The spatial distribution and diversity of metal-reducing bacterial assemblages belonging to Geobacteraceae were studied in groundwaters with different physicochemical characteristics by means of terminal-restriction fragment length polymorphism (T-RFLP) molecular fingerprinting, as applied to the 16S rRNA gene. The physicochemical conditions of these environments were unfavorable to support active-metal-reducing processes. The highest diversity of Geobacteraceae was observed in groundwater samples characterized by the highest dissolved Fe and Mn concentrations. T-RFLP analyses revealed major differences in the Geobacteraceae ribotype diversity and community composition of the groundwater samples as well as a considerable variability and spatial turnover of Geobacteraceae assemblages. Results from this work suggest that changes in the physicochemical characteristics of the aquifer deeply influence the richness and community structure of Geobacteraceae, even in those systems in which metal-reduction processes are not dominant.