The aim of this study was to assess the risk of S. aureus contamination in bottled drinking water and identify the factors that influenced the presence of S. aureus in raw water. Samples were collected at different stages of two drinking water plants, including raw water, soft water, reverse osmosis (R.O.) water, and finished water. Additionally, raw water samples and risk parameters such as pH, temperature, and residual chlorine were collected during the washing step at the packing house. Our findings revealed that the key factors contributing to S. aureus contamination in water were the processing time and pH of the water. The pH values for raw water, soft water, R.O. water, and finished water samples were 7.17, 7.24, 6.69, and 5.92, respectively, for Factory A (small scale), and 7.9, 7.44, 6.97, and 6.8, respectively, for Factory B (medium scale). The number of S. aureus detected in all water samples from both Factory A (2 CFU/ml) and Factory B (1 CFU/ml) were within the safe range for consumer consumption. Based on these findings, it is recommended to maintain a pH level between 6.5 and 7.5 for raw water and finished water to minimize pathogen contamination in bottled drinking water.