In the mining-impacted Rio Tinto, Spain, Fe-cycling microorganisms influence the transport of heavy metals (HMs) into the Atlantic Ocean. However, it remains largely unknown how spatial and temporal hydrogeochemical gradients along the Rio Tinto shape the composition of Fe-cycling microbial communities and how this in turn affects HM mobility. Using a combination of DNA- and RNA-based 16S rRNA (gene) amplicon sequencing and hydrogeochemical analyses, we explored the impact of pH, Fe(III), Fe(II), and Cl on Fe-cycling microorganisms. We showed that the water column at the acidic (pH 2.2) middle course of the river was colonized by Fe(II) oxidizers affiliated with and At the upper estuary, daily fluctuations of pH (2.7 to 3.7) and Cl (6.9 to 16.6 g/L) contributed to the establishment of a unique microbial community, including Fe(II) oxidizers belonging to , , and , identified at this site. Furthermore, DNA- and RNA-based profiles of the benthic community suggested that acidophilic and neutrophilic Fe(II) oxidizers (e.g., , , and ), Fe(III) reducers (e.g., ), and sulfate-reducing bacteria drive the Fe cycle in the estuarine sediments. RNA-based relative abundances of at the middle course as well as abundances of and at the upper estuary were higher than DNA-based results, suggesting a potentially higher level of activity of these taxa. Based on our findings, we propose a model of how tidal water affects the composition and activity of the Fe-cycling taxa, playing an important role in the transport of HMs (e.g., As, Cd, Cr, and Pb) along the Rio Tinto. The estuary of the Rio Tinto is a unique environment in which extremely acidic, heavy metal-rich, and especially iron-rich river water is mixed with seawater. Due to the mixing events, the estuarine water is characterized by a low pH, almost seawater salinity, and high concentrations of bioavailable iron. The unusual hydrogeochemistry maintains unique microbial communities in the estuarine water and in the sediment. These communities include halotolerant iron-oxidizing microorganisms which typically inhabit acidic saline environments and marine iron-oxidizing microorganisms which, in contrast, are not typically found in acidic environments. Furthermore, highly saline estuarine water favored the prosperity of acidophilic heterotrophs, typically inhabiting brackish and saline environments. The Rio Tinto estuarine sediment harbors a diverse microbial community with both acidophilic and neutrophilic members that can mediate the iron cycle and, in turn, can directly impact the mobility and transport of heavy metals in the Rio Tinto estuary.