The recurrent winter polynya in the Laptev Sea (Siberian Arctic) has been recognized as an area of intensive ice formation. The growth of new ice within the polynya induces a salt flux that should have a distinct effect on the hydrography of the Laptev Sea shelf. Because of the remoteness and hazardous weather conditions, direct oceanographic observations during the period of the most dynamic polynya openings in the Laptev Sea (November–March) do not exist. Motivated by the assumption that the polynyas are among the first polar systems to be impacted by climate change, two oceanographic moorings were deployed in 2007 in the area of the Laptev Sea shelf polynya for a period of 2 years. In parallel, ENVISAT synthetic aperture radar imagery was acquired from October 2007 until May 2009. This case study, which also includes field experiments at the polynya in April 2008 and in March and April 2009, was conducted within the framework of the Russian–German ‘Laptev Sea System’ project. Temperature and salinity data from the moorings (2007–2009) and field experiments demonstrate that the hydrography within the polynya in the southeastern Laptev Sea is dominated by a distinct salinity/density stratification of the water column (pycnocline) that survived even strong polynya events. The strong and persistent density stratification – caused by a high buoyancy input through river discharge and melting of sea ice during summer – is a characteristic of the central and eastern Laptev Sea. Even in March under-ice salinities below 15 PSU were observed prior to a major polynya opening event. During polynya events wind-induced turbulence in the pycnocline layer causes mixing of the low salinity surface waters with the more saline bottom waters, which results in a decrease of bottom water salinities during polynya events. This is in contradiction to the hypothesis that the polynyas in the southeastern Laptev Sea contribute to the formation of dense shelf water that might ‘feed’ the Arctic halocline.