These data include highly-branched isoprenoids (IP25, HBI II, HBI III and HBI IV) and isoprenoid GDGTs from marine sediment cores MD99-2269 and JR51-GC35 from the North Iceland Shelf. Total lipids were extracted and purified following standard procedures on an ASE and using silica-gel columns, respectively. HBIs were then analyzed on GC-MS and GDGTs on HPLC-MS. Both records have age models derived from radiocarbon-dated molluscs and foraminifera that are published elsewhere, and the above lipid biomarker records cover the last 8000 years. Temporal resolution varies between multi-centennial to sub-centennial. From MD99-2269, data also include complete planktic and benthic foraminifera assemblages. Foraminifera were wet-picked from sediment subsamples. Using established transfer functions, we also present SST and BWT records derived from the planktic and benthic foraminifera assemblages, respectively. Planktic assemblage data cover the last 10000 years whereas benthic assemblage data only cover the last 8000 years. Temporal resolution varies between multi-centennial to sub-centennial. These data were collected in order to document the Holocene paleoceanography of the North Iceland Shelf. In other words, to study when Arctic/Polar versus Atlantic Waters bathed the region, how the temperatures of these currents changed, when and how sea ice was advected to the region, and how pelagic productivity was impacted by all these oceanographic variables.