing a significant increase in megafaunal abundance from 12.1 ind. m-2 in 2004 to 35.2 ind. m-2 in 2007. At S3, megafaunal densities increased over time from 12.4 ind. m-2 in 2004 to a peak in 2015 (22.7 ind. m-2). Megafaunal community structure underwent significant changes over the study period, which is reflected in a significant overall increase in (γ) diversity at both stations, however, with varying contributions of α and β diversities. While the small-sized sea cucumber Elpidia heckeri increased significantly over time, the larger-sized Kolga hyalina decreased continuously. The trends will be discussed in the context of changes recorded in water temperatures, related changes in surface production and varying food availability on the deep seafloor. The results indicate that epibenthic communities from the deep seafloor are reactive and dynamic, with no “null” community state. Our study highlights the importance of long-term ecological research (LTER), as the megabenthic community composition appears to be characterised by continuous changes.