The aim of the study was to understand the effect of a long term metal exposure (110 years) on sediment microbial communities. Two freshwater sites, Férin and MetalEurop, differing by one order of magnitude in metal levels (MetalEurop: 3218 mg Zn kg–1; 913 mg Pb kg–1) were compared by shotgun metaproteogenomics. A total of 69–118 Mpb of DNA and 943–1241 proteins were obtained. PhymmBL analysis of the DNA sequences indicated that the phylogenetic profile was similar in both stations and that β-Proteobacteria were dominant. However, subtle but significant changes were observed for some bacteria: e.g., Pseudomonas (+0.4%), Leptothrix (–0.4%), Thiobacillus (+0.36%), Acidovorax (+0.48%). Using the STAMP software, the two communities were found to be functionally very similar. However, significant genetic differences (10–6 < P < 10–3) were observed for three SEED categories: synthesis of exopolymeric substances, virulence and defense mechanisms (including czcA metal efflux genes), and elements involved in horizontal gene transfer. The CzcA protein was found by metaproteomics in MetalEurop but levels were too low to allow comparisons. It is concluded that bacterial communities in freshwater sediments may adapt to high metal levels without broad changes in the structure of the population.