The need to reduce pollution and waste from sensitive industrial products, specifically the water used in the pharmaceutical industry, became a vital field of research. The use of chemical sanitization in water treatment processes is a significant source of pollution and can have harmful effects on drug products. This problem is compounded by the increasing demand for pure water and the need to protect pharmaceutical products from pollution in the inlet of the water process. The aim of this study is to assess the efficiency of sanitization based on the results of Microbial Count (MC) within the limits of the operational time. Samples were collected from the production and subjected to thermal or chemical sanitization. The sanitization samples were examined for their microbial counts. After 82 days of operation, thermal sanitization at 65 ºC yielded non-conformity results of 110 cfu/ml, whereas thermal sanitization at 85 ºC yielded conformity results of 34 cfu/ml. Chemical sanitization at 0.5 % and 5 % concentrations of H₂O₂ have been studied. A non-conformity microbial count results in 124 cfu/ml after 45 days at a 0.5 percent concentration of H₂O₂. After the 75-day operational period, the concentration of 5 percent H₂O₂ has conformity results of 97 cfu/ml. The study results in the optimum condition for the sanitization of water processes in pharmaceutical industries. The study explained that the thermal sanitization method at 85 ºC is the optimum condition and is used in sensitive pharmaceutical and semiconductor industries. Keywords: Cleaner Production; Biocontamination; Sanitization.