Tannery wastewater causes serious ecological and sanitary damage. Chemical analysis of water from Binlamdoune River of the medina of Fez was conducted and the results revealed the presence of toxic elements from tanneries and other industrial activities, which strongly affected water quality. To determine the effectiveness of bioremediation for depollution, we studied the abundance and diversity of bacteria residing in these polluted environments. Conducting denaturing gradient gel electrophoresis (PCR-DGGE) of the 16S rDNA area using primers related to bacteria showed a bacterial community belonging to eubacterial groups, that is, Epsilonproteobacteria, Clostridia, Lactobacillales, Bacteroidetes, Gammaproteobacteria, and Alphaproteobacteria. In addition, cloning displayed the presence of clones belonging to the Firmicutes group. Moreover, scanning electron microscopy revealed a significant heterogeneity of microorganism forms and structures. These endogenous microbes could have a significant role in the purification of Binlamdoune River and Fez tannery wastewater.