We analysed IODP Expedition 341 Site U1417 to understand the palaeoceanography in the Gulf of Alaska across the Pliocene and early Pleistocene (4-1.7 Ma). The data submitted here are productivity-related biomarkers (alkenone and brassicasterol accumulation rates), siliceous microfossils (total diatoms and silicoflagellate accumulation rates and diatom assemblages accumulation rates and relative abundance), biogenic silica accumulation rates, bulk carbon and nitrogen accumulation rates and stable isotope ratios (δ13C and δ15N), terrestrial and aquatic n-alkane accumulation rates, the Shannon-Weaver index and preservation value of diatoms (prev. value). The diatom assemblages include pelagic high productivity, pelagic warm water, coastal high productivity, coastal moderate productivity, benthic and freshwater habitats.