In Morocco, storage reservoirs are particular systems of water supply in rural areas (a case study in Assif El Mal Valley). These reservoirs are fed by rainwater and/or directly from the river through opened channels, and are used without any treatment as a drinking water by the surrounding population. This study was conducted to evaluate the bacterial contamination of drinking water reservoirs in this rural area using a molecular approach studying the 16S-rDNA bacterial diversity in water, via Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis (PCR-DGGE) technique. The application of PCR-DGGE techniques on stored water in the reservoirs showed a high bacterial diversity, including pathogens, namely Salmonella sp., E.coli, Sphingomonas spp. and Aeromonas sp., which indicated a high risk of infection for the user population. Comparative cluster analyses of the DNA based fingerprints revealed the six studied reservoirs according a gradient accumulation of bacterial contaminants from upstream to downstream. The molecular approach in this study gives a very helpful tool to confirm without any doubt the bacterial contamination of drinking water. Otherwise, this study provides an overview of the dominant bacterial groups in the traditional storage reservoirs of water in Moroccan rural area and the impact of environmental changes on bacterial diversity.