In semi-arid northeastern Brazil, where water is scarce, rainforest refugia can be seen along the coastal relief, where the trade winds bring in humidity from the Atlantic Ocean, or further inland, at the Araripe plateau where water comes from aquifer resurgence. In order to reconstruct past changes in water resurgence and in their associated vegetation types, we analyzed pollen, charcoal, and trace elements from sediment cores collected in the permanent swamps created by the resurgences. Our high temporal resolution analyses show that the vegetation was more sparse and drier than today until 2700 cal yr BP. Between 2700 and 2000 cal yr BP, palm swamp and evergreen forest tree taxa started to expand, suggesting an increase in water resurgence. At 2000 cal yr BP, the moist forest with Mauritia expanded and fire activity changed from mixed to woody fuel particles. During the last 200 cal yr BP, a decrease in the palm tree Mauritia flexuosa, an expansion of Poaceae and an increase in macrocharcoal particles are attributed to an increase in anthropogenic activities in the Araripe Basin. The Late-Holocene climatic trend seen at Araripe mirrors that of eastern Brazil and has controlled the aquifer activity, including during the major droughts that affected the region. This is highly relevant for the application of public policies that rely on the aquifers of Araripe for the 21st century.