Background: The threat of controlling water borne infectious diseases was always a challenge for health authorities because water related diseases are a major cause of morbidity and mortality worldwide. Faecal coliforms such as Esherichia coli (E. coli) are the indicators most commonly analysed to evaluate the level of faecal contamination in water. Objectives: The study aimed in the first part to compare different techniques for the best detection of E. coli from water. The chosen method was applied in the second part on samples from Wadi Hanifa and neighboring wells. Colonies considered as E. coli were subjected to single colony PCR targeting the genes hha (indicator of enteric bacteria) and tuf (indicator of E. coli), in order to determine if there is a correlation between positive results given with both genes, thus the gene hha could be used as an indicator of fecal contamination in water. Material and methods: 3 techniques of water concentration for the detection of E. coli in artificially contaminated tap water with K12 (E. coli) were compared: (i) The European directive ISO 9308-1 (ii) Ultrafiltration method (UF) and (iii) Membrane filtration followed by direct isolation of genomic DNA. The best technique was applied for E. coli detection in 156 samples collected monthly and during one year from Wadi Hanifa and neighboring wells in Riyadh. Presumptive E. coli strains were subjected to single colony PCR targeting the genes hha and tuf. Results: The comparison of the three techniques has shown that the ISO 9308-1 was more reliable, accurate and economic than the other two tested techniques. Ten (10) E. coli strains (6.41%) were found exclusively in the surface water of Wadi Hanifa whereas; no E. coli strain was detected in wells, fortunately. All E. coli strains tested positive for the gene tuf, were found also positive for the gene hha. Conclusion: The ISO 9308-1 was the technique of choice for the detection and enumeration of coliforms and E. coli in water samples. A good correlation was found between the two genes suggesting that the gene hha could be used as indicator of fecal contamination in water samples.