Abstract A 13 200-yr record of magnetic parameters from the Palmer Deep, western Antarctic Peninsula, records a sequence of five distinct shifts in glacimarine sedimentation coupled with century-scale variations in paleoproductivity. The five major shifts are manifested as abrupt, order of magnitude changes in low-field magnetic susceptibility, accompanied by changes in magnetic particle size and mineralogy. The Late Holocene (3.4–0 ka), the Early Holocene (11.5–9 ka), and the Last Glacial Maximum (prior to 13.2 ka) are intervals of strong low-field magnetic susceptibility and are characterized by multi-domain (MD) magnetite. MD magnetite is associated with zones of abundant gravel grains and is interpreted here as an indicator of material transported as ice-rafted debris. Deglaciation (13.2–11.5 ka) and the Middle Holocene (9–3.4 ka) were times of enhanced productivity. The Middle Holocene marks the onset of century-scale productivity cycles seen in high-field magnetic susceptibility, which is responding to variations in biogenic silica. Deglaciation and the Middle Holocene interval contain pseudo-single domain magnetite and titanomagnetite, respectively. These observations are surprising given the abundance of coarse MD magnetite available in local source rocks. The magnetic mineral assemblage in the Deglaciation interval, however, can be explained by density sorting in meltwater plumes. During the Middle Holocene, the magnetic mineral assemblage suggests the reduction or cessation of locally derived terrigenous sediment, and by inference, the reduction or cessation of iceberg generation. The Early Holocene–Middle Holocene shift in terrigenous sedimentation may be responding in part to sea level, which controls the position of the grounding line. The Palmer Deep Late Holocene interval coincides with the Neoglacial period, a time of glacier re-advances worldwide.