Understanding the dynamic of freshwater and sea-ice export from the Arctic is crucial to better comprehend the potential near-future climate change consequences. Here, we report nitrogen isotope data of a core from the Laptev Sea to shed light on the impact of the Holocene Siberian transgression on the summer stratification of the Laptev Sea. Our data suggest that the oceanographic setting was less favourable to sea-ice formation in the Laptev Sea during the early to mid-Holocene. It is only after the sea level reached a standstill at around 4 ka that the water column structure in the Laptev Sea became more stable. Modern-day conditions, often described as “sea-ice factory” were reached about 2 ka ago, after the development of a strong summer stratification. These results are consistent with sea-ice reconstruction along the Transpolar Drift, highlighting the potential contribution of the Laptev Sea to the export of freshwater from the Arctic Ocean.