This multi-proxy study of sediment cores from karstic Lake Estanya (Pre-Pyrenean Range, NE Spain) provides the first complete, continuous record of the hydrological evolution in the northeastern Iberian Peninsula over the last 9500 yr. Six sedimentary facies and four main sedimentary units have been defined after integration of sedimentological, mineralogical and geochemical analyses. The use of total sulphur content and sedimentary facies as paleohydrological proxies allows reconstruction of relative changes in lake level. The Estanya record shows a large increase in water availability after 9.2 ka, fluctuating lake levels and salinity during the period 9.2–4.2 ka; and generally higher lake levels after 1.7 ka. Periods of increased run-off and sediment delivery and less saline conditions occurred at 8.5–8.2, 6.7–5.9, and 4.9–4.2 ka. Dominant lower lake levels and concentrated waters during the period 4.2–0.8 ka were punctuated by a higher lake level, higher clastic input episode ca. 1.7–1 ka. Fluctuating, but higher lake levels occurred during the last 800 years. The main hydrological phases in Lake Estanya are coherent with Western Mediterranean and North Atlantic Holocene reconstructions, but they also show similarities with northern African records.