Background: The demand for water has necessitated the proliferation of bottled water companies in Kenya. This study evaluated if retailed bottled water in Nairobi Kenya complies with both local and international reference criteria. Methods: A total of 42 different water brands (25 approved by Kenya Revenue Authority (KRA) and 17 banned brands) were analyzed for both physicochemical and bacteriological quality. Spread plate method was used to obtain the total plate count of bacteria, while the membrane filter method was used to obtain total coliform count (TCC) and fecal coliform count (FCC). Structured interviews were used to gather company-related information. Results: Overall, 16% of KRA-approved and 35.3% of banned bottled water were contaminated with heterotrophic bacteria. Of the approved water brands, 4% were positive for total coliforms, compared with 17% of the banned brands. Similarly, 4% and 17% approved and banned water brands were positive for fecal coliforms, respectively. Escherichia coli (19.1%), Pseudomonas spp. (9.5%) and Klebsiella spp. (4.8%) were the most common bacterial types isolated from all water brands, most of which exhibited multidrug resistance. In multivariable analysis, water companies that cleaned pipework and bottles using chlorine-based disinfectants (OR 0.08, 95% CI 0.01 to 0.8), those that had food safety programs (OR 0.1, 95% CI 0.019 to 0.9), had standard operating procedures (SOP) for water sourcing (OR 0.1, 95% CI 0.012 to 0.9) and SOP for contamination protection (OR 0.1, 95% CI 0.02 to 0.9) remained independently associated with bottled water brands exceeding WHO TCC limits. Conclusions: A number of bottled water brands were contaminated with one or more types of indicator bacteria, some of which were multidrug resistant. Water bottling companies' processes contribute to contamination; rigorous regulation and monitoring will improve on water quality and safety.