Cooling water systems provide ideal aquatic environment for the microorganism multiplication. Copper and galvanized steel are frequently used in the construction of cooling towers because of their well-known antifouling property. The current study would examine the changes in total aerobic mesophilic heterotrophic bacteria (TAMHB) counts, the presence of Legionella and free-living amoeba on copper and galvanized steel surfaces and the presence of biocide in a cooling water system. In this study biofilm was confirmed by SEM on copper and galvanized coupons in experiments. Statistical analysis demostrated that heterotrophic bacteria counts were significantly (P<0.01) higher on the surface of galvanized steel coupons than on the surface of copper coupons. Our results showed that the isolates were characterized as members of genus Pseudomonas or were closely related to this genus. Free-living amoeba were detected on the surface of copper coupons and galvanized steel coupons whereas Legionella pneumophila was not established by culture method.