In the late 1990s, both German and Norwegian scientists established time-series transects in the waters surrounding Svalbard. While Norwegian research focussed traditionally on the water column of the inner Kongsfjord to the shelf break, the Alfred Wegener Institute for Polar and Marine Research (AWI) concentrated on the nearby bottom communities between 1000 and 5500m water depth (HAUSGARTEN). In 2008, the Norwegian oil company StatoilHydro funded a new project called KongHau within the scope of the EU-Project HERMES. The main goal of KongHau is to connect the Kongsfjord and HAUSGARTEN bathymetric transects. In a complementary approach, researchers from the Norwegian ARCTOS network have thus begun to sample the pelagic environment at selected HAUSGARTEN stations while AWI-scientists explore the seafloor at selected Kongsfjord stations to characterise the bottom communities. Our novel approach integrates existing and new data from different compartments of the ecosystem. This enables us to adapt and apply existing models on marginal ice zone pelagic-benthic interactions in shallow waters to the HAUSGARTEN data set. It also allows us to assess Arctic pelagic and benthic ecosystem changes in relation to climate factors such as sea ice, hydrography, NAO and AO indices.