Acid mine waters (AMW) collected during high- and low-flow water conditions from the Lousal, Aljustrel, and São Domingos mining areas (Iberian Pyrite Belt) were physicochemically analyzed. Speciation calculation using PHREEQC code confirms the predominance of Me and Me-SO species in AMW samples. Higher concentration of sulfate species (Me-SO) than free ion species (Me, i.e., Al, Fe, and Pb) were found, whereas opposite behavior is verified for Mg, Cu, and Zn. A high mobility of Zn than Cu and Pb was identified. The sulfate species distribution shows that Fe-SO, SO, HSO, Al-SO, MgSO, and CaSO are the dominant species, in agreement with the simple and mixed metal sulfates and oxy-hydroxysulphates precipitated from AMW. The saturation indices (SI) of melanterite and epsomite show a positive correlation with Cu and Zn concentrations in AMW, which are frequently retained in simple metal sulfates. Lead is well correlated with jarosite and alunite (at least in very acid conditions) than with simple metal sulfates. The Pb for K substitution in jarosite occurs as increasing Pb concentration in solution. Lead mobility is also controlled by anglesite precipitation (a fairly insoluble sulfate), where a positive correlation was ascertained when the SI approaches equilibrium. The zeta potential of AMW decreased as pH increased due to colloidal particles aggregation, where water species change from SO to OH species during acid to alkaline conditions, respectively. The AMW samples were supersaturated in schwertmannite and goethite, confirmed by the Me-SO, Me-Fe-O-OH, or Me-S-O-Fe-O complexes identified by attenuated total reflectance infrared spectroscopy (ATR-IR). The ATR-IR spectrum of an AMW sample with pH 3.5 (sample L1) shows well-defined vibration plans attributed to SO tetrahedron bonded with Fe-(oxy)hydroxides and the Me sorbed by either SO or Fe-(oxy)hydroxides. For samples with lower pH values (pH ~ 2.5-samples SD1 and SD4), the vibration plans attributed to Me sorption are not evidenced, indicating its release in solution. The sorption of heavy metals on the first precipitated simple metal sulfates was ascertained by scanning electron microscopy coupled with X-ray spectrometry (SEM-EDX), where X-ray maps of Cu and Zn confirm a distribution of both metals in the melanterite structure.