To evaluate changes in terrestrial and aquatic ecosystems in the Azores, we developed paleoecological and paleoclimate records from Lake Funda on Flores Island that span the last millennium. Vegetation composition (n-alkane average chain length) indicate when human activities began in the catchment area and biogenic silica tracks changes in diatom productivity. In addition, sterol hydrogenation and archaeal lipids (isoprenoid glycerol dialkyl glycerol tetraethers) trace changes in redox conditions and biogeochemical cycles, respectively. Finally, a high-resolution reconstruction using leaf wax hydrogen isotopes records changes in precipitation amount over the last millennium.