Sedimentological, geochemical and magnetic data in a ~ 7-m sequence from Marbore Lake (2612 m asl, central Pyrenees) provide information about environmental variability since the last glacier retreat (14.6 cal ka BP) in high-altitude Pyrenean environments. The sediment sequence is composed of millimeter- to centimeter-thick rhythmites made of finer greyish laminae and coarser-grain, carbonate-bearing laminae arranged in varied patterns throughout the sequence. Finer laminae are interpreted as deposition during periods of predominantly ice-covered conditions, whereas coarser, carbonate-bearing sediments reflect periods of higher runoff. The age model, based on 13 14C dates and a reservoir effect assessed with 210Pb and 137Cs, is coherent with known synchronous vegetation changes across the Pyrenees. Warmer intervals such as GI-1 (14.6–12.8 cal ka BP, Bolling/Allerod period), 10.4–8.2 cal ka BP in the Early Holocene, 7.5–5.2 cal ka BP in the Mid Holocene and the Medieval Climate Anomaly (AD 900–1300), are characterized by peaks in productivity and higher carbonate preservation. Deposition during colder periods such as GS-1 (12.8–11.7 cal ka BP), the Neoglacial (ca. 5.2–3.5 cal ka BP) and the Little Ice Age (last 400 years) show an increase in finer laminae. The presence of magnetite throughout the whole section suggests that Marbore Lake maintained predominantly oxic conditions since its formation. Changes in magnetic properties and the increase in magnetite from 3.5 cal ka BP to present, however, indicate a more oxic environment at the lake bottom during the last few millennia. The occurrence of Pb concentration peaks in sediments of Roman and modern age demonstrates the global distribution of heavy metal deposition, even into high-mountain lakes.