Hydrographic and stable oxygen isotope (H2 18O/H2 16O) sampling was carried out within the West New Siberian (WNS) coastal polynyas in the southern Laptev Sea in late winters 2008 and 2009. The impact of sea ice formation on the water column was quantified by a salinity/d18O mass balance. Several stations had vertically homogeneous physical properties in April/May 2008 and featured polynya-formed local bottom water with elevated signals of brine released during sea ice formation and elevated fractions of river water. The polynya-formed bottom water was fresher than surrounding bottom waters. At other stations, salinity/d18O correlation showed well-defined mixing lines for bottom and surface layers. In March–April 2009, surface waters were strongly influenced by Lena River water, and local polynya activity with elevated brine signals reached to intermediate depth but did not penetrate the bottom layer in the highly stratified water column. Inventory values of sea ice formation were comparable in both years, but freshwater distributions from the preceding summers were different. Therefore, the observed difference in the impact of polynya activity on the water column is not primarily controlled by the amount of sea ice formed during winter but by preconditioning from the preceding summer. Only in years when the river plume is mostly absent in the polynya region is stratification weak and allows winter sea ice formation to reach the bottom layer. Thus summer stratification controls the influence of local polynya water on the shelf’s bottom hydrography and, as bottom water is exported, impacts on the source water of shelf-derived halocline waters.