Burkholderia cepacia complex (BCC) have recently received a reasonable attention as one of the major risks in susceptible pharmaceutical products. This microorganism can easily spread and cause severe contamination especially to the water stations for pharmaceutical companies. It rapidly grow within the product and cause cystic fibrosis and septicemia in humans. Aim: The traceability of the sources of contamination of pharmaceutical non-sterile aqueous preserved products and how to control it during the manufacturing operations as it is concern with the public health. Materials and Methods: The samples collected for the analysis were taken from different sources provided from the pharmaceutical company such as: aqueous finished products, filling machines, preparation tanks and water stations, identified by API 20NE, Vitek 2 compact system and 16S rRNA. Results: From 213 different samples of finished product, 22 bacterial isolates had been identified as Burkholderia cepacia group. Raw materials and primary packaging materials did not result in any bacterial isolates while the machine surfaces and preparation tanks were contaminated. From 384 pharmaceutical water samples, 35 isolates were identified as B.cepacia. Conclusion:Our study suggests that the chlorine treatment and hydrogen peroxide have a significant effect on B.cepacia in water disinfection.