Two pilot-scale submerged-bed microbial biofilms were set up for the removal of Cr(III) and Pb(II) from groundwater, and the biological activities and structure of the bacterial communities developed in the presence of the heavy metals were analyzed. Artesian groundwater was polluted with Cr(III) or Pb(II) (15 mg/l) and amended with sucrose (250 mg/l) as carbon source. While Pb(II) was over 99% removed from groundwater during long-term operation (130 days), the efficiency of the removal of Cr(III) significantly decreased in time (95–73% after 60 days). Cr(III)-amended biofilms displayed significant lower sucrose consumption, ATP cell contents and alkaline phosphatase activity, compared to biofilms formed in the presence of Pb(II), while analysis of exopolymers demonstrated significant differences in their composition (content of carbohydrates and acetyl groups) in response to each heavy metal. According to transmission electron microscopy (TEM) and electron-dispersive X-ray analysis (EDX), Cr(III) bioaccumulated in the exopolymeric matrix without entering bacterial cells, while Pb(II) was detected both extra and intracellularly, associated to P and Si. Temperature-gradient gel electrophoresis (TGGE) profiling based on partial amplification of 16S rRNA genes was used to analyze the differences in the structure of the biofilm bacterial communities developed under exposure to each heavy metal. Prevalent populations in the biofilms were further identified by reamplification and sequencing of isolated TGGE bands. 75% of the sequences in the Pb(II) biofilter were evolutively close to the Rhodobacterales, while in the Cr(III) biofilter 43% of the sequences were found affiliated to the Rhizobiales and Sphingomonadales, and 57% to Betaproteobacteria.