The rainforests in the Alter do Chão Aquifer System play a crucial role in recharging the groundwater. By studying the soil, water chemistry, and isotopes, researchers found that the forest roots help water seep deep into the ground, increasing water flow. The aquifer system consists of different layers with varying water flow rates. Rainwater is the main source of recharge, with recent rainfall contributing significantly. The aquifer receives around 236,400 to 350,000 cubic meters of water per year, depending on the area.