Biofouling in the open recirculating cooling water systems may cause biological corrosion, which can reduce the performance, increase the energy consumption and lower heat exchange resulting in reduced efficiency of the cooling tower (CT). Seawater CTs are prone to bio-fouled due to the presences of organic and inorganic compounds which act as nourishment for various microorganisms like (algae, fungi, and bacteria) for their growth under certain environmental conditions. The most commonly being used method to control the biofouling in CT is by addition of biocides such as chlorination. In this study, diatom and green algae were added to the CT basin and its viability was monitored in the recirculating cooling seawater loop as well as in the CT basin. Three different types of oxidizing biocides, namely chlorine, chlorine dioxide (Chlorine dioxide) and ozone, were tested by continuous addition in pilot-scale seawater CTs and it was operated continuously for 60 d. The results showed that all biocides were effective in keeping the biological growth to the minimum regardless of algal addition. Amongst the biocides, ozone could reduce 99% of total live cells of bacteria and algae, followed by Chlorine dioxide at 97%, while the conventional chlorine showed only 89% reduction in the bioactivities.