We investigate Lake Estanya's diatom and pollen records from the Late Glacial (LG) to the Early Holocene (EH), in order to compare limnological and vegetation responses to common climate forcing. The biotic changes recognized in this study largely agree with the hydrological evolution of the lake described previously for the same period. The diatom record shows high sensitivity to fluctuations in both lake level and salinity concentration as consequence of climate shifts. In addition vegetation results indicate that the area could have played an important role as regional vegetation refuge. Shallow lake conditions during the Last Glacial Maximum (LGM) were punctuated by relatively deeper freshwaters between 19.3 and 18.6 cal kyr BP and at 18.0 cal kyr BP, as recorded by diatom shifts. A subsequent increasing aridity trend, coinciding with the Mystery Interval (MI), affected the diatom accumulation rates, which dropped to its minimum values between 17.2 to 14.7 cal kyr BP. Particularly dry and cold conditions during the LGM and MI are supported by the largest values of steppic pollen taxa of the whole sequence, which account for up to 40%. However, relatively high values of Betula during the Heinrich Event 1 suggest a plausible regional vegetation refuge. Abrupt cooling and warming episodes within the LG triggered remarkable ecological threshold crossings in the diatom communities, especially during the stadial/interstadial episodes. At this point, the vegetation reflect the onset of warm conditions during the Bølling/Allerød with the partial substitution of Betula by Marcescent and Evergreen Quercus, what probably indicates the arrival of temperate taxa to the area and the likely migration of birch to higher altitudes. The Younger Dryas Stadial shows a complex ecological response. Diatoms are very poorly preserved, but aquatic taxa reach their highest values. An increase in Marcescent Quercus during this cold stage lends further support to the hypothesis that this is a regional vegetation refuge. Low lake levels recorded during the EH affected the development and preservation of diatom communities. A delay in the onset of humid conditions for the EH is also supported by the vegetation composition, characterized by the maximum expansion of Juniperus.