The natural occurrence of acid waters in mountainous porphyry Cu systems poses challenges for water management considering the increasing water demand and global environmental change. Unraveling the transport and fate of minerals and metals in these types of acidic river systems is crucial for environmental management. To this purpose, we develop a transport and a hydrogeochemical model by coupling five components: (i) hydrology; (ii) hydrodynamics; (iii) sediment transport; (iv) solute transport; and (v) hydrogeochemistry. Our study domain is the Yerba Loca creek, a high-altitude acid rock drainage (ARD) basin located in the central Andes, Chile. Water in the upper basin shows a low pH (around 3) and high aluminum, copper, iron, manganese, and sulfate concentrations. Our model reproduced the observed mineralogical and chemical processes by inducing the expected pH dependence on mineral precipitation along the river. Results showed good agreement between modeled and field data, highlighting the main processes that control the transport and fate of minerals and metals in mountainous river systems.