The marine-based West Antarctic Ice Sheet (WAIS) is considered the most unstable part of the Antarctic Ice Sheet, with particular vulnerability in the Amundsen Sea sector where glaciers are melting at an alarming rate. Far-field sea-level data and ice-sheet models have pointed towards at least one major WAIS disintegration during the Late Quaternary, but direct evidence for past collapse(s) from ice-proximal geological archives remains elusive. In order to facilitate geochemical and mineralogical tracing of the two most important glaciers draining into the Amundsen Sea, i.e. Pine Island Glacier (PIG) and Thwaites Glacier (TG), we here provide the first multi-proxy provenance analysis of 26 seafloor surface sediment samples from Pine Island Bay. Our data show that the fingerprints of detritus delivered by PIG and TG are clearly distinct near the ice-shelf fronts of both ice-stream systems for all grain sizes and proxies investigated. Glacial detritus delivered by PIG is characterised by low εNd values (~−9), high 87Sr/86Sr ratios (~0.728), low smectite content (<10%), and hornblende and biotite grains with Late Permian to Jurassic (170–270 Ma) cooling ages. In contrast, glacigenic detritus delivered by TG is characterised by higher εNd values (~−4), lower 87Sr/86Sr ratios (0.714), higher smectite (20%) and kaolinite content (37%), biotite and hornblende grains with 40Ar/39Ar cooling ages of <40 Ma and ~115 Ma, and high content of mafic minerals. The geochemical and mineralogical fingerprints for PIG and TG reported here provide novel insights into sub-ice geology and allow us to trace both drainage systems in the geological past, under environmental conditions more similar to those envisioned in the next 50 to 100 years.