There are numerous studies measuring the rate and extent of bioturbation worldwide, however, information on mixing rates in the deep ocean, especially in the polar regions, are extremely scarce. The present study presents mixing rates and mixed layer depths for the deep seafloor at the LTER (Long-Term Ecological Research) observatory HAUSGARTEN in Fram Strait, Arctic Ocean. Two stations at similar water depths (HG-IV at 2492 m, and S3 at 2391 m) but different distances to the ice edge (approx. 65 km and 115 km, respectively) were chosen to carry out long-term in situ bioturbation experiments (2 and 4 years, respectively), using luminophores as a tracer. Enhanced bioturbation at the northern site, located closer to the high productive Marginal Ice Zone (MIZ) and thus expected to receive higher amounts of settling organic matter thereby supporting a richer benthic community, could not be confirmed. Instead, biodiffusion-like mixing rates (Db) at the experimental sites showed no significant differences (0.26 ± 0.27 SD cm−2 y−1 at station HG-IV; 0.28 ± 0.40 SD cm−2 y−1 at station S3). Moreover, mixed layer depths (L) at the two sites were almost identical; mixing of surface sediments occurred down to approx. 6–7 cm sediment depth. Indications for a non-local transport of sediment particles from the surface to deeper parts of the sediment, resulting in higher values for the Non-Local Index (NLI), could only be found for the central HAUSGARTEN site HG-IV. Differences in macro- and megafauna communities at the two experimental sites might be responsible for subsurface maxima in luminophore distribution and slightly (non-significantly) higher NLI values at this site (5.37 ± 3.35 SD at station HG-IV; 3.26 ± 1.82 SD at station S3). Temporal variations in benthic activities should have been levelled out in the multi-year experiments, thus providing reliable baseline data for the deep Fram Strait.