Stable isotopes and element compositions of the fine-grained matrix were measured for IODP Expedition 307 Hole U1317E drilled from the summit of Challenger Mound in Porcupine Seabight, northeast Atlantic, to explore the palaeoceanographic and palaeoclimatic background to development of the deep-water coral mound. The 155?m long mound section was divided into two units by an unconformity at 23.6 mbsf: Unit M1 (2.6–1.7 Ma) and Unit M2 (1.0–0.5 Ma). Results from 519 specimens show a difference in d13C value between Unit M1 (-0.6‰ to -5.0‰) and Unit M2 (-1.0‰ to 1.0‰), but such a distinct difference was not seen in d18O values (1.0‰–2.5‰), CaCO3 content (40–60 wt%), Sr/Ca ratio (2.0–8.0 mmol mol-1), and Mg/Ca ratio (10.0–20.0 mmol mol-1) through the mound. Positive d18O and negative d13C shifts at the mound base are consistent with the oceanographic changes in the northeast Atlantic at the beginning of the Quaternary. The positive d13C regression in Unit M2 suggests a linkage to the mid Pleistocene intensified glaciation in the Northern Hemisphere. Warm Mediterranean Upper Core Water of Mediterranean Outflow Water, Eastern North Atlantic Water and cold Labrador Sea Water of North Atlantic Deep Water are key oceanographic features that cause spikes and shifts in stable isotope and element composition. However, the stable isotope values of the sediment matrix could not primarily record the glacial–interglacial eustatic/temperature change, but indirectly indicate current regimes of the intermediate oceanic layer where the coral mound grew. Similarly, elemental ratios and CaCO3 content may not represent the productivity and temperature of surface sea water, respectively, but superpose the fractions from both surface and bottom water. It is concluded that palaeoceanographic change coupled to the Pleistocene glacial/interglacial cycles is a key control on the geochemical stratigraphy of the matrix sediments of the carbonate mound developed in Porcupine Seabight.