Volcanic aquifers have become valuable resources for providing water to approximately 2.5 million people in the Yogyakarta-Sleman Groundwater Basin, Indonesia. Nevertheless, hydrogeochemical characteristics at the basin scale remain poorly understood due to the complexity of multilayered aquifer systems. This study collected sixty-six groundwater samples during the rainy and dry seasons for physicochemical analysis and geochemical modeling to reveal the hydrogeochemical characteristics and evolution in the Yogyakarta-Sleman Groundwater Basin. The results showed that groundwater in the unconfined and confined aquifers exhibited different hydrogeochemical signatures. The Ca–Mg–HCO3 facies dominated groundwater from the unconfined aquifer. The groundwater facies evolved into a mixed Ca–Mg–Cl type along the flow direction towards the discharge zone. Meanwhile, groundwater from the confined aquifer showed mixed Ca–Na–HCO3, Na–HCO3, and Na–Cl–SO4 facies. The presence of Mg in the confined aquifer was replaced by Na, which was absorbed in the aquifer medium, thus showing the ion exchange process. The main geochemical processes can be inferred from the Gibbs diagram, where most groundwater samples show an intensive water–rock interaction process mainly influenced by the weathering of silicate minerals. Additionally, only groundwater samples from the confined aquifer were saturated with certain minerals (aragonite, calcite, and dolomite), confirming that the groundwater followed the regional flow system until it had sufficient time to reach equilibrium and saturation conditions. This study successfully explained the hydrogeochemical characteristics and evolution of a multilayer volcanic aquifer system that can serve as a basis for groundwater basin conservation.
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