Water cooling utilizing natural waters is typically used for cooling large industrial facilities such as power plants. The cooling water cycles are susceptible to biofouling and scaling, which may reduce heat transfer capacity and enhance corrosion. The performance of two fouling-release coatings combined with hypochlorite treatment were studied in a power plant utilizing brackish sea water from the Baltic Sea for cooling. The effect of hypochlorite as an antifouling biocide on material performance and species composition of microfouling formed on coated surfaces was studied during the summer and autumn. Microfouling on surfaces of the studied fouling-release coatings was intensive in the cooling water cycle during the warm summer months. As in most cases in a natural water environment the fouling consisted of both inorganic fouling and biofouling. Chlorination decreased the bacterial number on the surfaces by 10–1000 fold, but the efficacy depended on the coating. In addition to decreasing the bacterial number, the chlorination also changed the microbial species composition, forming the biofilm on the surfaces of two fouling-release coatings. TeknoTar coating was proven to be more efficient in combination with the hypochlorite treatment against microfouling under these experimental conditions.