This article consists on the implementation of a methodology for the Escherichia Coli (E. coli) detection in drinking water through alternative instrumental methods such as E-nose and E-tongue. For the making of each test, a group of bacteria samples was prepared, which consisted of individual E. coli, Pseudomonas aeruginosa and Klebsiella oxytoca colonies transferred to nutrient agar plates and suspended in sterile water. In order to validate the obtained results, the Membrane Filter Technique (MFT) was used and the measurement discrimination was made through PCA, reaching 99.4% of variance with the E-tongue. Similarly, a 97.6% variance was obtained for the bacteria discrimination with the E-nose. A Neural Network PNN was implemented only for the bacteria classification reaching 86% of accuracy, getting a very similar value in each one of the methods.