We collected filtered seawater samples from full water column profiles conducted near the Lena River delta during a winter expedition to the Laptev Sea. The samples were recovered during TRANSDRIFT XX Expedition in March and April 2012 using 2-l-Niskin bottles mounted on a frame equipped with a SBE 19plus CTD profiler (Sea-Bird Electronics Inc.). The dataset includes silicate, phosphate and oxygen concentration data of 28 seawater samples, which provide important information on nutrient sources and cycling in the Laptev Sea.