Paleolimnological reconstructions from the mid and high latitudes in the Southern Hemisphere are still relatively scarce. Anthropogenic impacts have evidenced trophic state changes and an increase in cyanobacterial blooms in the lacustrine system of San Pedro de la Paz in the last decades. Here, we reconstructed primary production and sedimentological changes spanning the past 2500 years in two coastal lakes in Mediterranean Chile. A multiproxy approach including sedimentological, biogenic silica, carbon and nitrogen isotopes and fossil pigments analysis in sediment cores was performed in Laguna Grande (LGSP) and Laguna Chica de San Pedro (LCSP). A marked change in the sedimentology of the lakes, likely related to the terrigenous sediment inputs derived by a transition from an arid condition in the mid-Holocene to a more humid condition in the late Holocene that favoured arboreal forest establishment at 100 BC–AD 150. A period of low primary production was identified between 850 to 1050 AC for LCSP, suggesting moist and cold conditions that were possibly related to La Niña events. In recent decades, there have been increases in primary production, probably resulting from anthropogenic disturbances. These likely include the clearance of native vegetation, the introduction of exotic tree species, and urbanisation, which in turn, resulted in nutrient inputs and hence eutrophication. We conclude that an integrated management program for both lakes is urgently needed.