The eastern north coast of Greenland is considered to be highly sensitive to the ongoing Arctic warming, but there is a general lack of data on modern conditions and in particular on the modern distribution of climate and environmental proxies to provide a baseline and context for studies on past variability. Here we present a detailed investigation of 11 biogenic proxies preserved in surface sediments from the remote High Arctic Wandel Sea shelf, the entrance to the Independence, Hagen, and Danmark fjords. The composition of organic matter (organic carbon, C:N ratios, δ13C, δ15N, biogenic silica, and IP25) and microfossil assemblages revealed an overall low primary production dominated by benthic diatoms, especially at the shallow sites. While the benthic and planktic foraminiferal assemblages underline the intrusion of chilled Atlantic waters into the deeper parts of the study area, the distribution of organic‐walled dinoflagellate cysts is controlled by the local bathymetry and sea ice conditions. The distribution of the dinoflagellate cyst Polarella glacialis matches that of seasonal sea ice and the specific biomarker IP25, highlighting the potential of this species for paleo sea ice studies. The information inferred from our multiproxy study has important implications for the interpretation of the biogenic‐proxy signal preserved in sediments from circum‐Arctic fjords and shelf regions and can serve as a baseline for future studies. This is the first study of its kind in this area.