© 2022 by the authors. Licensee MDPI, Basel, Switzerland.This work focuses on the physical-chemical characterization of a mining effluent affected by acid mine drainage (AMD) from its source to the confluence in the Odiel river, one of the most polluted rivers by AMD worldwide, in order to understand the reactions involved in the modifications in the chemical characteristics of water and precipitates resulting from water–rock–atmosphere interaction in an environment highly affected by mining activity without corrective measures. The channel starts in an open pit lake through one of the Concepción Mine main galleries, located in the Iberian Pyrite Belt, about 10 km northwest of Rio Tinto mining complex (southwest Spain). This gallery intercepts one of the largest and oldest underground mining work locations called “gallery Carmen”, allowing the exit of AMD affected waters. This channel is the first AMD polluting source in the Odiel basin. Thus, at the end of the rainy season, we conducted water sampling along this channel, from its source to its mouth, to further analyse its characterization and interpret the cause–effect relationships through the application of Fuzzy Logic and classical statistics tools. The interdependent relationship between the measured physicochemical parameters are set in order to propose a model, capable of describing the evolution of contaminants in response to the processes and reactions taking place within the affected channel and the Odiel river. The present work concluded the existence of natural attenuation processes for the mining channel, despite the entrances of other drainages in the AMD channel with different hydrochemical characteristics imposing modifications on it. This indicates that these media have a high vulnerability to external stimuli.