A rapid protocol of detection of the bacteria in water directly by PCR has been realized without having resort to the preparation of the total DNA. The results showed that (i) the direct detection of the bacteria by PCR is possible under the condition to concentrate the sample of water by filtration and centrifugation; (ii) the sensitivity of the protocol of detection established is function of the number of bacteria in the sample; (iii) and it increases with the volume filtered of the sample. This protocol of detection by PCR has been used for the study of three different natural waters (source water, well water, river water), for searching the presence of E. coli precisely, and the bacteria in general, using primers amplifying the uidA gene, and those amplifying the 16S rDNA, respectively. The PCR results showed the presence of bacteria in general and E. coli species in river water and well water, while in the source water, no PCR amplification was obtained indicating that this water is E. coli free, or contaminated with a lower concentration than the detection threshold. The three samples will allow characterizing further the degree of contamination of each water. According to this work we proved also that the PT-2/PT-3 primers amplifying a fragment of the uidA gene (?-D-glucuronidase) may be used to reveal the presence of E. coli in general and E. coli O157:H7, according to the annealing temperature of the PCR.