Delivery of safe water for human consumption is now considered a fundamental right. However, dwindling resources and faulty sanitation in Low and Middle- Income Countries makes the availability of safe water almost unattainable. It is therefore important to continuously evaluate the chemical and biological quality of drinking water. Failure to do so, people will be exposed to numerous water borne enteric diseases. Mombasa and the Coastal Region in general experience perennial water shortages. This cross-sectional study aimed to determine the frequency and characterization of Escherichia coli pathotypes from water samples collected from and wells in Mombasa County. One hundred and fifty-seven (157) water samples were collected from all four Sub Counties that is Mvita, Kisauni, Likoni and Changamwe Sub Counties using sterile techniques. Variables such chlorine treatment, distance to pit latrine, borehole or well covers, among others were recorded. The samples were then inoculated to double strength MacConkey broth and incubated at 370C for up to 48 hours. Positive results from the double strength MacConkey broth were compared to the 3 tube McCrady Most Probable Number table. The Escherichia coli were confirmed by Eijkman‟s test and antibiotic susceptibility carried out on confirmed isolates. The Escherichia coli were then molecularly characterized to determine the pathotypes using polymerase chain reaction. Out of 157 samples collected from around Mombasa County, one hundred and thirty-one (131) samples (83.4%) were contaminated by coliform bacteria. Of the contaminated samples, only 79 (60.3%) were confirmed to have E. coli. All the samples with E. coli tested (n = 77; 100%) were sensitive to Gentamicin, while all (n = 77; 100%) isolates were resistant to Ampicillin. Molecular characterization indicated that this study‟s isolates were typed as Enteroinvasive E. coli. These findings suggest that E. coli are major contaminants of water in wells and boreholes in Mombasa County. The E. coli showed a distribution of resistant and sensitivity patterns to commonly used antibiotics. The most dominant pathotype detected was Enteroinvasive E. coli.

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