The ISO reference method, defined by the European Drinking Water Directive for the enumeration of total coliforms and Escherichia coli in water intended for human consumption, has various limitations, especially related to discrepancies observed with the new taxonomic classification of the coliform group. A study was therefore performed to compare the above reference method with another rapid method, the DST/Colilert, and to evaluate the phenotypical characteristics of isolated microrganisms. The ISO reference method failed to detect a significant proportion of coliforms and E. coli in water and furthermore, it enumerated microrganisms belonging to other groups. The DST/Colilert method was found instead to be a suitable alternative method for the detection of bacterial indicators.